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Overview


Why does my country have so few members when I know there are more?

On the Statistics By Geography page you can see that there are tens of thousands of member who have decided not to identify their country. If you wish to identify yourself with a country, please update your profile.

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Why am I periodically asked to log into World Community Grid again?

The World Community Grid grants you the ability to use the website for a specific length of time after you log into the website. Once that length of time has been reached, you will be asked log in again. This is done in order to ensure that the member using the website is the member who logged in.

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How do I view the website in another language?

The World Community Grid web site will automatically display in the language to which your browser is set. If that language is not currently available on the site, the default language is English. To change to another language, simply use the drop-down menu on the main navigation bar to select the desired language. All of the areas of the site that are available in the selected language will be automatically translated.

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Why are some areas of the site only available in English?

There are some areas of the site that are dynamic and change frequently. There is no effective way to have these areas constantly updated in more than one language. The dynamic portions of the site include: What's New (on the home page), Help, and the forums. While the forums are not translated, posting in languages other than English is allowed.

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What happens if I check the box labeled 'Remember Me' when I sign into World Community Grid?

If you check the 'Remember Me' box when you sign into World Community Grid then you will be automatically signed into the website the next time that you visit from the same device. This means that you will not have to sign in again in order to access your My Contribution pages or post in the forums. You can have World Community Grid 'Remember' you on as many devices as you wish. If you wish World Community Grid to stop remembering you, then all you need to do is click on 'sign out' at the top right of our pages.

As a security precaution World Community Grid will not automatically sign you into the website if you have not accessed the website from a device for more than two weeks. Additionally, if you change your password, then World Community Grid will continue to remember you only on the device where you changed your password. However, next time you visit World Community Grid you can then check the 'Remember Me' box and World Community Grid will continue to remember you from that device.

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I checked the 'Remember Me' box when I signed in, but now the site is asking me to log in again.

As a security precaution, you must verify your member name and password in order to view pages that contain private member information.

For example, if you signed in a few days ago and checked the 'Remember Me' box, you won't be asked to sign in to view your My Statistics page. If you go to My Profile, you may have to sign in again since this page allows you to change your member name and email address (among other things).

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What are Project and Recruitment Badges?

Project badges recognize the contribution that a member has made to a research project running on World Community Grid, and recruitment badges recognize the member's contribution to introducing new volunteers to World Community Grid. All available project badges may be viewed here and all available recruitment badges may be viewed here.

Badges appear on a member's My Contribution page and next to their name in the forums.

Project Badges: There are 11 levels of badges awarded based upon how much computing time a member has contributed to each project:

  • Bronze - 14 days
  • Silver - 45 days
  • Gold - 90 days
  • Ruby - 180 days
  • Emerald - 1 year
  • Sapphire - 2 years
  • Diamond - recognizing higher levels of contribution of 5, 10, 20, 50 and up to 100 years of computing time
Recruitment Badges: There are 5 levels of badges awarded based on how many new people a member has recruited to World Community Grid:
  • Bronze - 1 new member
  • Silver - 5 new members
  • Gold - 10 new members
  • Ruby - 25 new members
  • Emerald - 50 new members
Members receive credit towards recruitment badges when someone signs up for World Community Grid using that member's unique recruitment URL and begins contributing computing power. You can get your recruitment URL and see which members you've recruited on your My Contribution page.

Recruitment badges are different from project badges in that they must be maintained. Recruited members must actively contribute computing power (return a result at least every 30 days) to count towards a member's recruitment badge. If an inactive recruited member becomes active again, they will once again count towards the recruitment total of the member who introduced them to World Community Grid.

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I'd like to put something about World Community Grid on my website; is there something that I can use?

If you'd like to promote World Community Grid and/or use the World Community Grid logo image on your website, you can make use of the World Community Grid widget. Click here for an FAQ explaining more about the World Community Grid widget.

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What is the World Community Grid widget?

The World Community Grid widget is a way for you to promote World Community Grid and show your team or personal contribution on your website or blog. It consists of a small piece of HTML code that you place on your website. This HTML code will display your custom widget with the most the current statistics for your or your team.

Here is an example:


To get your custom widget, just log in to World Community Grid, go to the Settings page, and click on the Create a Widget link in the left hand navigation. This will take you to a form where you can customize a widget with the World Community Grid logo, and your personal (or your team's) statistics. When you're happy with your widget, just copy the code at the bottom of the form, and paste it into your website!

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How do I find out the meaning of the messages on the Results Status Page?

A discussion of the results status page may be found here.

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What are the RSS, XML and atom buttons I see on certain World Community Grid web pages?

World Community Grid offers news feeds for News & Update articles published on the website and forum threads. If you don't know what a news feed is or how to use one, this video tutorial will be of assistance.

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How do I sign up for World Community Grid's feeds?

Click the RSS, XML or atom button on the page that contains the information you want to get feeds from. Then, select which Reader you would like to use to get the feeds and hit the 'Subscribe Now' button.

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Why do some work units remain on the Results Status page for a long period of time after they have been validated?

When more than one work unit for a particular research project shares the same input files, they are removed from the database in a different way than normal work units. All the work units that share the common input are left in the database until all work units that share the input files have completed successfully. If there a few work units in that group that error out, we then discuss with the research scientists how they would like the work units handled. In those cases, the work units will not be cleared from the database until we have agreement with the research scientists on how to proceed. This can cause some work units to stay in the database for an extended length of time.

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Forum Policy for Members

The Forum Policy for Members can be found here.

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Please remember our collective goal.

World Community Grid brings together people from across the globe to benefit humanity by creating the world's largest non-profit computing grid. We do this by pooling surplus processing power from volunteers' devices. We encourage your participation on the forums and provide information on team development and progress to make it easier for individuals to participate, to recruit new members and generally increase the amount of computing run time available for the humanitarian research projects we run. This web site is not a place to promote any other cause or issue.

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What do the Member Titles, underneath the Member Name, in the forums mean?

The following Member Titles are displayed based upon the number of posts a member makes:
0 - 49: Cruncher
50 - 149: Advanced Cruncher
150 - 499: Senior Cruncher
500 - 1499: Veteran Cruncher
1500 - 3999: Master Cruncher
4000+: Ace Cruncher

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How many characters may I use in a forum post?

The database limit is 32,700 characters. If special characters are used, the character count is decreased due to how special characters are stored in the database. If you have more than 32,700 characters, or utilize special characters, you will need to create 2 or more posts.

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What is a project timeline?

A project timeline displays that project's progress and status, including start date, estimated end date (when known), and the percentage of research tasks completed. This information can help volunteers know which projects are nearing completion and help them decide which projects to support with their computing resources.

The timeline also highlights key milestones and achievements, such as published papers and interesting research findings.

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Which projects have timelines?

The project timeline is currently available for active projects. At this time, it is not available for intermittent or completed projects.

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Where are project timelines displayed?

A high-level version of the timeline is displayed for each active project on the Research overview page. A more detailed timeline highlighting project achievements is also shown on at the top of the relevant project pages, within the Research section.

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What does the percentage on the timeline mean?

The percentage on the timeline on the Research overview page indicates how much of that project's work on World Community Grid has been completed.

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Why do some timelines not show end dates?

Many factors go into estimating how far a project is from completion - these factors change over time. Therefore, we only display the projected end date when the project will finish within about 6 months.

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How is the projected end date calculated?

The projected end date for an active project depends on a range of factors, including:

  • The quantity of research tasks that the researchers have provided to World Community Grid for the project.
  • The number of additional research tasks the researchers anticipate needing to run on World Community Grid. This is not always known and may change over time.
  • The rate at which volunteers contribute to the project. This depends on the number of active projects and the level of participation in each project compared to the other active projects.
  • Temporary pauses that may occur during the life of the project.
Where displayed, the end date is estimated based on the above factors. Since these factors may change from time to time, members should expect to see the end date change as well.

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What are the dates marked along a project timeline?

When you navigate to an active project's pages within the Research section, a timeline is displayed marking key dates in the lifespan of that project. Those dates represent important events, achievements and milestones for that project and link directly to the relevant News articles.

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Do you have an XML interface for the statistics?

You may obtain an XML version for most of the public statistics pages by simply adding either "?xml=true" if there are no other parameters in the URL or "&xml=true" if there already are parameters on the URL for the page.

Alternatively, you can view the XML page and follow the references provided on that XML document to go to locate pages that are in XML format.

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Do you have an JSON interface for the statistics?

You may obtain an JSON version for some of the public statistics pages by simply adding either "?format=json" if there are no other parameters in the URL or "&format=json" if there already are parameters on the URL for the page.

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Is there an API to get a list of in-progress and recently returned results for a member?

Yes. The URL for the API to access a members results is:

https://www.worldcommunitygrid.org/api/members/{member name}/results?code={verification code}

member name is the member name of the member whose results data you wish to access
verification code is found on the My Profile page of the member whose results data you wish to access

The default format is JSON.

Optional parameters are (can be combined):

  • Limit: Defines the number of results returned. Default is 25.
  • Offset: Defines how many results are skipped before the API returns any data. Default is 0.
  • SortBy: Defines the sorting order of the results. Options are: DeviceId, SentTime, ReportDeadline, ReceivedTime or CpuTime. Default is SentTime.
  • Format: The format of the data. Options are XML or JSON. Default is JSON.
  • ModTime: Return results which were last modified on or after this time. This value is a Unixtimestamp (number of seconds since midnight Jan 1 1970).
  • ServerState: Return results based on whether they are currently in progress or have already been reported back to World Community Grid. 4 would return in-progress results, 5 would return results which have already been reported back to the server.
  • Outcome: Return results based on the outcome of their processing. 1 means success, 3 means error, 4 means no reply, 6 means validation error, 7 means abandoned./
  • ValidateState: Return results based on the validation status. 0 means pending validation, 1 means valid, 2 means invalid, 4 means pending verification, 5 means results failed to validate within given deadline.
  • FileDeleteState: Return results based on their file delete state.  0 means not deleted.  1 means ready to delete.  2 means deleted.

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Is World Community Grid a non-profit organization?

World Community Grid is an IBM sponsored philanthropic initiative, started in November of 2004. Its purpose is to create the world's largest public computing grid for running research projects that benefit humanity. For more information, go to http://www.worldcommunitygrid.org/about_us/about_us.html

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How does World Community Grid get new projects?

First, a non-profit organization has to have a research project which benefits humanity for which they require some serious computer power in order to complete the research. Then someone from the research organization goes to the World Community Grid website and Submits a Proposal. At World Community Grid, we review the proposal to ensure it meets all requirements and is technically feasible to run on the grid. Then subject matter experts from IBM researcher review the proposal to ensure that the research is technically correct. After that, non-IBM subject matter experts review the proposal and also verify that the project is technically correct. After that, it is placed on the schedule for launch.

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Are the results produced by World Community Grid part of a commercial venture?

No. This is a philanthropic project, not for profit. The direct results of work done by the World Community Grid will be in the public domain.

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This sounds too good to be true. Am I missing something?

Everything benefits! Members who volunteer their unused processing power benefit by not only making their devices more productive, but also by helping make scientific inroads on humanitarian problems. Research organizations benefit by having access to huge amounts of computing power at no cost, enabling them to make more effective use of critical funds. The scientific community benefits because the project results are shared and made available in the public domain. The world benefits because humanitarian research is advanced.

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What is different about World Community Grid and other BOINC distributed computing projects?

Many of the BOINC projects are oriented toward one single research goal. And for those, the researchers have to set up their own infrastructure and manage the workload themselves. World Community Grid is able to accommodate multiple research projects. We run these projects for researchers from nonprofit organizations so that they do not have to manage the work and thus are able to focus on the science part of the research. For more information about how projects are selected to run on World Community Grid click here

To learn how to register and start participating in World Community Grid click here

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Will running the World Community Grid Software cost me more in electricity?

The amount of electrical energy consumed by your computer or other computing device is in many ways related to how much processing that it is doing at any given time. If it is sitting completely idle, then it uses relatively little power (usually about 50% of the maximum value). Actively using the device and simultaneously using more programs causes the device to consume more power. The World Community Grid software runs during times at which your device would otherwise be idle. This will cause it to use slightly more electricity (power) and therefore you may see a slight increase in your electricity costs. Exactly how much this increase will impact you depends on conditions where you live and how you have set your preferences. In most cases, the impact will be the equivalent of an additional low wattage light bulb. If these costs are a concern, you may limit the operational time for the software through preference settings on your Settings page or on your computer.

The default values of the BOINC agent are set so that the impact on average computers is minimal. Setting this to a higher value increases energy consumption and lowering it reduces energy consumption. We have chosen 60% because for most computers this figure seems to keep the energy consumption from increasing significantly and keeps laptop computers from getting too hot. In a multiple processor computer, reducing the number of processors permitted to run World Community Grid software may also control energy consumption. However, different machines vary in energy consumption patterns, so the maximum percent of the processor time and number of processors to be used by World Community Grid may be changed to custom values as follows:

  • To change your preferences for all computers under your member name, sign on to our website and go to your Settings page. Select “Device Manager”, then “Device Profiles from the left hand Navigation. Click the Profile Name that you want to alter and follow the instructions to change the preferences for your computer(s) and save. The new settings will take effect when the agent software next communicates with the servers.
  • To change the preferences for a particular computer under your member name. Double left click on the World Community Grid, or BOINC, icon in the system tray of the appropriate computer. Select Advanced View (if on Simple View) and from the menu at the top of the BOINC Manager select “Advanced”, then “Preferences” and designate your preferences and select “OK”. The setting changes made here take effect immediately and override those in the device profile above.
Changing the above settings will correspondingly increase or decrease the amount of contribution your computer is making to the research projects.

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What about connection costs?

The only costs associated with the connection depend on your service with your ISP. Uploads and downloads do not typically require lengthy connections, however busy periods or maintenance outages may impact your connection.

Additional information on connections may be found here.

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What energy benefits are realized by performing these computations on World Community Grid?

By utilizing idle capacity on existing computing devices, you arguably avoid the energy associated with manufacturing the additional servers which would be deployed to perform the computations. This realizes energy and resource savings for the materials and processes required to manufacture the servers and components.

By utilizing the power of World Community Grid, simulations can be run which mitigate the need to use materials, equipment, and living systems to perform research activities. While laboratory research will still be required to derive environmental or health benefits in the society at large, the research activities can be more finely focused, minimizing the laboratory research required and thus the materials and energy required to do the work.

The net societal benefit of the use of World Community Grid far outweighs the minimal additional energy which may be drawn from the otherwise idle devices. The power of the grid enables researchers to complete computations in months instead of years and bring new, exciting innovations and solutions to health and environmental issues which affect our communities, our global neighbors and the environment.

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How can I help reduce the energy usage associated with my computer?

The World Community Grid software and the workstation power management software may work in a complementary fashion. A World Community Grid participating computer may be set so that when it is in active use, the World Community Grid software harvests the unused CPU time. When a computer is not in active use for more than ten minutes, then power management software may be activated in accordance with the user's setting to enable energy saving. This may be enabled by going to your Device Profiles and selecting your 'Default' (or appropriate) profile and then selecting the 'Power Saving' option. There's plenty of computing power in the majority of our member's computers – enough to do their job, be productive, contribute to humanitarian research and still conserve energy at the end of the day.

By utilizing the Power–Saving Capability, we can all actively work towards reducing our energy use. And if you also participate in World Community Grid, you will be contributing to valuable humanitarian research.

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Does World Community Grid have a Twitter feed?

Yes, you can find World Community Grid on Twitter at: http://twitter.com/WCGrid

You can link World Community Grid to your Twitter account to automatically show your friends what you're doing to help solve the challenges facing our world. To do that, please click here.

For more information about Twitter, click here.

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Is World Community Grid on Facebook?

Yes, you can find the World Community Grid Facebook page here. Please click the 'Like' button to show your support for World Community Grid.

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What's new about Phase 2 of the FightAIDS@Home project? What will this phase of the project do?

Phase 2 of the project takes results from the molecular docking approach used in Phase 1 and produces a re-evaluation of the top hits found from the virtual screening, to further narrow down potential drug candidates.

While Phase 1 conducted virtual screening of chemical libraries using AutoDock and AutoDock Vina software tools, Phase 2 introduces a completely new computational method into the FightAIDS@Home effort: the BEDAM technique, implemented with Academic IMPACT software, a molecular simulation tool. Academic IMPACT models the thermodynamics of binding of a ligand to a protein including the reorganizational free energy of the docked complex. Much more computer time is needed to evaluate each docked complex, so only the top candidates from Phase 1's virtual screen are examined in this way.

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What benefits do you anticipate from this phase of the project?

The goal of the FightAIDS@Home project is to find new leads for HIV therapeutics. It is the first step in a long pipeline that may eventually lead to a new drug or therapeutic strategy. Subsequent to virtual screening in Phase 1 and further analysis in Phase 2 for hit identification, the compounds identified must be either purchased or synthesized to be tested experimentally. This is an expensive process, so if our list of hit compounds contains a large number of false positives, much time and money will be wasted. With the BEDAM post-processing of the virtual screening results, we can eliminate much of the false positive results from Phase 1 and save time and money in moving the drug candidates into the drug development pipeline.

Also, the methods that we use on HIV drug discovery are generic and can be applied to any other disease target. This means that other drug search projects on World Community Grid should benefit from our implementation of this computational pipeline.

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How does Phase 2 relate to Phase 1?

Phase 2 further refines the results from Phase 1 and helps us identify "false positives," thus saving time and money in future drug development processes.

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Are there plans to continue work on Phase 1 simultaneously?

Yes, we plan to continue to do virtual screens of large chemical libraries against a number of HIV targets. As the biology of the HIV life-cycle continues to be researched by the HIVE Center, and other efforts around the world, new targets and variations of existing targets are discovered and can be used in our Phase 1 activities. We are still currently screening many variations and sites from HIV Protease, Integrase and Reverse Transcriptase.

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How does this phase of the project build on the progress already made with FightAIDS@Home?

Significant new aspects of the biology of HIV have been discovered over the past 10 years. The research team's work on HIV protease has discovered new sites on the protein that represent targets that may result in new classes of drugs. Their work on HIV Integrase is exploring new chemical compounds that target a newly discovered mechanism to inhibit HIV infectivity. Again, this work may result in a new class of drugs that will work to defeat the virus and its ability to evolve drug resistance. The BEDAM approach being used in Phase 2 will help move us closer to the discovery of such drugs.

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What is BEDAM and how has it been used in the past?

BEDAM stands for “Binding Energy Distribution Analysis Method”. It is a method developed by the Levy group which uses advanced sampling and analysis techniques to calculate absolute binding free energies based on a foundation in statistical mechanics and data generated from molecular dynamics simulations.

In a collaboration between the Olson group at The Scripps Research Institute and the Levy group at Temple University, BEDAM techniques were recently developed and used in a computational challenge (SAMPL4) demonstrating that docking coupled with subsequent BEDAM processing gives more reliable hits. This challenge used blind data from a pharmaceutical company working on HIV Integrase inhibitors. The AutoDock Vina/BEDAM modeling performed the best among all automated computational predictions submitted in the challenge.

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Why is the BEDAM method useful to FightAIDS@Home? How is it different from other approaches previously used on the project?

The BEDAM approach uses Academic IMPACT, a computer program developed in the Levy Lab at Temple University to model the thermodynamics of protein-ligand binding. It is not a docking tool, but rather a method to evaluate the energetic and entropic components of the complexes from the molecular interactions predicted by docking. It would take prohibitively long to use the BEDAM approach for the millions of compounds without screening them first using the much faster docking software first, as done in Phase 1. Since the energetic estimates from the docking calculations are approximate -- to allow the high throughput needed to screen millions of compounds -- there are many so-called "false positives" in the list of top ligand protein complexes. The BEDAM analysis has been shown to potentially eliminate many of these false positive hits.

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What is unique about how research tasks are managed for FightAIDS@Home – Phase 2? How does this impact how work will be distributed to volunteers?

The simulations researchers need to carry out are typically very long running and complex, each of which would take several months to run on a single device. Instead, researchers split up each simulation for a given drug candidate into shorter running research tasks: much smaller and more manageable pieces. These pieces of work can be run independently and simultaneously on a volunteer devices.

However for FightAIDS@Home – Phase 2, the research tasks within a single drug candidate simulation are dependent on each other where the output of one task is used as the input to the next. This means longer research tasks within each drug candidate simulation which can’t be run simultaneously.

To handle this complexity, we are using two different, but related mechanisms called trickle messaging and intermediate uploads to allow us to track your progress through a research task and manage the handover of that task from one volunteer to the next to get it completed in the shortest time possible. This way, we can track the progress of the long simulations to ensure that computations are not delayed or lost, while the researchers get the valuable results back as quickly as possible. In addition, volunteers acquire their credits sooner too.

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What is trickle messaging?

Trickle messaging is a capability that allows your device to communicate with us while working on a research task to report the progress being made by your device. This allows us to determine whether work should continue on that research task or whether insufficient progress is being made and therefore that task should be handed over to another volunteer for processing.

This capability is particularly useful to a project like FightAIDS@Home – Phase 2 because of the nature of its research tasks, which may require more processing time to complete and can therefore be started by one volunteer and completed by another, without losing the progress made by the first volunteer.

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What is a trickle up message?

A trickle up message is when your device sends a message back to World Community Grid at certain processing milestones to inform us that you’re still making progress on the current research task. Along with intermediate results sent to us by your device, we use this information to:

  • Validate your work up to that point and grant credit accordingly;
  • Determine whether sufficient progress is being made by your device or whether the task should be handed over to another volunteer.

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Why is my device uploading result data (intermediate upload files) while a research task is still in progress?

We are using a mechanism called intermediate uploads whereby at certain processing milestones, your device would send us back partial results for the research task your device is currently working on. This allows us to validate the work you have completed up to that point and helps the researchers examine and interpret the results being returned by the volunteers.

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Why did my device stop processing a research task? And what is a trickle down message?

Using the information your device intermittently sends to us during the processing of a research task, we determine the likelihood of your device finishing the task before the completion deadline. If we determine that you are very likely to miss that deadline or you have already missed the deadline, we would send your device a trickle down message to instruct it to stop working on that research task and we then pass it along on to another volunteer.

There are two types of trickle down messages:

  • Soft stop: Instruction for your device to continue until the next milestone before stopping the computation of the current research task. This happens when your device is not making sufficient progress on the current calculation. We would then hand over your partial result to another volunteer to continue working on.
  • Hard stop: Instruction for your device to stop working on the current research task immediately. This happens when you have already passed the processing deadline without sending in the final full result or that there may be a communication error in sending us your progress. In this case, we would hand over the research task from the point of your last intermediate milestone to another volunteer to resume working on.
In either case, you will be awarded credit for the work you completed up to the point of the last checkpoint.

This mechanism allows work to be completed quicker and for the researchers to receive valuable results sooner.

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Why is this project using intermediate uploads and trickle messages?

Unlike many of our research projects, FightAIDS@Home – Phase 2 requires that research tasks within each simulation, and small processing steps within each task, to be carried out in sequence. This means that it would take much longer to get the results to the researchers.

Trickle messaging and intermediate upload capabilities allow us instead to move the same research task from one volunteer to the next, without losing progress along the way. Overall, this assures progress, shortens and stabilizes the processing time required to complete research tasks and speeds up the rate at which valuable results can be returned to the researchers.

While a typical FightAIDS@Home – Phase 2 simulation might take up to a year to complete, using these capabilities means that it can be completed in as little as two months.

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Why does this application require zero redundancy, i.e. no comparison of results across devices?

Unlike many of our research projects, FightAIDS@Home – Phase 2 does not require redundancy, where the same research task is sent to two devices and the results are compared for consistency. Instead, this project will be using various processing metrics during the computation of a research task to validate that the task is progressing without errors.

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What does the screen saver look like when FightAIDS@Home - Phase 2 is running?

Here is a video of the FightAIDS@Home - Phase 2 project graphics:

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What does the screen saver show?

The right portion of the screen saver shows both the target and candidate compound molecules, depicted as a collection of small spheres that represent the atoms of each molecule. These are the specific molecules that your device is currently working on.

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What does the progress bar in the screen saver represent?

The progress bar towards the bottom of the screen saver represents approximately how much of the current task your device has processed. When it reaches 100%, the computation is complete and the results will then be sent back to World Community Grid, where they will be packaged and delivered to the FightAIDS@Home researchers.

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What do the small spheres in the screen saver represent?

The small spheres represent the atoms in both the target molecule and candidate molecule currently being processed by your device.

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What does the Scripps Research Institute logo in the screen saver represent?

The Scripps Research Institute in La Jolla, California, is the largest private biomedical research institute in the US and the home of the research team behind the FightAIDS@Home Project.

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Where may I download pictures of the FightAIDS@Home - Phase 2 graphics?

A screenshot of the project graphics is available for download in the following resolutions:

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How can I help with this project?

You can help by joining World Community Grid and providing your computer or Android device's spare processing time. In addition, you can help support the researchers at their crowd sourced funding site at: www.crowdrise.com/CUREEBOLA
The researchers have turned to public support because the normal research grant process can take up to a year before any funds become available. Furthermore, because of public funding cuts and the sequester, fewer grants are available than in the past. The researchers are most grateful for any support you can give.

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Where can I learn more about the Ebola virus?

The following sites contain substantial information about the Ebola virus:

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What is Ebola?

The Ebola virus, first identified in 1976 and named after the Ebola river near its outbreak, is a member of the filovirus family. The virus, which is shaped like a long, flexible filament, attaches to and drives itself into the cell. It then replicates efficiently, budding out numerous copies of itself from the cell. The virus attacks several types of cells, including important cells of the immune system that circulate and carry the virus throughout the body. The damage includes inappropriate clotting, leakage from blood vessels, inflammation, organ failure and shock. When a person is first infected, there is a two to 21 day incubation period before the infected person shows symptoms. Initial symptoms can closely resemble those caused by flu or common tropical diseases and progress to include high fever, vomiting, diarrhea, dehydration and more. Contact with an infected person's fluids or the body of a patient that died from disease can infect the next person.

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How is Ebola currently controlled?

Infected people are best treated at special facilities which can best treat their symptoms and which can isolate their bodily fluids and keep them from infecting others. If special facilities are not available, bleach is used to disinfect everything that touches or comes from the patient. Treatment consists of re-hydration and treating the patients' symptoms. The patient may survive the disease if his own immune system is able to clear the virus before it has caused too much damage. Some experimental treatments have been used, but their efficacy is uncertain.

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What are the symptoms of Ebola?

When a person is first infected, there is a two to 21 day incubation period before the infected person shows symptoms. Initial symptoms can closely resemble those caused by flu or common tropical diseases. Symptoms progress to include high fever, vomiting, diarrhea, dehydration, bleeding and more.

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Where in the world is Ebola most common?

Most outbreaks have occurred in central Africa (Gabon, the Democratic Republic of the Congo, Uganda), but in 2014, a sustained epidemic in Western Africa sickened patients in Guinea, Liberia, Sierra Leone, Senegal, Nigeria, and Mali. Some of these people traveled to the United States, Germany, Spain, and England for treatment. Another species in the ebolavirus genus, Reston virus, exists naturally in Asia where it has been found among non-human primates and domesticated swine in China and the Philippines.

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What is the difference between a vaccine and an antiviral drug?

A vaccine gives your body immunity to the particular species of virus that the vaccine was manufactured to address. Once a person receives this vaccine and the immune system learns how to defend against the disease (typically 2 or more weeks), immunity to the disease is thought to last. Antiviral drugs are used to treat a viral disease once a person has contracted it and has no prior immunity, or if vaccination somehow failed to prevent infection. As of the start of this project, there are no approved vaccines or antiviral drugs that exist for Ebola. An antiviral drug could complement vaccines or antibody treatments because the antiviral would target the virus in a different way. Thus this project aims to discover an effective antiviral drug to fight Ebola.

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What does the screen saver look like when the Outsmart Ebola Together project is running?

Here is a video of the Outsmart Ebola Together project graphics when the Vina software is being used:

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What does the screen saver show?

The right portion of the screen saver shows both the target and drug candidate molecules, depicted as a collection of small spheres that represent the atoms of each molecule. These are the specific molecules that your device is currently working on. The left portion of the screen saver shows a scientist working in a laboratory.

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Where may I download pictures of the Outsmart Ebola Together graphics?

A screenshot of the project graphics is available for download in the following resolutions:

640x512
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What does the TSRI logo in the screen saver represent?

TSRI is the logo for "The Scripps Research Institute" in La Jolla, California, USA, which is the largest private biomedical research institute in the nation and the home of the research teams behind the Outsmart Ebola Together project.

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What does the Progress Bar in the screen saver represent?

The progress bar towards the bottom of the screen saver represents approximately how much of the current task your device has processed. When it reaches 100%, the computation is complete and the results will then be sent back to the World Community Grid servers, where they will be packaged and delivered to the Outsmart Ebola Together researchers.

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What do the small spheres in the screen saver represent?

The small spheres represent the atoms in both the target molecule and candidate molecule currently being processed by your device.

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What will this project do?

The project will compare about 200 million proteins encoded by the genes from a wide variety of known and unknown organisms. These genes came from organisms in samples taken from a range of environments, including water and soil, as well as on and in plants and animals. DNA from all the organisms in those samples (the metagenome) was extracted and analyzed to identify genes that encode proteins, most of which are enzymes. Uncovering Genome Mysteries will compare the proteins encoded by those genes to one another, both individually and in groups, to find genetic similarities. Such similarities can reveal the functions these organisms perform in various natural processes. Scientists can then use that knowledge to design solutions to solve important environmental, medical and industrial problems.

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Why are gene comparisons important?

Because of recent advances in DNA sequencing technology, there is now a huge amount of gene information available for a wide variety of organisms, with more being decoded every day. Many of these organisms, particularly microorganisms, have never been studied in detail before. We therefore know little about what they can do, and how they interact with their environment. However, it is likely that many genes from unknown organisms will be similar to genes from organisms that we know more about. When similarities are found, researchers get a head start in understanding previously unknown organisms.

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What will the results of this project be?

The researchers will publish an open-access database of the protein sequence comparisons computed on World Community Grid.

We expect that this information will help scientists discover new enzymatic functions, find how organisms interact with each other and the environment, document the current baseline microbial diversity, and better understand and model complex microbial systems.

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What are the expected benefits of this project?

There are two main areas where this research is expected to have a beneficial effect: current scientific research, and future technologies.

On the research side, the results should help improve scientific knowledge about gene and protein functions and biochemical processes in general, as well as helping scientists understand how microbial communities are changing in response to changing conditions in the natural world.

There are also several exciting ways in which this knowledge may help solve pressing world problems. For example, new knowledge about organisms should help identify, design and produce new antibiotics and drugs against diseases, as well as new enzymes for industrial applications, such as food processing, chemical synthesis, or the production of biodegradable plastics or biofuels. In the long-term this knowledge should help us manage the diverse organisms’ important functions in the world's ecosystem, in all environments, in industrial settings, and in human, animal and plant interactions.

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What is DNA?

DNA stands for deoxyribonucleic acid. DNA strands are molecules that act as blueprints for all living things. A single DNA molecule consists of a helical (coil shaped) strand or chain, consisting of four chemical “letters” that make up phrases (“genes”) and the genetic code. These letters are A, C, T and G and stand for the four types of compounds (adenine, cytosine, thymine, and guanine), which are assembled to form the DNA molecule’s gene codes.

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What are genes?

Genes are “DNA phrases” that encode for proteins. Specific three-letter DNA sequences each encode one specific amino acid. Chains of amino acids form proteins, some of which contribute to the structure of a cell (such as a microorganism) while others act as enzymes. Learn more.

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What are proteins?

A Protein is a chain of amino acids that folds in a particular structure necessary for the function of that protein. The chain can be composed of up to 20 different kinds of amino acids, and the types and order of those amino acids are encoded in the gene sequence (the genetic code). The amino acid sequence is also known as the “protein sequence” because there are multiple gene sequences that can specify the same protein sequence. A cell is made of thousands of proteins (in addition to fatty molecules called lipids, sugars and other chemicals) that can have either a structural function or an enzymatic activity. Enzymes are proteins that help break down other molecules or build new ones. Several enzymes can work in concert to convert molecules into other chemical building blocks for the cell (for example, sugar into lipids), or to extract energy from sugar.

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What are enzymes?

Enzymes are proteins that convert chemicals or act as catalysts. Certain enzymes in plants, for example, can assist in the absorption of carbon dioxide molecules and incorporate them into other cellular molecules.

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What is DNA sequencing?

DNA sequencing is a technology to determine the sequence of the four “letters” (A, C, T, G) that encode for genes, by chemically analyzing DNA molecules.

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How do you understand an organism's function from a DNA sequence?

In the first step we convert the DNA sequence into an amino acid sequence. This amino acid sequence then defines the properties of a protein. By comparing the amino acid sequence with other known sequences in databases, we can use the information about previously studied proteins to predict the functions of new proteins being investigated. If we know the function of all the proteins encoded by a genome, then we can ultimately understand how a cell or microorganism works.

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What is the difference between a genome and a metagenome?

A genome consists of all the genetic code for an individual organism, while a metagenome describes all genes and elements encoded in a group or community of organisms, for example, all of the microorganisms within a sample of soil or ocean.

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What are microorganisms?

Microorganisms are microscopically small life forms, mostly single celled, and include bacteria, archaea, protozoa, yeasts and microscopic algae. Members of these diverse groups are present in almost all environments on earth: in the air, water, earth, rocks, and even where conditions are very harsh, such as the deep ocean and polar environments. They play a crucial role in maintaining all ecological systems and interact closely with one another and with other life forms. They are present in and around other living systems, such as plants, animals and humans.

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Why are microorganisms important?

Microorganisms represent the great unseen and under appreciated majority of life on our planet. They are everywhere in the environment and in larger, more complex organisms. They are important for a huge variety of natural processes, including human health, agriculture and food production. For almost any kind of organic molecule, there will be a microorganism that has evolved the capacity to decompose, change, or construct it.

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Why is understanding microorganism function important?

Without a proper functioning of microorganisms the health of our planet would quickly deteriorate and higher organisms, including humans, would cease to exist. Despite their importance for our planet’s health, we know little about the diversity and function of microorganisms in the environment. Microorganisms also harbor new and unexpected functions that can be harnessed for biotechnological processes, such as food or drug production.

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What does the Uncovering Genome Mysteries project graphics show?

The graphics show a portion of a pair of protein sequences, which have been compared on your computer or device in the form of “letter codes”. The letters (A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V) represent the twenty types of amino acid molecules that are assembled in a chain to form the protein molecule. The matching letters in the two protein sequences are highlighted.

When sequences match, it means that the unknown organism produces a protein that is similar to a more well-known protein. This can indicate that the two proteins have similar functions, and give scientists a head start in understanding the unknown organism.

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What does the progress bar below the text show?

This graphically shows approximately how far along your device is in calculating the current task. It tells how many proteins have been compared against a set of other proteins. When your device has completed its work and the marker reaches the right end of the bar, the computation is completed and the results will then sent to World Community Grid before being packaged and sent back to the research teams.

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Where may I view a high quality video of the Uncovering Genome Mysteries project graphics?

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Where may I download images of the Uncovering Genome Mysteries graphics?

A screenshot of the project graphics is available for download in the following resolutions:

500x373
1000x745
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What are the potential benefits of the Mapping Cancer Markers project?

The project has three goals:

  • Identify sets of markers that may be able to predict if a person is at high risk of developing a particular cancer and increase the possibility of early detection.
  • Identify combinations of markers, which may predict a patient’s response to specific treatments. This would help make the treatment more personalized and could guide the development of customized therapeutic treatments for that patient.
  • Develop more efficient computational methods for discovering relevant patterns of markers.

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Is the Mapping Cancer Markers project similar to the Help Conquer Cancer project?

Although both projects relate to cancer research, the Help Conquer Cancer project (run on World Community Grid from 2007-2013) focused on basic science - discovering principles of protein crystallization and helping to determine 3D structure of over 15,000 proteins. Knowing the protein structure helps scientists to understand their function and design drugs that may provide novel treatment options for multiple complex diseases, such as cancer.

The Mapping Cancer Markers project focuses on clinical application - discovering specific groups of markers that can be used to improve detection, diagnosis, prognosis and treatment of cancer. As a second goal, the comprehensive analysis of existing molecular profiles of cancer samples will lead to unraveling characteristics of such groups of markers - and in turn improving our understanding how to find them more efficiently.

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What kinds of cancers are being studied in the Mapping Cancer Markers project?

Initially, we will focus on lung and ovarian cancer, followed by prostate, pancreatic and breast cancers. However, the project has been designed to accommodate other, less well-studied cancers if sufficient patient data exists.

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What will happen with the data generated by all these calculations?

After the scientists have received all of the computed results for the project, they will analyze the data and publish their findings. The raw data and algorithms will be made publicly available at that time.

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Some Mapping Cancer Markers jobs take longer to run than others. Why?

Each Mapping Cancer Markers task performs a search of multiple combinations of potential cancer biomarkers, representing a piece of a larger search strategy. It is difficult to split this extensive search into perfectly uniform pieces. Additionally, the machine-learning algorithms used to evaluate each combination of markers can take a variable amount of computing time to arrive at an answer. Together, these two factors make the run times of Mapping Cancer Markers tasks variable.

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What will the results of this project be?

The researchers will publish an open-access database of the protein sequence comparisons computed on World Community Grid.

We expect that this information will help scientists discover new enzymatic functions, find how organisms interact with each other and the environment, document the current baseline microbial diversity, and better understand and model complex microbial systems.

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What is a cancer marker and why is this a hard problem to solve?

Markers are specific genes (DNA segments), RNAs or proteins with differential activity. These molecules may be found in blood or tissue samples, and specific combination of these markers may be involved in a given cancer.

Even under healthy conditions, these genes, RNAs and proteins are activated and deactivated to perform specific functions. Cancer is caused by alterations to these activities. The Mapping Cancer Markers project focuses on discovering abnormal marker combinations, which may relate to cancer initiation and progression. It does so by comparing and analyzing data from many cancer patients and healthy control patients.

Extensive data mining and statistical analysis is needed to discover the subtle combinations of activity related to a cancer, and differentiate such signals from normal variation. This is done by systematically testing whether any of these combinations of markers are significantly correlated with the presence of the cancer.

Because there are thousands of possible markers, the number of their combinations becomes astronomical. Testing every combination would be impossible, even with all of the resources of World Community Grid. Various mathematical methods will therefore be used to zero in on the most likely combinations to be examined on World Community Grid.

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Are there any markers that are currently used?

There are several markers in clinical use. Two particular markers for breast and ovarian cancer, BRCA1 and BRCA2 recently received global attention after actress Angelina Jolie used them to assess her risk of developing the disease. In this particular case, only one marker BRCA1, in combination with family history was able to define her situation and to aid her in choosing her course of treatment.

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What is the difference between DNA, RNA, a gene and a protein?

DNA (deoxyribonucleic acid) is a long, helix shaped molecule that forms a chromosome. It acts as the master blueprint in charge of encoding genetic instructions used to develop all cells for a given organism. Specific sections of the DNA are called genes. A gene usually encodes information about how to build a particular protein molecule. RNA (ribonucleic acid) molecules are similar to DNA molecules, but are constructed from DNA information, and are used more directly to regulate and direct the machinery (other molecules) which creates proteins. The range of functions performed by these molecules is very broad and complex, and is a major subject in molecular biology. Typically, genes on the DNA (master blueprint) are “transcribed” into RNA, a process which is explained in this video. Other machinery then reads the RNA instructions and makes proteins such as hemoglobin, which is used to transport oxygen and carbon dioxide in blood.

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What are enzymes?

Enzymes are proteins that convert chemicals or act as catalysts. Certain enzymes in plants, for example, can assist in the absorption of carbon dioxide molecules and incorporate them into other cellular molecules.

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Why are microorganisms important?

Microorganisms represent the great unseen and under appreciated majority of life on our planet. They are everywhere in the environment and in larger, more complex organisms. They are important for a huge variety of natural processes, including human health, agriculture and food production. For almost any kind of organic molecule, there will be a microorganism that has evolved the capacity to decompose, change, or construct it.

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What do the Mapping Cancer Markers project graphics show?

While your computer carries out work for the Mapping Cancer Markers project, you may see the project’s graphics either on the World Community Grid screensaver, or within the World Community Grid software.

The graphics show a representation of the 23 pairs of human chromosomes in the right hand panel. Each chromosome is a DNA molecule containing genes and other information. The 23rd chromosome pair determines sex and comprises two “X” chromosomes for females or an “X” with a “Y” chromosomes for males. Genes are located at specific points along the length of these chromosomes. As your device analyzes certain combinations of genes, the approximate locations of those sets of genes within these chromosomes are highlighted in red.

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What does the Progress Bar at the top represent?

This graphically shows the approximate percentage of how far along your device is in calculating the current task. When it reaches 100%, the computation is completed and the results will then be uploaded to the servers at World Community Grid before being packaged and sent back to the research team.

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Where may I view a high quality video of the Mapping Cancer Markers graphics?


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Where may I download images of the Mapping Cancer Markers graphics?

A screenshot of the project graphics is available for download in the following resolutions:

500x300
1000x600
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Where is the Chesapeake Bay Watershed?

The Chesapeake Bay Watershed is the largest estuary in the United States and borders the Atlantic Ocean. Its land mass extends over parts of six Eastern states (New York, Pennsylvania, Maryland, Delaware, Virginia, and West Virginia) and the District of Columbia (Washington D.C.). It covers 64,299 square miles (166,534 square kilometers).

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Why is the restoration and sustainability of the Chesapeake Bay Watershed important?

Nearly 17 million persons live and work within the Chesapeake Bay Watershed today and its population continues to grow. With this population growth and the effects that it has on the streams and rivers and eventually the Bay itself, there has been a measurable decrease in the health of the Chesapeake Bay. According to the Chesapeake Bay Foundation, Bay health has poor grades, varying from year to year, depending on changing environmental conditions. For the Chesapeake Bay Watershed to improve and maintain a healthier condition, concerted action is needed.

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How is the health of the Chesapeake Bay measured?

The health of the Bay is typically measured in terms of the level of dissolved oxygen throughout the Bay. Scientists take measurements over the course of the year and at numerous locations around the Bay. The areas where the level of dissolved oxygen is too low to sustain aquatic life and vegetation are deemed anoxic. Areas that are marginally better are deemed hypoxic. The goal of restoring and sustaining the Chesapeake Bay is to significantly reduce the size of the anoxic and hypoxic areas returning the Bay to a healthier condition.

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What causes a decrease in the levels of dissolved oxygen?

Nutrients and sediment flow into the Bay from the land areas surrounding the Bay. These nutrients, such as nitrogen and phosphorus, lead to the growth of algae. This is commonly seen as a green film on the water’s surface. As these algae die, decompose, and sink to the bottom, they remove oxygen leaving the water with insufficient levels of oxygen to support life.

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Where do nutrients come from?

Although a small level of nitrogen and phosphorus enters the Bay through natural processes, the majority is the result of human activity. Agriculture contributes nutrients through farming methods, fertilization of the land, and tilling of the soil. Land development—the built environment—turns open land into impervious surfaces where rainfall and snow melt run off the surface rather than being absorbed into the soil. Waste treatment facilities provide for some nutrient removal, but many homes within the watershed use in-ground septic systems that eventually leach into the ground and reach stream and creeks flowing to the Bay. Manufacturing, power generation, and other human activities likewise contribute to nutrients flow.

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What has prompted action in the Chesapeake Bay Watershed?

Action to restore and sustain the Bay has had a long, though unsuccessful history. However, in May 2009, President Obama signed an Executive Order mandating the restoration and sustainability of the Chesapeake Bay Watershed. By this action, the various states and local communities will receive limits on the levels of nutrients they contribute to the Bay. Known as Total Maximum Daily Loads of nutrients and sediment, these communities must develop plans to curtail the impact of human activities on the levels of nutrients and sediment reaching the Bay.

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What kinds of actions might be taken?

There are various methods that can be adopted to reduce nutrient and sediment loads reaching the Bay. These are collectively known as “Best Management Practices (BMPs).” For example, farms can leave buffer areas between planted fields and bordering streams. They can minimize their use of fertilizers, plant cover crops in the winter (to absorb excess nutrients), and provide for the proper removal of animal waste. Municipalities can provide for separate storm water runoff systems and increase the frequency of street cleaning. Even individuals can affect change through household practices (reducing lawn fertilization, planting trees and shrubs) and limiting automobile driving. These types of actions are called non-point sources because they collectively contribute to the nutrient and sediment problem but are not individually measurable. Manufacturing, power generation, and other industrial contributors are point sources and these are regulated through existing policy and laws.

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How will the Computing for Sustainable Water project address the problem?

This project will, via a detailed simulation model of the entire Chesapeake Bay Watershed, test the impact of a large number of Best Management Practices (BMP)over a 20-year period. The proposed BMPs will be tested individually and in combination to assess their potential to effectively reduce the flow of nutrients and sediment into the Chesapeake Bay. Each of the various BMPs is expected to reduce the overall level of nutrients flowing into the Bay to some extent. However, scientists have no way of knowing in advance exactly how effective each might be. The project will provide an answer allowing policy-makers to choose those BMPs that will have the greatest impact.

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How will the results of this project help other watersheds and catchments?

The Chesapeake Bay Watershed is but one of over 400 major watershed/catchment systems globally. It is not unique in facing the challenges of population growth, increasing urbanization, and the challenges of changing environmental conditions. The results to be reported from this project can inform policy-makers worldwide as to best practices to employ to restore and sustain the globe’s precious water resources. More importantly, perhaps, information from this simulation can help citizens make better choices and help the private sector identify opportunities for new products, services, and processes that reduce nutrient flow.

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What is the difference between the Computing for Sustainable Water project and the Computing for Clean Water project?

The Computing for Sustainable Water project is studying how changes in human activities could help improve the quality of watersheds, critical for sustaining life and food sources. The Computing for Clean Water project is trying to develop less expensive water filters so that it would be more practical to produce clean drinking water from poor water sources.

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Screen saver/Graphics: What does the screen saver look like for Computing for Sustainable Water?

Here is a video capture of the Computing for Sustainable Water graphics:

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Screen saver/Graphics: Where may I download a high quality video of the Computing for Sustainable Water graphics?

You may download it here: Computing for Sustainable Water Video

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Screen saver/Graphics: Where may I download pictures of the Computing for Sustainable Water graphics?

You may get them by clicking the links for the resolutions below of the example screen shot.

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Screen saver/Graphics: What does the screen saver show?

The center portion of the screen saver shows a map of the Chesapeake Bay watershed area being simulated. The green on the left represents the surrounding land and the blue on the right, the Atlantic Ocean. The colored regions in the center show the overall nutrient level according to the color scale shown on the right. As each simulated time step is computed, the screen saver shows the change in nutrient level in each region from the prior time step. This color change is repeatedly displayed until a new time step is computed. The regions shown are aggregates of much smaller regions being used in the calculations. The color of the land to the left and ocean to the right does not correspond to a nutrient level.

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Screen saver/Graphics: What does the Computing for Sustainable Water logo represent?



The logo is intended to capture the goal of sustainability. The clasped hands, green representing sustainability and blue representing water, represent the idea that it is only through concerted, cooperative human action that we can realize this goal.

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Screen Saver/Graphics: What does the Progress Bar represent?

This graphically shows the approximate percentage of how far along the processing of the current work unit has progressed. When it reaches 100%, the computation should be completed and the results will then be sent back to the servers at World Community Grid.

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Screen saver/Graphics: What does the changing color scale represent?

The color scale shows the overall level of combined nutrient quantities, from low to high, aggregated by the respective land regions, as they change over the time span being simulated.

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What is schistosomiasis?

Schistosomiasis is a tropical disease caused by parasitic worms of genus Schistosoma that is transmitted by freshwater snails. The disease kills 200,000 people each year and affects over 207 million people.

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How is schistosomiasis currently treated?

Antimony, oxamniquine, mirazid, and metrifonate are drugs that have been used to treat schistosomiasis, but these drugs are either not highly effective, have been discontinued, or work against only certain forms of the disease. An orally administered drug called praziquantel is currently the best treatment for schistosomiasis. However, there is evidence that Schistosoma may become resistant to praziquantel.

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How is schistosomiasis transmitted?

The parasite's larvae, released by freshwater snails, penetrate the skin and eventually travel to the liver via the blood stream. Feeding on the host's blood, the parasites mature and move through the veins to other parts of the body such as the bladder and intestines. During their lifetime, which can be decades, they can produce hundreds of eggs per day. Some of the eggs are excreted in urine or feces, then hatch and infect more snails.

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What are the symptoms of schistosomiasis?

The body's immune response to the eggs, which remain in the body, is the main cause of the disease. The immune response is the body's natural defense mechanism to foreign invaders and normally causes temporary inflammation of the affected tissues. However, the disease causes continued inflammation, which damages the affected organs and so the problem becomes more severe. Schistosomiasis can affect various organs such as the liver, spleen, intestine, and kidneys, and can lead to death. One species of Schistosoma can also cause bladder cancer.

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How many people are affected by schistosomiasis?

700 million people worldwide are at risk of getting schistosomiasis. Currently over 207 million people in 74 countries are infected. As many as 200 thousand die each year from the disease.

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Are any animals involved in Schistosoma transmission?

Fresh water snails are the primary carriers of Schistosoma. In addition to humans, other wild and domestic animals can be infected, in some cases acting as a reservoir for the disease.

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Does schistosomiasis kill?

About 200,000 people die from schistosomiasis, primarily due to kidney failure and haematemesis (vomiting blood).

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What areas of the world are affected by schistosomiasis?

Schistosomiasis is most common in Asia, Africa, South America, and in tropical areas with freshwater snails.

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Is there a vaccine for schistosomiasis?

There are currently no vaccines available for schistosomiasis.

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Screen saver/Graphics: What does the screen saver look like for Say No to Schistosoma?

Here is a video capture of the Say No to Schistosoma graphics:

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Screen saver/Graphics: Where may I download a high quality video of the Say No to Schistosoma graphics?

You can download it here: Say No to Schistosoma Video

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Screen saver/Graphics: Where may I download pictures of the Say No to Schistosoma graphics?

You can get them by clicking the links for the resolutions below of the example screen shot.

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Screen saver/Graphics: What does the screen saver show?

The screen saver will cycle through sixteen images. In the graphic above, the right portion of the screen saver reflects the atoms in both the target molecule and drug candidate molecule currently being processed by your device. Each ball represents an atom. However, only a limited number of atoms are shown when the molecule is very large.

The five images on the left portion of the screen saver are thumbnail versions of the recently viewed, currently viewed and upcoming images to be viewed on the right of the screen. There are sixteen total images which are self-explanatory or have text included. The screen saver cycles through these showing the molecule picture after every fourth or fifth image.

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Screen saver/Graphics: What does the INFORIUM logo represent?

The INFORIUM logo represents Information technology making our lives better.

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Screen saver/Graphics: What does the Say No to Schistosoma logo represent?

The Say No to Schistosoma logo represents the stages of the life cycle of Schistosomiasis.

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Screen Saver/Graphics: What does the Progress Bar represent?

This graphically shows the approximate percentage of how far along the processing of the current work unit has progressed. When it reaches 100%, the computation should be completed and the results will then be sent back to the servers at World Community Grid.

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Screen saver/Graphics: What do the balls represent?

The small spheres represent the atoms in both the target molecule and drug candidate molecule currently being processed by your device.

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How is my computing time helping fight schistosomiasis?

There are many approaches that can help combat not only schistosomiasis, but many infectious diseases, whose genome is sequenced and proteins annotated. Using computational methods or bioinformatics, it is possible to predict or identify molecules that are essential to the survival of these organisms, so they can be then evaluated as drug targets or vaccines. Furthermore, it is also possible to identify whether a drug could interact and inhibit an essential protein of the parasite, in order to kill it or to stop its multiplication. For the design of new drugs, it is very useful to identify molecular targets in microorganisms, and then based on these targets, to design new drugs or evaluate some previously synthesized and used for other purposes. The availability of the complete genome of Schistosoma (http://www.sanger.ac.uk/resources/downloads/helminths/schistosoma-mansoni.html) will facilitate prediction of critical or important gene products, such as those involved in pathways or metabolic essential processes for the Schistosoma parasite.

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What is malaria?

Malaria is one of the three deadliest infectious diseases on Earth. Plasmodium falciparum, the protozoan parasite that causes the most severe form of malaria, kills more people than any other parasite on the planet. Four other species of Plasmodium can also cause malaria infections in people (Plasmodium vivax, Plasmodium malariae, Plasmodium ovale, and Plasmodium knowlesi), but these four species tend to cause a milder form of malaria that is rarely fatal. Plasmodium vivax causes the largest number of malaria infections each year, but Plasmodium falciparum causes about 90% of the deaths that result from malaria infections. Consequently, most of our research on GO Fight Against Malaria will focus on Plasmodium falciparum, but we will also perform some research against the molecular targets from Plasmodium vivax.

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How is malaria transmitted?

Malaria infections are transmitted to humans by certain types of mosquitoes. Female mosquitoes from the genus Anopheles are the specific kinds of mosquitoes that are responsible for hosting and then spreading malaria infections. Since male mosquitoes eat plant nectar instead of blood, only the females transmit malaria infections. Female mosquitoes become infected with the malaria parasite when they drink the blood of a human who has a malaria infection. After being ingested by a mosquito, the parasite progresses through specific stages of its life cycle that can only occur when it is inside a mosquito (see the FAQ below on the parasite’s life cycle). When that infected female mosquito then feeds on a different person, its saliva contains the malaria parasite, which gets injected into the person’s skin.

In very rare cases, blood transfusions can also transmit malaria infections, but female mosquitoes are the main culprit.

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How is malaria currently controlled?

Since the female Anopheles mosquitoes tend to feed on human blood at night, insecticide-treated bed nets are a common tool that helps prevent malaria infections. The bed net makes it harder for mosquitoes to bite people, and the specific insecticide that coats it can kill some of the mosquitoes. Insecticides are also sprayed indoors to help kill or deter the mosquitoes. These strategies are called “vector control,” since they focus on decreasing the ability of mosquitoes (the vector) to spread the infection to humans. Although these approaches can help decrease the spread of malaria, malaria infections are still very widespread. In addition, mosquitoes that are resistant to the insecticide can eventually arise, similar to the way in which malaria parasites that are resistant to the drugs eventually evolve.

After a person has become infected with malaria, "chemotherapeutic approaches" are employed (that is, a drug or a combination of different drugs is used to cure the malaria infection). There are many different drugs that can be used to cure malaria infections; however, the parasites that cause malaria eventually evolve “drug resistance” against the specific chemicals that are used to eliminate the parasites (see the FAQ below on “multi-drug-resistant mutant superbugs”). For example, in the past the drug chloroquine was very useful for curing malaria infections, but the Plasmodium parasites eventually evolved drug resistance against chloroquine. Later, the dual drug combination of sulfadoxine plus pyrimethamine was developed. For several years it was very useful for curing malaria infections, and it helped save millions of lives. But then the Plasmodium parasites evolved resistance to this dual drug combination, too. Since resistance to sulfadoxine plus pyrimethamine started becoming very prevalent, the World Health Organization now recommends that artemisinin-based combination therapies (“ACTs”) be used to treat malaria infections. Unfortunately, Plasmodium falciparum parasites that are able to resist treatment with artemisinin, and its derivatives, have recently started to appear at the Thai-Cambodian border. The drug resistance phenomenon is the reason why discovering and developing new drugs that can eliminate multi-drug-resistant malaria infections is a global health necessity, and it’s the reason why we created the GO Fight Against Malaria project.

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What are the symptoms of malaria?

When the Plasmodium falciparum parasites infect red blood cells, which the parasites use for food and then burst, the symptoms of malaria start to appear. Fevers, headaches, and vomiting are common symptoms of malaria, and these symptoms tend to appear within ten to fifteen days after the person is bitten by an infected mosquito. Other symptoms of malaria include shivering, convulsions, joint pain, retinal damage, an enlarged spleen, an enlarged liver, hypoglycemia, renal failure, and anemia. Whitening of the retinas can also be associated with “cerebral malaria,” which can sometimes help doctors tell the difference between malaria and other causes of fevers. Since the parasite diminishes the patient’s supply of red blood cells, it starts to cut off the supply of nutrients that are needed for the patient’s internal organs to function properly. If the malaria infection is not treated promptly and properly, then malaria can lead to comas and death. Even if malaria does not kill the infected patient, it can still cause severe brain damage and other developmental impairments.

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How many people are affected by malaria?

Over three billion people are at risk of becoming infected with malaria. There are over two hundred million clinical cases of malaria each year, and approximately one million people are killed by malaria infections every year. The groups of people who are especially vulnerable to malaria infections are children and pregnant women.

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Does malaria kill people?

Yes, malaria infections kill almost one million people each year, and most of those who die from malaria are children under the age of five. Every 30 to 45 seconds, a child dies of malaria.

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What areas of the world are affected by malaria?

Malaria thrives in tropical and subtropical regions. Malaria infections are found in at least 106 different countries. It predominantly infects people in Africa, South-East Asia, and South America. However, in this era of globalization, it affects almost all sub-populations of the world, either physically, mentally, or monetarily. Millions of people from developed countries visit or work in malaria-infested regions each year.

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Is there a vaccine for malaria?

There is not yet an approved vaccine for malaria, but this is an active area of research being performed by many labs throughout the world. Recently, progress has been made in the development of a vaccine to protect children against malaria infections. This new vaccine, called “RTS,S,” is made by GlaxoSmithKline, and in a pilot study it decreased the risk of severe malaria infections by almost 50%. Although this new vaccine represents very exciting progress against malaria, the general goal for vaccine development is to reduce the risk of infection by at least 90%. Thus, more work still needs to be done to effectively prevent malaria infections.

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What is the life cycle for the malaria parasite?

When an infected female mosquito bites someone’s skin, the Plasmodium parasite is injected. The parasite quickly invades liver cells (within a matter of minutes after it was injected). The parasite hides in the liver cells, where it undergoes asexual multiplication. This stage in the liver tends to last for eight to thirty days, during which the symptoms of malaria do not yet appear. The parasites escape the liver by rupturing the infected cells. The parasites then invade red blood cells, where they continue to undergo asexual multiplication. When these malaria parasites replicate themselves in red blood cells (which the parasites use for food and then burst), the symptoms of malaria appear (see the FAQ above on the symptoms of malaria). If another mosquito then feeds on that infected person’s blood, that mosquito becomes infected. Plasmodium parasites can only sexually reproduce when they are inside a mosquito.

Detailed descriptions and amazing visualizations of the malaria parasite’s life cycle in both mosquitoes and humans were created by Drew Berry and are available at: http://www.youtube.com/watch?v=_OIY-M6GnCU (part 1 = human stages) and http://www.youtube.com/watch?v=7sHB56AjHQ8 (part 2 = mosquito stages).

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What is GO Fight Against Malaria?

GO Fight Against Malaria is a project of the Olson laboratory (http://mgl.scripps.edu). The project uses distributed computing to help accelerate research on the discovery of new drugs which can cure infections of multi-drug-resistant mutant “superbugs” of Plasmodium falciparum, the parasite that causes the deadliest form of malaria.

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What are multi-drug-resistant mutant superbugs?

Being “resistant” to a drug means that the specific target protein molecule, whose activity the drug blocks, has mutated (changed), which makes the drug lose its effectiveness at treating the infection. But at the same time, the mutation does not prevent the superbug from surviving and reproducing. Being “multi-drug-resistant” means that the pathogen has acquired mutations that allow it to escape treatment with multiple different types of drugs, while still allowing the pathogen to survive and multiply. Since the ability to escape treatment by the drugs helps the parasites survive and multiply, drug-resistant strains of the parasite have a selective advantage and become widespread throughout the malaria-infested regions.

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How do I join the GO Fight Against Malaria project?

Joining the GO Fight Against Malaria project and the other projects at IBM’s World Community Grid is a simple process. Detailed, step-by-step instructions are available at: http://www.worldcommunitygrid.org/reg/viewRegister.do. After installing BOINC and registering to become a member of World Community Grid, your computing device is then automatically put to work on these projects, and you can continue using your device as usual.

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How does the GO Fight Against Malaria software work?

The GO Fight Against Malaria project uses software that automatically downloads small amounts of input data and then performs calculations that model how well different drug candidates interact with various molecular targets from the malaria parasite. After your device finishes one set of calculations, the results are sent by World Community Grid to a computer at The Scripps Research Institute. The Scripps research team then analyzes the results produced by all of the different donor machines on World Community Grid.

This project uses AutoDock 4.2 and the new AutoDock Vina computer software to evaluate how well each candidate compound (molecule) attaches ("docks" or "binds") against a malarial target (usually a protein molecule.) Millions of candidate compounds will be tested against 14 different molecular drug targets from the malaria parasite in order to discover new compounds that can block (inhibit) the activity of these multi-drug-resistant mutant superbugs. These candidates will be tested by docking flexible models of them against 3-D, atomic-scale models of different protein drug targets from the malaria parasite, to predict (a) how tightly these compounds might be able to bind, (b) where these compounds prefer to bind on the molecular target, and (c) what specific interactions are formed between the candidate and the drug target. In other words, these calculations will be used to predict the affinity/potency of the compound, the location where it binds on the protein molecule, and the mode it uses to potentially disable the target. Compounds that can bind tightly to the right regions of particular proteins from the malaria parasite have the potential to “gum up” the parasite’s machinery and, thus, help advance the discovery of new types of drugs to cure malaria.

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What are AutoDock 4.2 and AutoDock Vina?

These are two different types of “docking” programs, which allow us to computationally search for new compounds that might be able to bind to and block the activity of molecular drug targets from the malaria parasite. Both of these docking programs were created and developed by the Olson lab at The Scripps Research Institute (http://mgl.scripps.edu).

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How do these docking programs work?

AutoDock is a suite of automated docking tools designed to predict how “small molecule compounds,” such as substrates or drug candidates, bind to a receptor (target) of known 3-D structure and to estimate how tightly that small molecule binds to that receptor. That is, it predicts both the small molecules “binding mode” and estimates its potency against the target. The AutoDock algorithm is essentially a high dimensional stochastic search utilizing a “Lamarckian genetic algorithm” approach with flexible models of the small molecules. When docking any given drug candidate against a particular protein target, the space of all possible configurations must be explored to find the best energetic fit between the two molecules. Any given docking protocol must explore all possible degrees of freedom that are specified in the system. AutoDock consists of two main programs: autodock performs the docking of each compound against a set of grid maps that describe the energetic landscape of the target protein, and autogrid pre-calculates these grid maps before autodock is run, which greatly increases the speed of the autodock phase of these calculations.

AutoDock Vina also uses pre-calculated grid maps (which are generated internally, instead of using a separate program, such as autogrid). Vina also uses flexible models of the small molecules, and it also treats the docking process as a stochastic global optimization of the scoring function. But Vina utilizes a different scoring function and a different search algorithm than AutoDock, and Vina’s search process is guided by the gradients in the energetic landscape of the target protein (unlike AutoDock4.2).

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Will my device only be working on the GO Fight Against Malaria project?

You get to decide which project or projects your computing time will help advance; however, only some projects are available for mobile devices. You can select from the active projects that are being performed on World Community Grid by visiting the My Projects page. Follow that link, and you can view all the available projects and choose those in which you want to participate.

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How can I learn more about malaria?

More information about malaria can be found at the World Health Organization’s website, the Medicines for Malaria Venture website, and on Wikipedia.

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Screen saver / Graphics: What does the screen saver look like for the GO Fight Against Malaria?

Here is a video capture of the GO Fight Against Malaria project graphics:

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Screen saver / Graphics: Where may I download a high-quality video of the GO Fight Against Malaria graphics?

You may download it here: GO Fight Against Malaria Video

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Screen saver / Graphics: Where may I download a high-quality picture of the GO Fight Against Malaria graphics?

You may download this picture by clicking any of the resolution links below of the example screen shot.

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Screen saver / Graphics: What does the screen saver show?

The screen saver shows the target and drug candidate molecules, depicted with small spheres representing a subset of the atoms that make up the molecules. These are the molecules the program is working on with your device.

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Screen saver / Graphics: What does the GO Fight Against Malaria logo represent?

The circular logo shows a world map in the background, a mosquito in the center, and surrounding hexagonal lines representing a common organic chemistry bond structure for a benzene ring. This logo represents the GO Fight Against Malaria project at The Scripps Institute in La Jolla California, USA.

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Screen saver / Graphics: What does the progress bar represent?

This graphically shows the approximate percentage of how far along the processing of the current work unit has progressed. When it reaches 100%, the computation should be completed and the results will then be sent back to the servers at World Community Grid.

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Screen saver / Graphics: What do the rotating balls represent?

The small spheres represent a subset of the atoms in both the target molecule and drug candidate molecule currently being processed by your device.

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What is Leishmaniasis?

Leishmaniasis is a disease caused by a protozoan parasite of the genus "Leishmania." It is transmitted by sand flies and causes skin lesions, with some forms affecting internal organs, possibly leading to death. The disease is a severe public health problem in 97 countries around the world, and is seen in other countries due to tourism. The disease affects more than two million people per year. In Colombia and Latin America the disease has increased so significantly that now Colombia is second only to Brazil in number of cases of Leishmaniasis in the Americas.

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How is Leishmaniasis currently controlled?

Currently, control of the disease is accomplished primarily via chemotherapy and with measures to control the spread via insects and animals. The drugs used in the treatment of disease present problems of toxicity and other side effects. These adverse effects sometimes cause patients to discontinue treatment, which leads to drug resistance. In addition, the high cost of anti-Leishmania compounds is an inhibitor, because the disease is common mostly in developing countries.

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How is Leishmaniasis transmitted?

Leishmaniasis is transmitted through the bite of sand flies of the genus Lutzomyia in the Americas and the genus Phlebotomus in other parts of the world. The female insects need blood meals to develop eggs, and in the process of feeding, infected insects inject the parasite into the new host.

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What are the symptoms of Leishmaniasis?

Leishmaniasis is presented mainly under three clinical forms: cutaneous, mucocutaneous and visceral. The cutaneous form causes ulcerated lesions, but may also appear as warty lesions or spots. The mucocutaneous form causes cell death in mucous membranes, especially the nose and also the throat. The visceral form is characterized by infection of the spleen, liver, lymph nodes and bone marrow. This form causes anemia, clotting problems, weight loss, and enlarging of the spleen, liver and lymph nodes.

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What treatments exist for Leishmaniasis?

Although pentavalent antimonials (commercially known as Pentostam or Glucantime) have been the drugs of choice to treat this disease, there have been frequent reports of treatment failure due to resistance by the parasite. In addition, these drugs can cause mild to severe adverse effects, including death. Second-choice drugs, such as amphotericin B, pentamidine and paromomycin, also have toxic effects, sometimes requiring hospital management. Miltefosine, an oral drug, is one of the compounds used recently in the treatment of Leishmaniasis, but its effectiveness has only been tested with some species of the Leishmania protozoans. Although its administration is oral and effective against some species of Leishmania, its prescription is contraindicated in pregnant women because of the potential of causing birth defects.

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How many people are affected by Leishmania?

An estimated 350 million people are at risk of contracting the disease, and approximately 2 million people suffer from the disease in 97 endemic countries each year. Of these 2 million people affected, approximately 1.5 million cases are of the cutaneous form of Leishmaniasis and about 500,000 cases are of the visceral form. A smaller proportion of cases are of the mucocutaneous form.

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Are any animals involved in Leishmania transmission?

In some parts of the world, mice and rodents have been involved, while in other areas, some bears and foxes are often involved in transmission of cutaneous or mucocutaneous Leishmaniasis. Dogs seem to be the most important animal in the transmission of the visceral form of the disease.

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Does Leishmaniasis kill?

The cutaneous and mucocutaneous forms are not fatal, but the visceral form of the disease may cause death if the patient is not treated properly in time.

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What areas of the world are affected by Leishmaniasis?

Leishmaniasis is endemic in five continents: the Americas (from southern U.S.A. to northern Argentina), Asia, Africa and Europe (on the Mediterranean coast). Relatively recently, a case of Leishmaniasis has been discovered in Australia.

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Is there a vaccine for Leishmaniasis?

Although there have been attempts to develop a vaccine against Leishmaniasis, there is currently no vaccine available.

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What is the life cycle for the Leishmania parasite?

Leishmania is a parasite transmitted by the bite of a female sand fly of the genus Lutzomyia. The insect injects humans or other animals with promastigotes, the infective stage of the parasite. Once injected into the skin, the promastigote is consumed by immune system cells such as macrophages and other mononuclear phagocytic cells. Within these cells, the promastigote transforms into the tissue stage of the parasite, known as an amastigote, which multiplies inside the cell by simple division, moving on to infect other phagocytic mononuclear cells. Various factors of the parasite and host determine which form of the disease appears in the host. The insects become infected by sucking infected cells of the host during a blood meal. In the insect´s gut, the cells rupture, releasing amastigotes, which are transformed back into promastigotes. They multiply and develop in the gut. After several days, depending on the species, the parasites migrate to the mouthparts of the insect, where they are ready again to be transmitted to a host during the next blood meal.

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Screen saver/Graphics: What does the screen saver look like for Drug Search for Leishmaniasis?

Here is a video capture of the Drug Search for Leishmaniasis graphics:

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Screen saver/Graphics: Where may I download a high quality video of the Drug Search for Leishmaniasis graphics?

You may download it here: Drug Search for Leishmaniasis Video

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Screen saver/Graphics: Where may I download pictures of the Drug Search for Leishmaniasis graphics?

You may get them by clicking the links for the resolutions below of the example screen shot.

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Screen saver/Graphics: What does the screen saver show?

The left portion of the screen saver shows the target and drug candidate molecules, depicted with small spheres representing the atoms that make up the molecules. These are the molecules the program is working on with your device.

The right portion of the screen saver shows various images relating to Leishmaniasis with captions.

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Screen saver/Graphics: What does the PECET logo represent?

PECET is the logo for "Program for the Study and Control of Tropical Diseases" at the University of Antioquia, in Medellín, Colombia

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Screen Saver/Graphics: What does the Progress Bar represent?

This graphically shows the approximate percentage of how far along the processing of the current work unit has progressed. When it reaches 100%, the computation should be completed and the results will then be sent back to the servers at World Community Grid.

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Screen saver/Graphics: What do the balls represent?

The small spheres represent the atoms in both the target molecule and drug candidate molecule currently being processed by your device.

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How is my computing time helping fight Leishmaniasis?

There are many approaches that can help combat not only Leishmaniasis, but many infectious diseases, whose genome is sequenced and proteins annotated. Using computational methods or bioinformatics, it is possible to predict or identify molecules that are essential to the survival of these organisms, so they can be then evaluated as drug targets or vaccines. Furthermore, it is also possible to identify whether a drug could interact and inhibit an essential protein of the parasite, in order to kill it or to stop its multiplication. For the design of new drugs, it is very useful to identify molecular targets in microorganisms, and then based on these targets, to design new drugs or evaluate some previously synthesized and used for other purposes. The availability of complete genomes of several Leishmania species, one from the Americas (L. braziliensis) and two from other parts of the world (L. major and L. infantum) (GeneDB) will facilitate prediction of critical or important gene products, such as those involved in pathways or metabolic essential processes for the parasite Leishmania.

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Why is clean water important?

In some parts of the world, people take clean water for granted. But in much of the developing world, water is a scarce and often unavailable commodity. In the year 2000, about 8% of the world’s population lived in countries chronically short of water. But by 2050 it is estimated that this number will rise to 45% of the world’s population – by then the equivalent of 4 billion people.

Even where water is available, if it is not clean, it can become one of the biggest factors in spreading debilitating and often fatal diseases. Millions of people, including an estimated 1.4 million children, die annually most often from diarrhea, caused by drinking unsafe water.

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How does ultrafiltration work?

Ultrafiltration refers to the process of reducing or eliminating very small particles from water by passing water under very high pressure through a membrane containing very fine pores. The unwanted particles have a harder time getting through the membrane than the water molecules, so fewer of them appear on the other side. The high pressure needed for ultrafiltration requires expensive equipment and much energy.

Any way to reduce the pressure needed in ultrafiltration can make water purification a cheaper and more accessible process. This is precisely what the Computing for Clean Water Project is ultimately aiming to achieve, by first studying in detail how the water molecules flow through filters.

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How does reverse osmosis work?

To understand reverse osmosis, first consider osmosis. Osmosis is the movement of a solvent, such as water, through a semi-permeable membrane to equalize the concentrations of a solute, such as salt, on each side of the membrane. If, for example, unequal concentrations of salt solutions were placed on each side of a suitable membrane, the water would move from the lower concentration side through the membrane to the side with the higher concentration of salt. By applying pressure on the higher concentration side, the process can be reversed, hence reverse osmosis. So reverse osmosis can effectively reduce salt concentrations, and is one of several major approaches used to remove salt from seawater.

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What is a carbon nanotube?

A carbon nanotube is made from graphite, the same material that is used in pencil leads. Graphite is a form of carbon – another well-known form of carbon is diamond. Graphite is made of sheets of carbon, just a fraction of a nanometer thick. One nanometer is a billionth of a meter. Under certain conditions, it is possible to grow such sheets so they wrap around and form tubes. The diameter of these tubes is only a few to tens of nanometers, so that is why they are called nanotubes.

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How do you make nanotube membranes?

A nanotube membrane typically consists of nanotubes that have all been aligned in one direction, like the bristles of a brush, embedded in another material that is impermeable to water. One recipe for making such membranes is to first grow the carbon nanotubes on a silicon surface so they all stand up on end. This can be done by first putting nanoparticles of a metal like nickel on the silicon, then letting a chemical vapor containing a carbon compound react with the nickel catalyst, resulting in the carbon growing out of the particles as nanotubes.

Once the nanotubes have been grown, a thin film of silicon nitride is deposited around them, so the nanotubes are embedded in it. Silicon nitride is an insulating material similar to glass. Then the underlying silicon is etched away with a chemical that does not affect the silicon nitride nor the nanotubes, leaving a free-standing membrane of nanotubes embedded in silicon nitride. Finally, etching in a vacuum chamber with reactive ions removes the closed ends of the nanotubes, so that nanometer scale pores through the membrane open up.

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How does a molecular dynamics simulation work?

Newton wrote down simple equations of motion to describe how balls fly through the air or apples fall. The world of atoms and molecules is subject to quantum mechanics, which is a good deal more complex than classical Newtonian mechanics. Yet it turns out that by making certain approximations and simplifications, it is possible to simulate the molecular world by letting large numbers of atoms or molecules interact according to Newton’s laws.

So the idea of a molecular dynamics simulation is to let things evolve using a computer program which can track every detail of what happens to each molecule over time as it is buffeted by all the surrounding ones. But to get a statistically meaningful picture from such simulations it usually requires repeating the simulations thousands or even millions of times with slightly different starting conditions. It is this computational challenge that this project addresses, by getting volunteers to provide more than a thousand times the computing power that a typical research group would have access.

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How much computing power does this project need, and why?

Based on the molecular dynamics simulations that the researchers have done up to now, using a cluster of 20 nodes (160 CPU cores) for a couple of months at a time, they estimate that to extend the simulations to water-flow velocities typical of practical nanotube filters, they will require another factor of 400 or more in compute time. And to simulate a representative range of membrane pore sizes would require a further factor of 10, for a total of order 106 thousand single-core-CPU-years. Add on to this a wide variety of contaminants they would like to add to the water in the simulations, and the sky is the limit!

Of course, the researchers will have to go one step at a time, and a lot of the computing effort will be to verify previous results at each stage and to make sure the results are reliable.

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What is the expected practical outcome of this project?

The research is primarily driven by a desire to understand, at a fundamental level, why experimental results show that water can flow through some nanotube filters far more easily than expected according to the classical laws of hydrodynamics. By getting a better understanding of these fundamentals, the research aims to shed light on ways in which such filters could be improved even further, and lead to more affordable and more energy efficient types of water filters for cleaning and desalinating water.

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Where will the results of this research be published?

The researchers expect to publish papers in a number of academic journals. Typically, Physical Review Letters and Applied Physics Letters are targeted for similar sorts of research topics. Really big breakthroughs might get into prestigious multidisciplinary journals like Science and Nature. Of course, for any publication that gets accepted, the volunteers on Computing for Clean Water will be the first to know, and will be duly acknowledged in the articles.

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Screen saver/Graphics: What does the screen saver look like for Computing for Clean Water?

Here is a video capture of the computing for clean water graphics:

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Screen saver/Graphics: Where may I download a high quality video of the Computing for Clean Water graphics?

You can download them here: Computing for Clean Water Video

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Screen saver/Graphics: Where may I download pictures of the Computing for Clean Water graphics?

You can get them by clicking the links for the resolutions below of the example screen shot.

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Screen saver/Graphics: What does the screen saver show?

The main center of the screen saver shows the atoms of a carbon nanotube surrounding a sampling of water molecules inside. The positions of the atoms match the computation your device is performing at that time. The carbon atoms are shown in blue. The water molecules consist of oxygen and hydrogen atoms shown in red and green. About every five minutes, the nanotube is shown alternately in full size or as a close-up near the wall of the nanotube. More of the water molecules are shown in the close-up view. At the left, the "Prog: nn.n%" shows the progress computing the current work unit in percentage complete. The dark blue background shows waves of water which move slowly and climb in level along with the progress of the work unit.

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Screen saver/Graphics: What does the CNMM logo represent?

CNMM is the logo for the project team at Tsinghua University. It stands for "Center for Novel Multidisciplinary Mechanics".

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Screen Saver/Graphics: What does the Progress Bar represent?

This shows the approximate graphical and percentage value of how far along the processing of the current work unit has progressed. When it reaches 100%, the computation should be completed and the results would then be sent back to the servers at World Community Grid.

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Screen saver/Graphics: What does the blue tube-like object represent?

The blue tube-like object represents the carbon nanotube through which the water is passing in the simulation. The blue spheres are carbon atoms. In some of the work units, the carbon nanotubes may have two layers of carbon atoms and in some there may be just one layer. The size of the carbon nanotube may also vary with work unit. Every 5 minutes the screen saver switches between a large view and a close-up view near the wall. The close-up view shows more of the water molecules present there in the simulation. In the larger version, only a sampling of the water molecules are drawn. This is done to limit the computing time required to show the picture.

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Screen saver/Graphics: What do the green and red bubble-like objects inside the blue tube represent?

The red and green spheres represent the atoms forming water molecules. Each water molecule has two hydrogen atoms (green) and one oxygen atom (red). Not all of the water molecules are drawn to limit the use of computing time spent on creating the graphics images.

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Screen saver/Graphics: What do the waves in the background represent?

The dark blue waves in the background are a background decoration. They move slowly and their level rises with the percentage completion of the particular work that your machine is working on.

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Why is solar energy important?

It is expected that by the year 2050 the world's energy requirements will be twice today’s demand. Energy is without doubt a prerequisite for economic stability in both the developed and developing world; however, despite its importance, the actual energy system is far from being self-sustainable. Achieving a completely sustainable energy system will require technological breakthroughs that radically change our paradigms on how we produce and use energy. A possible solution to this problem is solar energy. Every hour, enough solar energy reaches Earth to supply our energy need for an entire year. Finding the means to convert the incident solar energy into usable forms to maintain current ways of life represents a main objective of The Clean Energy Project.

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How does an organic solar cell work?

Organic solar cells convert sunlight into electricity. The first step is that the organic solar cell must absorb light. This absorbed light adds energy into the material, causing the electrons in the material to increase their energy and move through the material, leaving behind a hole. Second, electrons must travel to a region where they can be collected by an acceptor material, lowering their energy (i.e., the donor-acceptor interface, see Figure 1). Once the electrons are collected, they can be extracted to give a current, or they can remain in the device to give rise to a voltage. The electrons that leave the organic solar cell as current can deliver their energy to whatever is connected to the circuit.


Figure 1. Illustration of how an organic solar cell works. (1) Light absorption and formation of an exciton (electron-hole pair); this step is followed by the promotion of an electron into the lowest unoccupied molecular orbital (LUMO) of an electron donor semiconductor (i.e., pentacene molecule); (2) electron transfer from the LUMO of the electron donor semiconductor to the electron acceptor semiconductor (i.e., C60 molecule); and (3) subsequent transport of the electrons to the electrodes. Note: HOMO is the Highest Occupied Molecular Orbital.

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How will The Clean Energy Project help find solar cell materials?

Understanding the properties of new materials that are the basis of alternative sources of renewable energy represents one of today’s major scientific challenges. Many of these materials are composed of large organic molecules that contain hundreds of atoms. These atoms can be rearranged in multiple ways to fine-tune the properties of the desired material. With the aid of World Community Grid, researchers will evaluate the conductive properties of at least 1,000,000 molecular structures (created by combinatorial methods) that are suitable for organic solar cells applications. The results of such an enormous number of computations will be used to create a public database of molecular properties for data mining.

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What is the efficiency in a solar cell?

Solar cells are commonly characterized by the percentage of the incident solar light that they can convert into electrical power. Thus, the efficiency is given as a percentage. In general, the efficiency is determined by the material from which the solar cell is made and by the technology used to construct it. Efficiencies for commercially available solar cells range from about 5% to about 17%. Although inorganic-based solar cells have reached a maximum efficiency of up to 40%, these are expensive to produce and pollute when thrown away. The maximum efficiency reached for organic-based solar cells is around 8% as of 2010. Therefore, there is still a lot of work to be done to improve them.

If researchers could find an organic-based solar cell whose efficiency reached 10%, these cells would be commercially feasible and would revolutionize the field of solar materials. Additionally, if these cells covered 0.16% of the surface of the planet, they would produce about an additional 20 TW (Terawatts, a trillion Watts), which would make up for the estimated increase in energy for the year 2050.

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What other technological applications will be relevant to this project?

Another technological application that will spawn from this project is the study of molecular electronics, where molecules are used for building electronic components. A good organic semiconductor for solar cells would also be good for potential applications in molecular electronics such as transistors. This means that The Clean Energy Project (CEP) has a potential to extend Moore's Law.

The CEP also plans to host a range of other calculations for cleaner energy capture and storage such as solar concentrator and polymer fuel cell. It is only with your help that researchers will be able to pursue these pure and applied directions of research.

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Screen saver/Graphics: What does the screen saver look like for The Clean Energy Project - Phase 2?

Here is a video capture of the computing for clean water graphics:

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Screen saver/Graphics: Where may I download a high quality video of The Clean Energy Project - Phase 2 graphics?

You can download them here: The Clean Energy Project - Phase 2

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Screen saver/Graphics: Where may I download pictures of The Clean Energy Project - Phase 2 graphics?

You can get them by clicking the links for the resolutions below of the example screen shot.
600x480
1000x800
3977x3016

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Screen saver/Graphics: How are The Clean Energy Project plots on the screen saver created?

The 3D graph of the screen saver plots the evolution of a matrix that is being diagonalized by Q-Chem to obtain the electronic structure of the molecules. The size of this matrix is determined by the size of the molecule (i.e. number of electrons and number of nuclei) as well as the accuracy of the calculation. For example, a bigger molecule as well as a calculation with better accuracy would result in a bigger matrix. The spikes in the graph represent the magnitude of each matrix element.

A set of parameters can be extracted from this matrix once the diagonal elements no longer change and most of the off-diagonal elements are minimized. These will reveal the electronic structure of the molecule. Understanding the electronic structure of the candidate molecules is crucial for predicting solar cell properties such as light absorption, conduction and stability.

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Screen saver/Graphics: What is Q-Chem?

To obtain the electronic structure of molecules, one needs to use Quantum Mechanics. Q-Chem is a suite of electronic structure programs which can calculate molecular structures, electronic spectra, molecular vibrations and many other parameters solving quantum mechanical equations. Q-Chem is the electronic structure software preferred by the CEP team. All these properties will contribute to find ideal molecules for organic photovoltaics.

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Screen saver/Graphics: How can we increase awareness of energy and environment?

Everyone knows that fossil-based energies are finite and can be exhausted in the near future, no question about it. But, how can we help to maintain the energy needs of today and the future? To increase our awareness of this problem, The Clean Energy Project team at Harvard University decided to create animated images, or "scipplets" (science applets), that show factoids of the current and future energy needs of today’s society.

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Screen saver/Graphics: What are The Clean Energy Project "Scipplets" all about?

"Scipplets" stands for Science Applets. "Scipplets" appear as pictures on the screen saver. In these pictures, we include energy-related facts that represent the main motivation of our project. Also, we expect to incorporate more "scipplets" as the project moves along, so that they become an informative tool for those interested in knowing more about alternative sources of energy.


"Scipplets" is a new word coined by Harvard which stands for SCIence and aPPLET.

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Screen saver/Graphics: What is a gigajoule (GJ)?

A gigajoule is a unit of energy. You can break the word into "giga" and "joule". "Giga" is a Greek prefix used to denote 1,000,000,000 and a joule (J) is a unit of energy (equal to the amount kinetic of added to a one kilogram object to which one newton of force is applied as the object moves one meter in the direction of the applied force).

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Screen saver/Graphics: What does The Clean Energy Project blue plant leaf object represent?

This is our rendition of a solar cell modeled after a plant. It actually represents our goal for the project in the sense that we are working to discover materials that will be able to convert solar energy into a useable energy, as plants do every day.

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How does The Clean Energy Project benefit humanity?

The Clean Energy Project is focused on understanding the fundamental science of how flexible solar cells work, so scientists can design more efficient energy-related technologies. The results of the project will eventually help us reduce our dependence on fossil fuels to lower our carbon emissions, keep our air cleaner, and contribute to the fight against global warming. Our research will facilitate the development of cheap, flexible solar cell materials that we hope will be used worldwide.

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Why is Phase 2 of the Clean Energy Project an opt-in project?

These calculations require work units that may run longer, have higher memory, disk space and data transfer requirements. Therefore, we are providing the users the option to opt-in to the project.

In addition, The Clean Energy Project is the first World Community Grid project to use an external server. That is, your result data is directly uploaded to the Harvard research server. Security checks are in place to make certain that uploaded data is transferred correctly and validated by the Harvard research server that is receiving the data. World Community Grid controls which servers the data is sent to and the Harvard servers will not send data files to the member machines.

Therefore, if you're interested in advancing the science of solar cells, please help us out in this great effort!

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Who are the people in the picture on the World Community Grid - BOINC Manager?

The people in this picture are The Clean Energy Project research team from Harvard University.

Front Row, Left to Right: Leslie Vogt, Anna Brockway, Dr. Sule Atahan.

Back Row, Left to Right: Roberto Olivares-Amaya, Dr. Johannes Hachmann, Dr. James Cuff, Prof. Alán Aspuru-Guzik, Dr. Jerry Lotto, Prof. Carlos Amador-Bedolla.

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What are the potential benefits of the "Discovering Dengue Drugs - Together - Phase 2" project?

This project has the potential to yield novel antiviral drugs for infectious diseases that greatly impact global health. Specifically, the aim is to identify and develop antiviral drugs against Dengue, Hepatitis C, West Nile, and Yellow fever viruses. In addition, this study will provide the foundation for a new and more efficient approach to drug development for other diseases that plague the world.

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What computers can run the "Discovering Dengue Drugs - Together" Project?

This project is distributed using the BOINC client, which is available for download on this site for computers with Windows, Macintosh, or Linux operating systems. For system requirements, click here.

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What is the difference between Phase 1 and Phase 2 of the Discovering Dengue Drugs - Together project?

The first phase performs a faster screening on a larger set of potential drug candidates and the second phase performs a more time consuming screening of the best candidates identified in the first phase. See the following FAQ for more information: "What will World Community Grid's calculations produce?".

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Where can I find information about Phase 1 of the Dengue Fever project?

Information for Phase 1 of the Dengue Fever Project may be found by selecting "Research" from the upper navigation bar and searching for "Discovering Dengue Drugs - Together" under the heading COMPLETED RESEARCH or by clicking here.

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What will World Community Grid's calculations produce?

The calculations done on World Community Grid will predict which small molecule compounds, out of the millions contained in a library database, should be tested for their ability to inhibit the flavivirus protease. This is a major step towards the ultimate goal of discovering new drugs to stop flavivirus infections.

Phase 1 of this project predicted how each small drug molecule might bind to the active site of the viral protease. This phase also produced preliminary "energies" that coarsely rank the strength of the intermolecular interactions between the compounds and viral protease.

Phase 2 will accurately predict free energies of binding between each drug compound and the viral protease. This calculation utilizes the binding orientations calculated in Phase 1. Due to computation time required for each free energy of binding calculation, only compounds with "good" scores from Phase 1 will be selected for Phase 2 calculations.

As an analogy, Phase 1 will tell us how two people might hold hands, whereas Phase 2 will tell us whether or not they want to hold hands.

Phase 2 of our project is designed to reduce the number of Phase 1 false positives (i.e., dead ends) that are tested in our laboratory. Phase 2 will take several thousand Phase 1 hits, run each hit through computationally demanding free energy calculations, and remove many of the false positives from the hit list. Phase 2 is expected to produce an updated list of hits that contains ~80% true positives. Testing Phase 2 hits in the laboratory will be much more productive, efficient, and rewarding than testing Phase 1 hits. For instance, to find 25 small molecules that stop dengue virus replication in the laboratory, we would need to synthesize and test either 250-500 Phase 1 hits or ~30 Phase 2 hits.

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When will the "Discovering Dengue Drugs - Together - Phase 2" project be completed?

Phase 1 began in August 2007 and finished in August 2009. Phase 2 started in February 2010 and may finish by the end of 2010.

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What will happen with the data generated by all these calculations?

After completion of the project and internal analysis by the research groups, all data will be made available on the Discovering Dengue Drugs-Together web site.

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What is meant by "binding free energy?"

Binding free energy is a thermodynamic measure of the difference in energy between a bound and an unbound state. In this project, it is the energy difference between a small molecule bound to the protease in solution, and a small molecule alone in solution. Large negative binding free energies correspond to molecules that tightly bind to the protein, and thus can effectively stop the viral protein from functioning.

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What is molecular docking and virtual screening?

Docking is the process of bringing together two objects. For example, a ship docks with a pier in a harbor. Molecular docking refers to a computer simulation in which two molecules are brought together. In our case, we dock a "small" molecule (i.e., a possible drug) to a target molecule (i.e., the viral NS3 protease). A docking program predicts the orientation or pose of the small molecule when bound to the target. This is accomplished by maximizing favorable interactions and minimizing unfavorable interactions between the two molecules. In addition, the program gives each pose a score based on these interactions and the conformation of the small molecule.

Virtual screening is the process of systematically screening a database of small molecules against a defined target molecule. The scores provided by the docking programs rank how well the small molecule docks to the target protein relative to other molecules in the database. Unfortunately, these rankings typically produce a large number of false positives. In this project, binding free energy calculations, combined with docking scores, will provide an accurate prediction of compounds that most strongly bind to the target protease.

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What are viruses?

Some scientists refer to viruses as "cellular parasites." Viruses are composed of a protein coat and the genetic material (RNA or DNA) that encodes the proteins needed for replication. They are dependent on a host cell and the cellular machinery for translation of the genetic material into those proteins. Without a cell, the virus cannot replicate.

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Does this study address diseases other than Dengue Fever?

This study is addressing viruses that belong to the family Flaviviridae. This includes dengue fever, West Nile virus, yellow fever, Hepatitis C, Japanese encephalitis and others. See the FAQ: "What types of viruses belong to the family called Flaviviridae?"

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What types of viruses belong to the family called Flaviviridae?

The viruses that belong to the family Flaviviridae include three genera: the flaviviruses, the hepaciviruses, and the pestiviruses. The two genera on which this project focuses include the flaviviruses and the hepaciviruses. The genus flavivirus includes (but is not limited to) the mosquito-borne Dengue, West Nile virus, and Yellow Fever virus. It also includes the tick-borne encephalitis viruses. The genus hepacivirus includes Hepatitis C virus.

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How are virus and protein structures determined?

Cryo-electron microscopy is one way to determine the approximate structure of a virus or large protein. After isolating and concentrating particles, one can quickly freeze them on a microscope grid. The freezing allows the particles to be preserved "intact." Images of the particles on the grid are then obtained with an electron microscope. By reconstructing thousands of images, one can obtain a final three-dimensional structure with enough detail to observe the entire virus particle, as well as the individual structural proteins that comprise the particle.

Another method of obtaining virus and protein structures is X-ray crystallography. For this method, virus (or the viral protein of interest) is isolated, purified, concentrated, and crystallized. High-powered X-rays are beamed onto the crystal, and the diffraction pattern is analyzed computationally and ultimately reveals a structure of the molecule of interest.

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What proteins do these viruses make?

While the flaviviruses and the hepaciviruses have some differences in their genome and coding strategies, the proteins they encode are very similar. They all encode the structural proteins that surround the nucleic acids. These include the envelope glycoproteins, the capsid protein, and the membrane protein. In addition, they encode non-structural proteins. These include a helicase, polymerase, methyl transferase, and the protease. It is the highly conserved protease that is the target of inhibition for this study.

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What antiviral drugs exist?

About half of the antiviral drugs that exist are targeted against HIV. These include protease inhibitors, reverse-transcriptase inhibitors, nucleotide and non-nucleotide analogs, and a fusion inhibitor. There are a few antiviral drugs that target herpes virus, including nucleotide analogs and drugs that disrupt virus uncoating. There are also a few drugs that target influenza virus, cytomegalovirus, and hepatitis B virus. Many of these drugs have very limited efficacy.

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Why is it so difficult to develop new drugs?

Finding drugs that can be used safely remains one of the major difficulties in producing new drugs. Millions of compounds may need to be screened to discover a handful of compounds with a desired activity. Unfortunately, many compounds that show activity are either toxic or poorly absorbed in the human body. Since it is difficult to accurately predict the behavior of drug leads in the human body, perhaps only 1% of drug leads eventually become drugs.

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Screen saver/Graphics: What does the screen saver look like for Discovering Dengue Drugs - Together - Phase 2?

Here is a video capture of the Discovering Dengue Drugs - Together - Phase 2 graphics:

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Screen saver/Graphics: Where may I download a high quality video of the Discovering Dengue Drugs - Together - Phase 2 graphics?

You may download them here: Discovering Dengue Drugs - Together - Phase 2 Video

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Screen saver/Graphics: Where may I download pictures of the Discovering Dengue Drugs - Together - Phase 2 graphics?

You may get them by clicking the links for the resolutions below of the example screen shot.

600x480
1000x800
4000x3200

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Screen Saver/Graphics: What is represented in the box on the left?

This is a picture of the drug candidate molecule your computer is analyzing at the current time. The spheres represent atoms in the molecule.

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Screen Saver/Graphics: What is represented under the box on the left?

This provides some information about the name of the work unit being processed and the points the member has accrued.

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Screen Saver/Graphics: What does the Progress Bar represent?

This shows the approximate graphical and percentage value of how far along the processing of the current work unit has progressed. When it reaches 100% the computation should be completed and the results would then be sent back to the servers at World Community Grid.

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Where are the Help Cure Muscular Dystrophy - Phase 2 FAQs?

FAQs about the project are in the Resesarch section under Project FAQs.

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Will this project help stop the current H1N1 flu outbreak?

No. A search for potential drugs to combat influenza is a lengthy process and is unlikely to be helpful in the current outbreak. Once the computational portion of the project identifies the chemical compounds that are the best candidates, a considerable amount of laboratory testing and drug development is required before a drug is ready for safe and effective public use. The current H1N1 influenza outbreak is a reminder of how quickly influenza mutates and how easily new strains of the virus emerge. Seasonal outbreaks of influenza cause hundreds of thousands of deaths around the world each year. We want to leverage this understanding to encourage more people to volunteer their idle computer time and help us to accelerate this important research. However, with the large computational power of World Community Grid and your individual contributions of spare time from your computers, we can greatly accelerate the process, examine a much larger pool of chemicals and focus laboratory research on the best candidates for new treatments. Researchers will be well positioned to help respond to outbreaks of potentially more severe (or drug-resistant) influenza viruses in the future.

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Why can't influenza immunizations solve the problem?

Each year, scientists and manufacturers work to create a new influenza vaccine to be used before the flu season. However, influenza can mutate rapidly into new varieties and these cannot always be anticipated many months before the season starts, when vaccine production begins. Since the flu virus is always mutating and new strains appear, this type of research is always valuable.

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How will my computer make a difference on this project?

While your computer is powered on, much of the time the processor inside your computer is just waiting for something to do, such as processing your next keystroke or mouse click. These idle times add up to a very large amount of processor time, when multiplied across millions of computers, that could be tapped and used for productive purposes such as this project. This can accelerate the research dramatically. Some of these projects would take hundreds or thousands of years to accomplish with the normal resources available to the scientists, and thus are likely not to even be attempted. World Community Grid and your contributions make projects such as these possible for the first time.

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How soon is a new influenza drug going to be available?

In just several weeks, we will start identifying candidates for laboratory examination from the analysis on World Community Grid. It will then take anywhere from a few months to years to complete the entire process of distributing new drugs. During this time, when good candidates are found, they will proceed to laboratory testing phases. These ultimately lead to clinical trials and hopefully a drug available for use. The entire process can take years depending on the details and any problems encountered. Thus, we do not know how long it will really take nor when and if suitable candidates will be found.

However, we do know that the process of searching for drug candidates among the millions of potential compounds can be greatly accelerated using World Community Grid, compared to using conventional laboratory work or the limited resources typically available to the researchers.

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What is the difference between influenza immunizations and antiviral drugs like Tamiflu and Relenza?

Influenza vaccine injections give your body immunity to the particular strains of influenza virus that the specific vaccine was manufactured to address. Once a person receives this vaccine, immunization for those strains typically lasts for many years. However, this immunization usually does not work for new strains. Because influenza mutates rapidly, new strains are formed all of the time. Influenza antiviral drugs are used to treat sever cases of the disease once a person has contracted an influenza strain for which he or she is not immune. Antiviral drugs such as oseltamivir (commercial name Tamiflu) and zanamivir (commercial name Relenza) help retard the spread of the virus in the body, once a patient has contracted influenza. However, these drugs are not effective against all types of influenza and in addition new drug-resistant strains are evolving. This is why this type of antiviral research is important. The antiviral drugs should only be used under the guidance of a doctor because other uses can encourage drug resistant strains of the virus to develop.

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How do I keep from getting H1N1 influenza?

There is no guaranteed way to avoid getting influenza. However, the following CDC guidelines of everyday actions could help you stay healthy:

  • Cover your nose and mouth with a tissue when you cough or sneeze, and throw the tissue in the trash after you use it.
  • Wash your hands often with soap and water, especially after you cough or sneeze. Alcohol-based hands cleaners are also effective.
  • Avoid touching your eyes, nose or mouth. Germs spread that way.
  • Stay home if you get sick. CDC recommends that you stay home from work or school and limit contact with others to keep from infecting them.

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I think I may have H1N1 influenza. What should I do?

We recommend that you check with your doctor and visit the following sites for advice:

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What is the first picture on the Influenza Antiviral Drug Search detail page?

This is an image of the project's seal/icon and was designed by Tzintzuni Garcia and Robert Malmstrom. The background contains a stylized influenza virus particle with its characteristic spikes. The eight gray bars inside the particle represent eight segments of the influenza genome. The stylized virus particle is overlaid with the image of a compound signifying the search for an antiviral drug.

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What is neuroblastoma?

Neuroblastoma is one of the most frequently occurring solid tumors in children, especially in the first 2 years of life, when it accounts for 50% of all tumors. Neuroblastoma comprises 6–10% of all childhood cancers, and 15% of cancer deaths in children.

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What is the cause of neuroblastoma?

The cause of neuroblastoma is currently unknown, though most physicians believe that it is an accidental cell growth that occurs during normal development of the adrenal glands and sympathetic ganglia.

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What are the potential benefits of the Help Fight Childhood Cancer project?

The Chiba Cancer Center Research Institute and Chiba University are using the computational power of World Community Grid to identify new candidate drugs that have the right shape and chemical characteristics to block three proteins – TrkB, ALK and SCxx, which are expressed at high levels, or abnormally mutated, in aggressive neuroblastomas. If these proteins are disabled, scientists believe there should be a high cure rate using chemotherapy.

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What will our calculations for the Help Fight Childhood Cancer project produce?

The researchers have prepared a library of 3 million compounds - or potential drug candidates (called ligands) – and are using World Community Grid to simulate laboratory experiments to test which of these compounds block the TrkB, ALK and SCxx proteins. The best molecules will be selected from the project and tested in a laboratory for efficacy against neuroblastoma.

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What is the benefit of conducting this research on World Community Grid?

In the absence of the computational power of World Community Grid, researchers would have to undertake their investigation through individual docking simulations which would take approximately 8,000 years to complete. With World Community Grid, analysis can be carried out in parallel, and researchers estimate this will reduce the time required to about 2 years.

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Where do the paintings / pictures on the Help Fight Childhood Cancer project research pages and BOINC client come from?

The paintings were donated by the Children's Cancer Association of Japan (CCAJ). CCAJ is the only non-profit organization in Japan to support children with cancer and their families and was established in October 1968, by parents who had lost their children to cancer.

The paintings were done as follows:

  • "Lion" was painted by a 5 year old cancer patient who had Acute Lymphocytic Leukemia. The patient passed away at the age of 6.
  • "Pink seeds" was painted a 9 year old cancer patient who had Cerebellar medulloblastoma. The patient is currently 17 years old.
  • "Radio-Exercises" was painted by 5 year old cancer patient who had Acute Lymphoblastic Leukemia. The patient passed away at age 7.

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Screen saver/Graphics: When I look at the screen saver image, what is my device working on?

It means that your device is processing one of the millions of drug candidates for the Help Fight Childhood Cancer project. It is simulating a laboratory experiment to test if this particular drug candidate could potentially block a protein involved with the cancer. The shape in the center of the circle of children represents the protein molecule being targeted in the experiment running on your device.

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Screen saver/Graphics: What does the circle of children represent?

Because the Help Fight Childhood Cancer project focuses on a disease that afflicts children, the circle of children represents children who are surrounding a potential cancer-related molecule. This is the molecule that is being processed on your device at the time you are looking at the screen saver. The children are hopeful that a cure for neuroblastoma will be found using your computing time.

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Screen saver/Graphics: What does the molecule represent?

For the Help Fight Childhood Cancer project, the molecule is a graphical representation of the protein molecule (one of TrkB, ALK, or SCxx proteins) being tested against a particular drug candidate in the work unit that is running on your device at the time that you are looking at the screen saver. Occasionally, when a possible docking position is calculated between the protein and drug molecules, the docking position is represented by a small colored ball.

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Screen saver/Graphics: What does the Progress Bar represent?

The Progress Bar tells you how much of the current work unit is finished. Since the main recipients of the benefits of the Help Fight Childhood Cancer project are children, the progress bar is made up of children.

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Screen saver/Graphics: What do the figures between the Chiba Cancer Center logo and the Chiba University logo represent?

These figures represents the parents of a child with cancer and the child. These figures are placed between the two logos to show that Chiba Cancer Center Research Institute and Chiba University work together to help cancer patients.

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What are the buildings in the slideshow images for Help Fight Childhood Cancer?

There are two photos of buildings in the slide show. One comes after the picture of the Help Fight Childhood Cancer scientists. This is a picture of the Chiba University campus with cherry blossom trees in bloom. The second picture which comes immediately after the first is a picture of the Chiba Cancer Center Research Institute.

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Why is solar energy important?

It is expected that by the year 2050 the world's energy requirements will double today’s demand. Energy is without doubt a prerequisite for economic stability in both the developed and developing world; despite its current importance, the actual energy system is far from being self-sustainable. Achieving a completely sustainable energy system will require technological breakthroughs that radically change our paradigms on how we produce and use energy. A possible solution to this problem is to use solar energy. Every hour, our sun produces enough solar energy to supply the whole world’s annual energy requirements. Finding the means to convert the incident solar energy into usable forms to maintain the current way of life represents a main objective of The Clean Energy Project team.

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How does an organic solar cell work?

Organic solar cells convert sunlight into electricity. The first step is that light must be absorbed in the organic solar cell. This absorbed light causes the electrons in the material to increase their energy. Second, electrons must travel to a region where they can be collected (i.e., the donor-acceptor interface, see Figure 1). Once the electrons are collected, they can be extracted to give a current, or they can remain in the device to give rise to a voltage. The electrons that leave the organic solar cell as current can deliver their energy to whatever is connected to the circuit.



Figure 1. Illustration of how an organic solar cell works. (1) Light absorption and formation of an exciton (electron-hole pair); this step is followed by the promotion of an electron into the lowest unoccupied molecular orbital (LUMO) of an electron donor semiconductor (i.e., pentacene molecule); (2) electron transfer from the LUMO of the electron donor semiconductor to the electron acceptor semiconductor (i.e., C60 molecule); and (3) subsequent transport of the electrons to the electrodes. Note: HOMO is the Highest Occupied Molecular Orbital.

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How will The Clean Energy Project help find solar cell materials?

Understanding the properties of new materials that are the basis of alternative sources of renewable energy represents one of today’s major scientific challenges. Many of these materials are composed of large organic molecules that contain hundreds of atoms. These atoms can be rearranged in multiple ways to fine-tune the properties of the desired material. With the aid of World Community Grid, researchers will evaluate the conductive properties of at least 100,000 molecular structures (created by combinatorial methods) that are suitable for organic solar cells applications. The results of such an enormous number of computations will be used to create a database of molecular properties for data mining, which will be publicly available.

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What is the efficiency in a solar cell?

Solar cells are commonly characterized by the percentage of the incident solar light that they can convert into electrical power. Thus, the efficiency is given as a percentage. In general, the efficiency is determined by the material from which it is made and by the technology used to construct the solar cell. Efficiencies for commercially available solar cells range from about 5% to about 17%. Although inorganic-based solar cells have reached a maximum efficiency of up to 40%, these are expensive to produce and polluting when thrown away. The maximum efficiency reached for an organic-based solar cell is around 6% as of 2007. Therefore, there is still a lot of work to be done to improve them.

If researchers could find an organic-based solar cell whose efficiency reached 10%, these would be commercially feasible and would revolutionize the field of solar materials. Additionally, if these cells covered 0.16% of the surface of the planet, they would produce about an additional 20 TW (Terawatts, a trillion Watts), which will make up for the estimated increase in energy for the year 2050.

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What other technological applications will be relevant to this project?

The study of solar cells is similar in form to other fields. For instance, the interaction of titania (TiO2) with organic molecules in dye-sensitized solar cells is very similar to (heterogeneous) catalysis, the act of accelerating the rate of a reaction, where a metal particle or surface interacts with an organic molecule or a group of molecules.

Another technological application that will spawn from this project is the study of molecular electronics, where molecules are used for building electronic components. This means that we will potentially provide the means to extend Moore's Law.

Furthermore, the CEP plans to host a range of other calculations for cleaner energy such as work on solar concentrator and fuel cell materials. It is only with your help that researchers can go ahead and try to answer these questions of both pure and applied research.

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Screen saver/Graphics: How are The Clean Energy Project plots on the screensaver created?

The plots on the screen saver show how the energy and temperature of the molecules changes over time during a Molecular Dynamics Simulation (MDS). In this case, MDS are in some respect very similar to “real” bench-type experiments because we can use this computational technique to measure the properties of interest during a certain time interval.

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Screen saver/Graphics: Why are we interested in determining the energy and temperature of a molecular system for The Clean Energy Project?

We are interested in knowing the energy and temperature of a given molecular material because we need to investigate its stability (i.e., finding a the optimal arrangement of the molecules) and performance (i.e., functionality). Also, these two parameters can be later used to evaluate whether or not a particular molecular structure is suitable for alternative energy applications.

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Screen saver/Graphics: What does "kcal/mole" and "K" mean on these plots for The Clean Energy Project?

The energy units are kilocalorie per mole (symbol: kcal/mole), where a kcal is the amount of energy needed to increase the temperature of one kilogram of water by one centigrade degree (1˚C) and a mole is a measure of how many molecules are in the system.

The temperature units are Kelvin (symbol: K), which is a unit of absolute temperature. A change of 1 K corresponds to a change of 1˚C. In fact, 0 K represents the theoretically coldest temperature where all the molecular and atomic motion ceases. On the Kelvin scale, the freezing point of water is 273 (273 K = 0˚C = 32˚F).

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Screen saver/Graphics: Why are we interested in investigating alternative sources of energy for The Clean Energy Project?

Everyone knows that all the oil-based energies are finite and they can be exhausted in the near future, no question about it. But, how can we help to maintain the energy needs of today and the future? To increase our awareness on this problem, the Clean Energy Project team at Harvard University decided to create animated images, or "scipplets" (science applets), that show factoids of the current and future energy needs of today’s society.

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Screen saver/Graphics: What is the green object in The Clean Energy Project screen saver?

This is a small set of atoms that are being simulated on your computer; each atom is represented by a green sphere. This a "green project", after all!

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Screen saver/Graphics: What are The Clean Energy Project "Scipplets" all about?

"Scipplets" stands for Science Applets. In these pictures, we include energy-related facts that represent the main motivation of our project. Also, we expect to incorporate more "scipplets" as the project moves along, so that they become an informative tool for those interested in knowing more about alternative sources of energy.

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Screen saver/Graphics: The Clean Energy Project Scipplets refer to something called gigajoules (GJ). What is a gigajoule?

A gigajoule is a unit of energy. You can break the word into "giga" and "Joule". "Giga" is a greek prefix used to denote 1,000,000,000 and a Joule (J) is a unit of energy (the amount of force needed to move one kilogram of something one meter). So a gigajoule is 1 billion joules.

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Screen saver/Graphics: What does The Clean Energy Project blue plant leaf object represent?

This is our rendition of a solar cell modeled after a plant. It actually represents our goal for the project in the sense that we are working to discover materials that will be able to convert solar energy into a useable energy, as plants do everyday.

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Screen saver/Graphics: How does The Clean Energy Project benefit humanity?

The Clean Energy Project is focused on understanding the fundamental science of how flexible solar cells work, so scientists can design more efficient energy-related technologies. The results of the project will eventually help us reduce our dependence on fossil fuels to lower our carbon emissions, keep our air cleaner, and contribute to the fight against global warming. Our research will facilitate the development of cheap, flexible solar cell materials that we hope will be used worldwide.

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Why rice?

Rice, maize and wheat are the three main cereal grains in the world, accounting for 43% of the world's food calories. The rice genome is the only cereal genome that has been sequenced. While the rice genome is different from the human and other mammalian genomes, it is a good model for the other cereal grains. Lessons learned about how the functions and interactions of rice genes interact are likely to be useful in understanding the genetics and biology of other major crops.

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What is a protein?

Proteins are large biomolecules consisting of one or more chains of amino acids. The sequence and identity of the amino acids making up the chain determine the structure and the properties of the proteins. Proteins are made by transcribing and translating the DNA sequence of the corresponding gene. So, while DNA may be thought of as the blueprint of life, proteins carry out the instructions contained in the blueprint.

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What do proteins do?

What don't they do? Some proteins are structural such as collagen and keratin which makes up the hair, skin and nails. Some are enzymes that catalyze the chemical reactions necessary for all activities like metabolism. Others have important signaling and feedback functions that ensure that cells do what they are meant to and don't grow out of control.

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What does protein structure tell us?

Proteins are governed by the same rules as any other molecule. The structure of a protein, or how it folds, determines its function. For example, the precise arrangement of active chemical groups from different amino acids in the protein chain at the active site of an enzyme accounts for its catalytic activity. Another example is the location of positively charged groups on the surface to allow DNA binding proteins to bind to the negatively charged phosphate backbone of DNA. In addition, one can often identify the role of a protein of unknown function by comparing its structure to structures of known proteins.

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What do proteins look like?

Proteins are too small to be seen by common visible light microscopy. It is possible to see larger proteins and protein arrays using transmission electron microscopy or atomic force microscopy. The protein structures that you usually "see" are depictions based upon high resolution structures as determined by X-Ray crystallography or Nuclear Magnetic Resonance (NMR).

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Why do we need to predict protein structure?

Prediction is the only viable alternative to experimental techniques which can be extremely labor intensive and require many months or years of effort.

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How is Protinfo different from other approaches?

Protein structure prediction is an active area of research, and no one method or methodology is "best" for all situations. The public success of projects like Folding@Home, POEM@Home, Human Proteome Folding, and Rosetta@Home are evidence of the interest in solving this computationally challenging problem. We wish to offer another approach that differs in certain subtle but significant ways that can provide complementary and competitive results.

Some approaches (like Folding@Home and POEM@Home) simulate the protein folding process as we believe it occurs in real life, where physical energies are minimized. Protinfo (like Human Proteome Folding and Rosetta@Home) uses a minimization of "statistical energies" to identify likely protein structures, but with a slightly different approach. Rather than relying on a single complex energy function, Protinfo uses a simple, easily evaluated function and chooses the best structures by following up with a set of more sophisticated functions. Another difference is that Protinfo uses a novel continuous sampling methodology that enables us to explore good structures more finely. The continuous sampling methodology incurs little memory overhead and evaluating our compact energy function is very fast. This allows Protinfo to run on almost any computer.

The Protinfo structure predictions have been ranked as some of the best by the Critical Assessment of Structure Prediction (CASP) competition since 1994. You can read more about Protinfo on the researchers' page about this project.

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Why is protein structure prediction so difficult?

Two factors that make protein structure prediction challenging are the nature of the energy functions, and the vast search space.

The environment of a protein is populated with many other atoms and molecules. If the program were simulating a process that happened in vacuo or even in a non-polar solvent (instead of the aqueous environment of the cytoplasm) it would be much easier. The presence of polar and polarizable solvent molecules make accurate calculation of electrostatic forces extremely difficult. In addition, the main "force" in protein folding is the hydrophobic effect. This arises from the interactions between atoms within the protein, their interactions with the solvent atoms and the interactions between the solvent atoms. In simulations such as Protinfo, Human Proteome Folding, and Rosetta@Home, the effect of these solvent dependent interactions is approximated in the statistical energies. The development of better solvent models and simulations is another active area of research that will eventually address these problems.

The other limiting factor is the number of possible structures, or conformations, that need to be sampled for a protein. Even with a completely accurate energy function, there is still a need to sample the possible conformations finely enough to find the right one. Not only is the number of possible conformations huge (see
Levinthal paradox), it is made even more difficult by the extremely complicated energy landscape. Most of the usual global optimization techniques that could be used with a well behaved function will fail when applied to protein folding. Luckily, of the two problems, this is probably the lesser. With increased CPU power and improved sampling techniques generally some accurate structures are usually generated - but without the completely accurate energy function we are not always able to identify them.

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Screen saver/Graphics: What is the rotating shape in the center of the Nutritious Rice for the World graphics?

It is a representation of the latest structure predicted by your computer.

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Screen saver/Graphics: What is the red graph titled RAPDF in the Nutritious Rice for the World graphics?

This is the score of the best structure over time. The score comes from the Residue-specific All-atom conditional Probability Discriminatory Function (RAPDF), which measures how similar a predicted protein structure is to real structures. Good structures have a low score. You can read more on the researchers' page about this project.

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Screen saver/Graphics: What is in the background of the Nutritious Rice for the World graphic?

The background is a photo of a rice field in Asia.

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Screen saver/Graphics: May I look at the information in the Nutritious Rice for the World graphic a different way?

When you are viewing the graphics, there are keyboard controls that will change the way the information is displayed. These keys only work in the standalone graphics mode, they won't do anything when viewing the screensaver.

Workunit:

Mtoggle member info (show/hide)
Itoggle progress graph size and position (large/small)

Protein visualization:

Btoggle backbone shape (show/hide)
Stoggle structure atoms (show/hide)
Ccarbon (C and Cα)
Acarbon (Cα)
Nnitrogen
Ooxygen

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What are the potential benefits of the "Help Conquer Cancer" project?

There are several direct and indirect benefits of the project. For the first time, scientists will execute a comprehensive image analysis and classification of crystallography images. This will lead to better understanding of the crystallization process, and will enable scientists to improve the accuracy and speed of CrystalVision. Improved understanding of the crystallization process and improved CrystalVision also will enable more disease proteins to be crystallized faster. Finally, more 3D structures will improve our understanding of disease and potentially its treatment, and will lead to improved in silico (performed on a computer or via computer simulation) structure prediction.

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What will World Community Grid's calculations produce?

On the lowest level, CrystalVision will compute thousands of image features for each crystallography image. This data objectively measures characteristics of the image, which will enable scientists to use a system to discern image classification. In turn, this will allow them to automatically and objectively characterize results from the high-throughput crystallization screens, and then apply data mining techniques to optimize future crystallization experiments.

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What will happen with the data generated by all these calculations?

After careful analysis, evaluation and interpretation, all results will be published in the public domain. The scientists' first goal is to improve the CrystalVision system to enable automated, accurate and fast crystallography image classification. This algorithm will then be deployed at Hauptman-Woodward Medical Research Institute to ensure that this public high-throughput crystallography screening facility will speed up crystallization of many disease-related proteins.

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Screen saver/Graphics: When I look at the Help Conquer Cancer graphic, what is my device working on?

Each work unit is a photograph of a protein crystallization experiment (one out of 1,536 images per protein, photographed six times over a period of one month), a visual record of the state of a protein sample dissolved in a solution of crystallizing agents. This photograph is shown in the background of the agent window. The Grid agent performs a computer vision analysis of the image in order to interpret its contents, first determining important image features, which are then used to classify (or label) the result of the experiment. During the feature image computation, intermediate steps of this analysis are displayed in the colored circles appearing in the foreground of the agent window.

The analysis is a search for four large categories of features in the image: microcrystals, straight lines, discrete objects, and textural features. Intermediate steps of the texture analysis are displayed in the colored circles that appear in the foreground of the agent window. As each step is completed, the computed result appears in the agent window. Each circle is a copy of a region of the original image, transformed to highlight a different texture.

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Screen saver/Graphics: What is the moon-crater object in the middle of the Help Conquer Cancer graphic background?

The background image is a photomicrograph of a protein crystallization experiment. The experiment takes place in a droplet of water the size of a pinhead (200 nl), suspended in an oil-filled chamber. The circular wall of the chamber, and the roughly circular droplet contained within are visible in the photo. Inside the droplet, precipitated protein or salt, or even protein crystal may be visible.

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Screen saver/Graphics: In the Help Conquer Cancer graphics: What are the round disks? Each disk has a different color. What does that mean?

Each disk is a visualization of a different texture measure applied to the background image. Thus, when two disks are differently colored, it means only that different textures are more or less prominent in different regions of the image. Twenty-six measures of texture are visualized in the Grid agent.

Each measure is related to frequencies of the grey-scale values of pairs of pixels found in the image, and summarizes these frequencies according to pixel-pixel contrast, correlation, variance, or entropy. Each of 13 categories of statistics is measured multiple times by changing the distance and relative orientation of the pixel-pairs.

Each disk visualizes the results of a search for a particular texture in the original image. The texture search is done in three steps. The first step records fine-grained changes in the grey-tones of the image, the second step records medium-grained changes, and the third step records coarse-grained changes. The three steps are visualized together by using red (step 1), green (step 2), and blue (step 3) colour channels to create a full-colour image representing the whole process. A blue region of the disk would then indicate a region of the original image where the texture is most apparent in coarse-grained grey-tone changes.

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Screen saver/Graphics: I noticed that the right most disk in the Help Conquer Cancer graphic is occasionally replaced by a new disk and all the other disks move to the left and the last one falls off. What is going on?

The Grid agent will only display the results of the last 10 image analysis steps. As the next step is completed, its result is displayed, and the oldest is removed.

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Why are my work units failing with exit code 232 “ERROR: .\VerifyGPU.cpp:65 Unknown”?

This failure occurs for work units running on the graphics card during a test of the ability of your graphics card to run the work unit. If you see this error, make sure you are using the latest video driver for your graphics card. Also, remote desktop connections can have an effect on graphic card applications and it is recommended not to have an active remote desktop connection while the Help Conquer Cancer graphics card application is running.

You may learn more about updating your video drivers at the website of your graphics card manufacturer: Nvidia or AMD

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Why are my work units failing with exit code 233 “ERROR: Kernel execution time estimate too high, exiting”?

At the beginning of each work unit run on your graphics card, a small portion of the workload is run to estimate the execution time of a single kernel execution on the graphics card. If this estimate is too high, the application will exit to reduce the risk of Windows restarting the display driver due to the Timeout Detection and Recovery feature of Windows. If this occurs, the above error message will be written to the stderr log. If this occurs multiple times, it is likely the graphics card is not capable of running the project. Please refer to the "What graphics cards are not able to participate in the Help Conquer Cancer research project?"FAQ for a list of graphics cards which are not supported.

If it occurs occasionally but not on every execution, it could be that other graphics intensive work is interfering. We recommend that you set your preferences to not allow World Community Grid to run while you are actively utilizing your computer. This option is available on the Device Profile page under the custom options section. This option is labeled "Do work on my graphics card while computer is in use?". Select "no" and save.

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Why are my work units failing with exit code 234 “Error: cl_khr_local_int32_base_atomics extension required by this program is not supported”?

The Help Conquer Cancer graphics card application requires the OpenCL extension cl_khr_local_int32_base_atomics and will not run on cards that do not support this extension. If you see the error above it is because your graphics card does not support the extension.

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What is climate?

Climate is the average long-term pattern of weather activity over a region.

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What is a General Circulation Model (GCM)?

A GCM is a global, three-dimensional computer model of the climate system, which can be used to simulate the earth's climate. GCMs are highly complex and represent the effects of such factors as reflective and absorptive properties of atmospheric water vapor, greenhouse gas concentrations, clouds, solar heating, sea temperatures and ice boundaries. The most advanced GCMs include global representations of the atmosphere, oceans, and land surface.

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What is a Regional Circulation Model (RCM)?

A RCM is a comprehensive physical high resolution (less than 50km) climate model that covers a limited area of the globe, usually including the atmosphere and land surface components of the climate system, and containing representations of the important processes within the climate system (e.g., cloud, radiation, rainfall, soil hydrology).

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What are climate model parameters?

Climate model parameters are numbers that quantify certain factors in the rules of a climate model. Quantities related to land surface types such as vegetation, land, water, or amounts of atmospheric convection, etc. are examples of climate parameters. Climate model parameters also include the specification of factors that are not simulated but rather prescribed, such as the amount of rain from a given amount of humidity, wind and temperature.

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Why was this project just looking at Africa?

Africa is already vulnerable to extremes in climate, and current climate change projections suggest that the region will be more vulnerable in the future. Thus a climate study for this region is important both for economic reasons and for understanding future vulnerability. The climate modeling techniques developed here may be applied to other regions of the world in the future.

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Why did this project download and upload so much data?

Climate simulations require three-dimensional information about temperature, pressure, wind, humidity and surface properties for the entire region being studied at a detailed grid level. In addition, information arriving at the boundary of the region over the time span being studied is needed. This requires a considerable amount of input data, and as the simulation runs, a large quantity of output data is produced.

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What are the potential benefits of the "AfricanClimate@Home" project?

The project will lead to the identification of combinations of key parameterizations that best simulate the varying climates of Africa. More accurate models will give researchers a better understanding of the implications of various natural and man-made influences on the African climate. In turn, this will enable policy makers to make important adaptation and mitigation decisions based on the best available information.

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What computers can run the "AfricanClimate@Home" Project?

AfricanClimate@Home can run on computers that use a high speed internet connection and that run the Windows and Linux operating systems. AfricanClimate@Home will be available using the BOINC agent. You can check to see if you are using the BOINC agent by following the information available here. For system requirements, click here.

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What will World Community Grid's calculations produce?

World Community Grid will produce a significant amount of atmospheric and surface data that will be analyzed and interpreted by researchers to better understand the ability and constraints faced by models simulating African climate.

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What will happen with the data generated by all these calculations?

The generated data will eventually be released to the general scientific community, as well as others interested in doing non-commercial climate research over the African region.

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Why were there so many copies of a work unit sent out for AfricanClimate@Home?

Each computer that receives a work unit for AfricanClimate@Home will compute a two week period for the climate model based on the same starting conditions as other computers that receive a copy of the same work unit. The result data for AfricanClimate@Home is very large (greater then 100MB). Very few computers are able to return a result of this size. Therefore the result file is divided between each computer computing the work unit and each returns a unique section of the result file. Additional information is returned as well to ensure that the section of the result file returned is correct.

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Why do I have to opt into AfricanClimate@Home in order to participate?

The AfricanClimate@Home downloaded work unit size is anticipated to be approximately 77MB, which means it is approximately 150 times larger than a typical FightAIDS@Home or HPF2 work unit. Thus, a 756kbps network connection will take approximately 12-15 minutes to download the work unit. We have estimated that only about 33 percent of registered computers have enough bandwidth to be eligible to participate in this project.

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What version of WRF was being used for the AfricanClimate@Home project?

AfricanClimate@Home presently uses WRF Model Version 2.2 (December 2006). In addition, this project is not using the Chemistry model of WRF.

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When will this project be completed?

The first phase of the project ran through July, 2008.

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Screen saver/Graphics: What did the variable Temperature @ 2m on the right graph of the AfricanClimate@Home graphic represent?

The variable Temperature @ 2m represents the model simulated air temperature 2 meters above the ocean/land surface.

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Screen saver/Graphics: What did the variable Humidity @ 2m on the right graph of the AfricanClimate@Home graphic represent?

The variable Humidity @ 2m represents the model simulated absolute humidity (expressed as the mass of water vapor per kilogram of air) 2 meters above the ocean/land surface.

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Screen saver/Graphics: What did the variable Precipitation on the right graph of the AfricanClimate@Home graphic indicate?

It indicated the amount of rainfall simulated by the model at the surface.

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Screen saver/Graphics: What did the graph on the right side of the AfricanClimate@Home graphic represent?

It showed the change as time progresses in the mean value of Temperature/Humidity/Precipitation over the whole domain.

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Screen saver/Graphics: What did the map on the left side of the AfricanClimate@Home graphic represent?

The map on the left represented southern Africa with country boundaries. The island of Madagascar is on the right hand side of the map, which is derived from a blue marble image, courtesy of NASA's earth observatory. The shaded box represents the domain (boundaries) of the climate model, centerd on South Africa. Within that domain can be seen the model simulation of the local weather patterns.

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What are the potential benefits of the "Discovering Dengue Drugs - Together" project?

This project has the potential to yield novel antiviral drugs for infectious diseases that greatly impact global health. Specifically, our aim is to identify and develop antiviral drugs against dengue, hepatitis C, West Nile, and yellow fever viruses. In addition, this study will provide the foundation for a new and more efficient approach to drug development for other diseases that plague the world.

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What computers can run the "Discovering Dengue Drugs - Together" Project?

This project is distributed using the BOINC client, which is available for download on this site for computers with Windows, Macintosh, or Linux operating systems. For system requirements, click here.

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What will World Community Grid's calculations produce?

The calculations done on World Community Grid will predict which small molecule compound, out of the millions contained in our library database, should be tested for their ability to inhibit the flavivirus protease. This is a major step towards our ultimate goal of discovering new drugs to stop flavivirus infections.

Phase 1 of this project will predict how each small molecule might bind to the active site of the viral protease. This phase also produces preliminary "energies" that coarsely rank the strength of the intermolecular interactions between the compound and viral protease.

Phase 2 will accurately predict free energies of binding between each compound and the viral protease. This calculation utilizes the binding orientations calculated in phase 1. Due to computation time required for each free energy of binding calculation, only compounds with "good" scores from phase1 will be selected for phase 2 calculations.

As analogy, phase 1 will tell us how two people might hold hands, whereas phase 2 will tell us whether or not they want to hold hands.

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What will happen with the data generated by all these calculations?

After completion of the project and internal analysis by our groups, all data will be made available on the Discovering Dengue Drugs-Together web site.

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When will the DDD-T project be completed?

Phase 1 began in August, 2007 and finished in August, 2009. Phase 2 is expected to start in late 2009 and may finish by mid 2010.

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What is molecular docking and virtual screening?

Docking is the process of bringing together two objects. For example, a ship docks with a pier in a harbor. Molecular docking refers to a computer simulation in which two molecules are brought together. In our case, we dock a "small" molecule (i.e., a possible drug) to a target molecule (i.e., the viral NS3 protease). A docking program predicts the orientation or pose of the small molecule when bound to the target. This is accomplished by maximizing favorable interactions and minimizing unfavorable interactions between the two molecules. In addition, the program gives each pose a score based on these interactions and the conformation of the small molecule.

Virtual screening is the process of systematically screening a database of small molecules against a defined target molecule. The scores provided by the docking programs rank how well the small molecule docks to the target protein relative to other molecules in the database. Unfortunately, these rankings typically produce a large number of false positives. In this project, binding free energy calculations, combined with docking scores, will provide an accurate prediction of compounds that most strongly bind to the target protease.

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What is meant by "binding free energy?"

Binding free energy is a thermodynamic measure of the difference in energy between a bound and an unbound state. In this project, it is the energy difference between a small molecule bound to the protease in solution, and a small molecule alone in solution. Large negative binding free energies correspond to molecules that tightly bind to the protein.

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What are viruses?

Viruses are composed of a protein coat and the genetic material (RNA or DNA) that encodes the proteins needed for replication. They are dependent on a host cell and the cellular machinery for translation of the genetic material into those proteins. Without a cell, the virus cannot replicate. Some scientists refer to viruses as "cellular parasites."

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What types of viruses belong to the family called Flaviviridae?

The viruses that belong to the family Flaviviridae include three genera: the flaviviruses, the hepaciviruses, and the pestiviruses. The two genera on which this project focuses include the flaviviruses and the hepaciviruses. The genus flavivirus includes (but is not limited to) the mosquito-borne dengue, West Nile virus, Japanese encephalitis, and yellow fever virus. It also includes the tick-borne encephalitis viruses. The genus hepacivirus includes hepatitis C virus.

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How are virus structures determined?

Cryo-electron microscopy is one way to determine the structure of a virus. After isolating and concentrating virus particles, one can quickly freeze them on a microscope grid. The freezing allows the particles to be preserved "intact." Images of the particles on the grid are then obtained with an electron microscope. By reconstructing thousands of images, one can obtain a final three-dimensional structure with enough detail to observe the entire virus particle as well as the individual structural proteins that comprise the particle.

Another method of obtaining virus structure is X-ray crystallography. For this method, virus (or the viral protein of interest) is isolated, purified, concentrated, and crystallized. High-powered X-rays are beamed onto the crystal, and the diffraction pattern is analyzed computationally and ultimately reveals a structure of the molecule of interest.

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What proteins do these viruses make?

While the flaviviruses and the hepaciviruses have some differences in their genome and coding strategies, the proteins they encode are very similar. They all encode the structural proteins that surround the nucleic acids. These include the envelope glycoproteins, the capsid protein, and the membrane protein. In addition, they encode non-structural proteins. These include a helicase, polymerase, methyl transferase, and the protease. It is the highly conserved protease that is the target of inhibition for this study.

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How are protein structures determined?

A primary method for determining atomic resolution protein structures is X-ray crystallography. For this method, the protein of interest is isolated, purified, concentrated, and crystallized. High-powered X-ray is beamed onto the crystal, and the diffraction pattern is analyzed computationally and ultimately reveals the protein structure.

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What antiviral drugs exist?

About half of the antiviral drugs that exist are targeted against HIV. These include protease inhibitors, reverse-transcriptase inhibitors, nucleotide and non-nucleotide analogs, and a fusion inhibitor. There are a few antiviral drugs that target herpes virus, including nucleotide analogs and drugs that disrupt virus uncoating. There are also a few drugs that target influenza virus, cytomegalovirus, and hepatitis B virus. Many of these drugs have very limited efficacy.

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Why is it so difficult to develop new drugs?

Finding drugs that can be used safely remains one of the major difficulties in producing new drugs. Millions of compounds may need to be screened to discover a handful of compounds with a desired activity. Unfortunately, many compounds that show activity are either toxic or poorly absorbed in the human body. Since it is difficult to accurately predict the behavior of drug leads in the human body, perhaps only 1% of drug leads eventually become drugs.

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Screen saver/Graphics: Where do the student writings that appear on the Discovering Dengue Drugs - Together graphic come from?

Students from Lanier Middle School (Houston, Texas, USA) graciously contributed their original writings for this project's screen saver. The dedicated teachers at Lanier Middle School, in particular Ms. Tracy Thibodeaux, Mr. Michael Giroir, and Principal Julia Dimmitt, helped direct this writing project. The student writings complement the humanitarian focus of this research project, the mission of World Community Grid, and the philosophy of Lanier Middle School.

The unedited student writings serve as part of this project's screen saver and are sent to thousands of participating computers around the world. This type of screen saver is appealing for several reasons; it increases student awareness of global computer technology and biomedical science by involving them in an advanced biomedical research project. It also encourages student interest in science, technology, writing, and world issues. Finally, it empowers students to proactively search for solutions to their concerns and spread humanitarian goodwill.

Sidney Lanier Middle School is one of the premier public schools within the Houston Independent School District. Its dedicated teachers instruct truly remarkable students in grades 6 through 8, and support both neighborhood students and an extensive Vanguard gifted/talented program that draws students from throughout Houston.

The student writings reflect the opinions of an individual student, and do not necessarily reflect the opinions, mission, or beliefs of the organizations and people involved in this project or World Community Grid.

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Where are the Help Cure Muscular Dystrophy FAQs?

FAQs about the project are in the Resesarch section under Project FAQs.

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What is the status of the Help Cure Muscular Dystrophy project?

The first phase of Help Cure Muscular Dystrophy was completed in June, 2007. The scientists are currently analyzing the phase 1 results in preparation for phase 2. We expect phase 2 to start in early 2009. You may read about the Help Cure Muscular Dystrophy project and the preparation for Phase 2 here.

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What is Genome Comparison?

Genome Comparison is a project of the Bioinformatics Team at the Department of Biochemistry and Molecular Biology of Fiocruz that used the compute power of World Community Grid to calculate the sequence similarity level among the whole protein content encoded in completely sequenced genomes of hundreds of organisms, including humans and several other species of medical, commercial, industry, or research importance. The calculated similarity indices will be used, together with standardized Gene Ontology, as a reference repository for the annotator community, providing an invaluable data source for biologists.

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Why did the Genome Comparison project compare protein sequences?

Only a fraction of the predicted protein content encoded in completely sequenced genomes has actually had their biological function and expression confirmed through laboratory analysis. The assignment of predicted biological functions and structural features to raw sequence data is called annotation, and is accomplished mostly by comparing them to predicted proteins or protein coding genes with information stored in different public domain databases around the world. However, annotation is often incomplete, uses non-standardized nomenclature or can be incorrect when inferred from previous incorrectly annotated sequences. Thus, an all against all controlled comparative database would be of great use as a reference.

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How proteins were compared in the Genome Comparison Project?

Biological sequences (DNAs, RNAs, and proteins) are mostly compared in pairs through a process called pairwise sequence alignment, which consists of putting two sequences side-by-side in such a way that the number of identical positions between them is maximized. The sequences can be globally (taking the whole sequences) or locally (taking parts of the sequences) aligned, depending on the context and the purpose. The sequence similarity comparison program used in the Genome Comparison Project is called SSEARCH (W.R. Pearson [1991] Genomics 11:635-650), a freely available implementation of the Smith-Waterman rigorous algorithm (T. F. Smith and M. S. Waterman, [1981] J. Mol. Biol. 147:195-197) (algorithm is an organized procedure for performing a given type of calculation or solving a given type of problem), which finds the mathematically best local alignment between pairs of sequences.

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What are the potential benefits of the Genome Comparison Project?

  • The resulting all against all comparative database will be of great use as a reference for many research projects on functional aspects, biochemical pathways, evolutionary aspects, and an invaluable source for correct annotation of previously sequenced and newly obtained genome sequences
  • Precise annotation, assignment of possible functions to hypothetical proteins of unknown function, and the description of evolutionary relationships between proteins will be a major step forward towards our understanding of genome composition, genome evolution and cellular function
  • The contribution to the understanding of host-pathogen relationships, and the means to develop new drugs and vaccines, will be of utmost benefit to the scientific community at large
  • Research on biodiversity and new organisms will greatly benefit from reliable comparative data
  • Future new sequence releases will build upon the growing cross-referenced database

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What is the status of the Genome Comparison project?

The Genome Comparison project was completed in July, 2007. You may read about the Genome Comparison project here. Findings from the Genome Comparison research scientists will be posted here.

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How did the Genome Comparison software work?

The software automatically downloaded small pieces of data (predicted protein sequences) and performed sequence comparisons to accurately calculate the similarity level among them. After the information was processed by members computers, the results were sent by World Community Grid to Fiocruz where they are being analyzed by the Bioinformatics Team at the Department of Biochemistry and Molecular Biology. Large-scale comparative analysis applying Smith-Waterman algorithm is computationally intensive and demanded exceptionally huge computational power, which is why it was a perfect project for World Community Grid.

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Screen saver/Graphics: What did those circles, symbols and letters in the Genome Comparison graphic mean?

The panel presented in the Genome Comparison agent application window represented the entities involved in the comparison process and a summary of the result achieved for a pair of them.

The small circles on the left side symbolized two different genes, pertaining to two distinct genomes or to a single genome. Inside of each circle we could see the unique number that identified the predicted protein sequence encoded by the gene in the source database.

The large circle on the right side of the panel showed the corresponding protein sequences, their descriptions, and the abbreviated name of the similarity scores and their calculated values for the particular pair of sequences.

The protein sequences were represented by an ordered string of letters (as encoded in their respective genes). Each of those letters stands for a different amino acid (M for methionine, S for serine, and so on) in the protein.

Most protein sequences are hypothetical or putative, which means that their existence have been computationally predicted but their expression by the respective cell or organism have not been experimentally confirmed yet.

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What is Tissue Microarray technology?

Tissue Microarray (TMA) technology is a relatively new investigative tool for harvesting small cylinders of tissue from a range of standard histological sections and arranging them on a on a single microscope glass slide in a grid-like manner. The arrays are subsequently treated with antibodies (proteins which specifically detect and bind to molecular targets of interest) that are complexed with a staining medium to determine the protein and molecular signatures of the underlying pathology of the tissue samples. This technique allows maximization of tissue resources by analysis of small core biopsies of blocks, rather than complete sections. Using this technology, a carefully planned array can be constructed with cases from pathology tissue block archives, such that a 20-year survival analysis can be performed on a cohort of hundreds patients, simultaneously using just a few micro-liters of antibody.

Using TMA technology investigators are beginning to unveil the underlying mechanisms by which healthy tissues are transformed into malignancies and are gaining unparalleled insight as to which patient populations are most likely to respond to a given treatment regimen. TMA’s hold tremendous promise for improved accuracy in prognosis, therapy planning and drug discovery.

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What does a Tissue Microarray slide look like?

Below is a photo of an actual Tissue Microarray slide. Each of the colored dots is a tissue slice which was an image for a work unit. That image corresponds to the large circle on the left side of the agent (above).

Tissue Microarray slide

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How long does the scanner take to scan in a whole slide?

Usually under an hour, but it depends on how many discs are on the specimen.

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What is the average number of tissue slices per slide?

Most slides have 300-400 discs. However some of them only have around 100 discs.

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Was an automatic slide feeder used?

No, scanning TMAs required manual monitoring.

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Where can I find out more on Tissue Microarrays?

The UMDNJ - Robert Wood Johnson Medical School has a site that can help to explain things further.

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Why were there not as many work units for the Help Defeat Cancer project?

The data images used in the Tissue Microarrays took a lot of computer processing themselves to assemble into work units. The preprocessing alone required for the generation of the work units was quite sizable. The Cancer Institute of New Jersey had as many computers as they could spare working on creating work units for this project. Unfortunately, there was no way to put the work unit creation process on our grid, but we added the new work units to our grid as soon as they were generated.

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How can I find the latest status on the Help Defeat Cancer Project?

The latest status on the Help Defeat Cancer Project may be found here.

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Is there a podcast for the Help Defeat Cancer Project?

Yes, you may find a podcast by Dr. David Foran on the News & Media page.

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Screen saver/Graphics: What was the large circle on the Help Defeat Cancer graphic, and what did the Distance and Filter mask graphics mean?

The round image at the left side of the application window showed the image of a slice of tissue sample, which the members computer processed. The tissues may have been stained with certain compounds to better highlight certain features, such as the nuclei of cells. The square "Filter Mask" in the upper right showed how one of many of the mathematical filters responded to a particular square subsection outlined in the tissue image at the left. The shading showed that particular filter's response value for each point ranging from dark (low response) to light (high response). You could see some correspondence between the outlined area and the Filter Mask. The shading in the "Distance Mask" at the lower right showed how the particular filter's response is relevant to a mathematical pattern being developed over all of the filters. This is a highly oversimplified description of what was displayed and computed. But, it does let you see a glimpse of the computation that was performed.

Help Defeat Cancer Agent Graphics

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What is FightAIDS@Home?

FightAIDS@Home is a project of the Olson laboratory at The Scripps Research Institute that uses volunteer computing technology which allows you to contribute your device's idle resources to accelerate research into new drug therapies for HIV, the virus that causes AIDS.

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How do I join the FightAIDS@Home Project?

All you need to do to join FightAIDS@Home is download and install the free software. Once that has been done, your device is then automatically put to work, but you can also continue using it as normal. Click here to get started.

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How does the FightAIDS@Home software work?

At any one time, the project uses one of two software docking tools to automatically download small pieces of work to your device and performs calculations that model how drugs interact with various HIV virus mutations. After your device processes the information, the results are sent back to World Community Grid and then sent on to The Scripps Research Institute where they are analyzed by the Scripps research team. The process takes an enormous amount of computing time, which is why World Community Grid needs you (and your friends!) to participate in FightAIDS@Home project.

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Will my computing time only help the FightAIDS@Home project?

Your device will contribute to whatever projects you choose; however, only certain projects will be available for mobile devices. You can select from the projects currently active at World Community Grid by visiting the My Projects page. There you can view all available projects, and choose those in which you want to participate.

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Are there any additional FAQs for FightAIDS@Home?

Yes, there are more FAQs on the FightAIDS@Home website.

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How can I find the latest status on the FightAIDS@Home Project?

You may find the latest status on the FightAIDS@Home Project here.

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What is the difference between the Vina and AutoDock software packages used in the FightAIDS@Home project?

AutoDock and Vina are automated docking software tools. They are designed to predict how a small molecule, such as a substrate or drug candidate, binds to a receptor molecule of known 3D structure. In the context of this project, these docking tools are being used to find potential drug compounds which may inhibit the HIV-1 protease (a protein which encourages and controls the progression of the virus).

The two software programs use different algorithms, each of which may provide better results depending on the types of molecules being docked. The FightAIDS@Home project uses both software tools in its calculations: the Scripps researchers determine ahead of time which software package is more suited to the particular task at hand, and the selected software for those work units then runs on World Community Grid. The project may therefore switch back and forth between the two software packages depending on its needs. As a contributor to the FightAIDS@Home project, you may notice either of those software packages being run for this project, each of which has a unique screen saver (see below for details on both screen savers).

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Screen saver/Graphics (AutoDock version): Current Dockings

Click on the on your agent application window in the lower right hand corner. You then will see a graphics window similar to the following AutoDock screen saver image:



What is the white arrow, helix and loopy structure?
Ribbon diagrams are simplified drawings of proteins that make it easier for scientists to view and understand what is shape is. The three-dimensional "skeleton" of HIV-1 protease is shown as a white ribbon diagram on the screen and is magnified about 10,000,000 times.

In this panel, you can see the shape that the particular sequence of amino acids in HIV-1 protease makes in three dimensions. For clarity, we are not showing the details of all of the atoms in the protein molecule, just the backbone. Remember, all proteins, including HIV-1 protease, are made up of strings of amino acids, linked like beads on a string. There are twenty different naturally-occurring amino acids, and you can think of them as different kinds of building blocks. These strings of amino acids have parts that like to stick to others while repelling others. The different parts of the protein's amino acid chain clump together into characteristic three-dimensional shapes.

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Screen saver/Graphics (AutoDock version): What are the colored spheres in Panel A?

The search algorithm used in AutoDock is not just looking at one possible solution of one candidate drug molecule (ligand) but is actually evaluating many possible solutions at once. The spheres show places where the best drug molecule to HIV-1 protease dockings have been calculated and the color shows how good they are.

AutoDock is trying to find the best way that the current ligand, the one your agent has downloaded, can fit together with the target HIV-1 protease. You can think of the ideal drug we are trying to find as a "key," and the HIV-1 protease as a "lock." Unlike keys in the real world, however, many drug molecules bend to change shape. In this respect, molecules are like a dancer's body; the same body is able to adopt many different poses and shapes. Unfortunately, we do not know what shape a candidate drug will adopt until we try millions of different possibilities and then select the best one.

To find the best fit, we are using an algorithm. An algorithm is just a recipe, a list of ingredients and instructions on how to do or make something. We are actually applying the principles of evolution in our search algorithm to find the best way that our candidate drug molecule would best fit together with the target, HIV-1 protease. Like evolution in the real world, we have a "population" of possible solutions to the problem.

This is what you are seeing when you look at the different colored spheres dotted around the white ribbon diagram. The colors correspond to the same colors of the crosses in panel B. Those representing more negative energy are considered better dockings. AutoDock uses a representation for each of these ligand dockings that says where the ligand's center is, what its orientation is, and what shape it has currently adopted. AutoDock applies genetic operations on the representations of random pairs of ligand shapes to generate two new representations and hence potentially better solutions. You can see how well AutoDock is doing by looking at the graph in panel C.

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Screen saver/Graphics (AutoDock version): Docking Energies

We see here the energy breakdown for each candidate ligand docking of the current population of possible solutions. The total energy of a ligand binding to the HIV-1 protease consists of an electrostatic energy component and a non-bonded energy component. The electrostatic energy measures how many like-charges and unlike-charges are interacting between the ligand and the protease. The non-bonded energy measures non-electrostatic attraction between the two.

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Screen saver/Graphics (AutoDock version): What is electrostatic energy?

You can see electrostatic forces in action if you rub a balloon on a dry wooly sweater, and then gently place the balloon against a wall: It sticks! This is because all objects are made of atoms. Each atom has an equal number of electrons and protons. Electrons have a negative charge, while protons have a positive charge. These charges balance one another exactly to make objects neutral, or uncharged. When we rub the balloon against a sweater, the friction causes electrons to be rubbed off the sweater and onto the balloon. The balloon becomes charged with static electricity, and it now has more electrons than protons, so it is negatively charged; the wall is more positively charged than the balloon so the balloon sticks.
If you were to rub a second balloon on your sweater, and hang the two balloons from a string, you would see the two balloons repel one another.

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Screen saver/Graphics (AutoDock version): What is non-bonded energy?

Non-bonded energy arises because atoms are "sticky" when they get close to one another. The amount of "stickiness" depends on the two atoms that are interacting. However, atoms repel one another when they are pushed too close together. Between two touching molecules, there are many of these non-bonded interactions. They are called "non-bonded" because these interactions are not permanent like chemical bonds.

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Screen saver/Graphics (AutoDock version): Best Docking Energy

We see here the best docking energy in the current population, plotted over the course of the current docking, shown as a green solid line. The red-dotted line shows the same kind of graph, but for the best docking achieved so far. As the current docking proceeds, at the end of every generation, the green graph gets updated.

The vertical axis shows the best energy. The more negative the energy, the better, i.e. the more precisely we predict this particular ligand will bind to the protease. You can see times when the energy is not changing (the horizontal lines in the graph) and times when the energy dropped (the vertical lines) when AutoDock has found a better solution than the previous generation.

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Screen saver/Graphics (AutoDock version): Current Progress Bar

The Current Progress Bar shows how much of the current work unit has been completed. The work units are specified by the researchers at The Scripps Research Institute and transmitted via the servers at World Community Grid to your machine. Each work unit has just one candidate drug molecule, out of a vast library of candidate drug molecules we are virtually screening. The software running under the grid agent on your device is called AutoDock, and it tries to determine the best way the current ligand fits into the target HIV- 1 Protease. When the work unit is finished, the best results are sent back to Scripps via World Community Grid for further analysis, to find the best candidate protease inhibitors for further testing in the laboratory.

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Screen saver/Graphics (Vina version): What does the screen saver look like when the FightAIDS@Home project is running?

Here is a video of the FightAIDS@Home project graphics when the Vina software is being used:

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Screen saver/Graphics (Vina version): What does the screen saver show?

The right portion of the screen saver shows both the target and drug candidate molecules, depicted as a collection of small spheres that represent the atoms of each molecule. These are the specific molecules that your device is currently working on. The left portion of the screen saver shows a view of the Earth and a red AIDS ribbon representing the worldwide fight against AIDS.

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Screen saver/Graphics (Vina version): Where may I obtain a high quality video of the FightAIDS@Home graphics?

You may download it here: FightAIDS@Home Video

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Screen saver/Graphics (Vina version): Where may I download pictures of the FightAIDS@Home graphics?

Images are available to download in the following resolutions:


640x512
1000x800
4000x3200

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Screen saver/Graphics (Vina version): What does the SCRIPPS logo represent?

SCRIPPS is the logo for "The Scripps Research Institute" in La Jolla, California, USA, which is the home of the research team behind the FightAIDS@Home project.

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Screen Saver/Graphics (Vina version): What does the Progress Bar represent?

The progress bar towards the bottom of the screen saver represents approximately how much of the current task your device has processed. When it reaches 100%, the computation is complete and the results will then be sent back to the World Community Grid servers, where they will be packaged and delivered to the FightAIDS@Home researchers.

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Screen saver/Graphics (Vina Version): What do the balls represent?

The small spheres represent the atoms in both the target molecule and candidate molecule currently being processed by your device.

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What was the first phase of the Human Proteome Folding project all about?

Each project on World Community Grid contains its own information page. Click here for the Human Proteome Folding page.

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How long did it take to finish work on a protein?

Task execution progress increased slowly. We tuned work units so that they took an average of about a week of wall clock time to complete. However, if you had a very fast computer it might have finished much sooner. In addition, the time to complete depended on the difficulty of folding a particular protein and on how long the computer was running.

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What is the status of the Human Proteome Folding project?

The first phase of the Human Proteome Folding Project was completed in July, 2006. You may read about the Human Proteome Folding Phase 1 results here.

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HPF1 vs. HPF2: Scoring different structures at higher resolutions

Balancing resolution with computational efficiency:
Protein structure prediction procedure must strike a delicate balance between the computational efficiency of the procedure and the level of physical detail used to model protein structure within the procedure. Low-resolution models can be used to predict protein topology/folds and sometimes suggest function (Bonneau et al. 2001b). Low-resolution models have also been remarkably successful at predicting features of the folding process such as folding rates and phi values (Alm and Baker 1999a; Alm and Baker 1999b). It is clear, however, that modeling proteins (and possibly bound water and other cofactors) at atomic detail, and scoring these higher resolution models with physically derived, detailed, potentials is a needed development if higher resolution structure prediction is to be achieved. Recent progress has focused on the use of low-resolution approaches for finding the fold followed by a refinement step where atomic detail is added (side chains added to the backbone) and physical scoring functions are used to select and/or generate higher resolution structures. Several recent studies have illustrated the usefulness of using de novo structure prediction methods as part of a two stage process in which low-resolution methods are used for fragment assembly and the resulting models are refined using a more physical potential and atomic detail (e.g. rotamers) to represent side chains (Bradley et al. 2003; Misura and Baker 2005; Tsai et al. 2003). In the first step Rosetta is used to search the space of possible backbone conformations with all side chains represented as centroids. This process is well described and has well characterized error rates and behavior. High confidence or low scoring models are then refined using potentials that account for atomic detail such as hydrogen bonding, van der Waals forces and electrostatics.
One major challenge that faces methods attempting to refine de novo methods is that the addition of side-chain degrees of freedom combined with the reduced length scale (reduced radius of convergence) of the potentials employed require the sampling of a much larger space of possible conformations. Thus, one has to correctly determine roughly twice the number of bond angles to a higher tolerance if one hopes to succeed.

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HPF1 vs. HPF2: Hydrogen Bonds

An illustrative example of the difference in HPF1 and HPF2 is the difference between low-resolution methods and high-resolution methods for the scoring of hydrogen bonds. In HPF1 we used the strand packing score, now, for HPF2, we use the hydrogen bond score, you can see this score on the client window. In the HPF1 procedure backbone hydrogen bonding is scored indirectly by a term designed to pack strands into sheets that simply looks to see that strands are aligned. Hydrogen bonding in helices is not modeled and it is assumed that hydrogen bond are satisfied in helices. See the series of pictures below to see hydrogen bonds in proteins. This low-resolution method first reduces strands to vectors (ignoring helical secondary structure fragments) and then scores strand arrangement (and the correct hydrogen bonding implicit in this arrangement) via functions dependent on the angular and distance relationships between the two vectors. Thus, the scoring function is robust to a rather large amount of error in the coordinates of individual atoms participating in backbone hydrogen bonds (as large numbers of residues are reduced to the angle and distance between the two vectors representing the strands). In the high-resolution, refinement, mode of Rosetta an empirical hydrogen bond terms with angle and distance dependence between individual electro-positive and electro-negative atoms is used (Rohl, 2005). This more detailed hydrogen bond term has a higher fidelity and a more straightforward connection to the calculation of physically realistic energies (meaningful units, physicists won’t make as much fun of us for using this one) but requires more sampling, as small changes in the backbone can cause large fluctuations in computed energy. Here is a small protein with the chain colored from N-terminus/start/blue to C-terminus/red.



Now I'll show just the two strands in this protein that are hydrogen bonded (a few hydrogen bonds) to each other:



Here is the protein if I color by atom type (C = green, N = Blue, O = red, S = yellow, H = white):


Here I've removed the fancy trace of the backbone everywhere but over the two strands:



And lastly I show the Hydrogen bonds as black zig-zags between the Nitrogens on one chain and the oxygens on another.


Here is another small protein that has no strands. Hydrogen bonds and help hold together the alpha helices.



Here it is with the helices drawn (same orientation, and colored by atom type):


And again, here is the protein with a few hydrogen bonds drawn as black zig-zags keeping the helix together:


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HPF1 vs. HPF2: Solvation - modeling the protein in water at higher resolution

Another major challenge with high-resolution methods is the difficulty of computing accurate potentials for atomic-detail protein modeling in solvent; with electrostatic and solvation terms being among the most difficult terms to accurately model. Full treatment of the free energy of a protein conformation (with correct treatment of dielectric screening) is not a problem with an efficient solution and the computational cost of full treatment of electrostatic free energy (by solving the Poisson-Boltzmann or linearized Poisson-Boltzmann equations for large numbers of conformations) is high. In spite of these difficulties several studies have shown that refinement of de novo structures with atomic-detail potentials can increase our ability to select and or generate near native structures. These methods can correctly select near native conformations from these ensembles and improve near native structures, but still rely heavily on the initial low-resolution search to produce an ensemble containing good starting structures (HPF2 like methods rely on initial search with HPF1 like methods) (Lee et al. 2001; Misura and Baker 2005; Tsai et al. 2003). Some recent examples of high res predictions are quite encouraging, and an emerging consensus in the field is that higher resolution de novo structure prediction (structure predictions with atomic detail representations of side chains) will begin to work if sampling is dramatically increased (thus the grid!). The solvation score is depicted in one of the three score panels in the HPF2 client.

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HPF1 vs. HPF2: Res-res pair score

The pair score in HPF2 is like the pair score in HPF1, but HPF2-pair score takes the position of Rotamers (a way of efficiently representing all side chain atoms) instead of centroid positions (representing the amino acid as a blurred out single point). So think of the HPF2 pair score as a all-atom version of the HPF1 pair score (appropriately re parameterized, of course).

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Higher resolution is important for other methods as well

Progress in high-resolution structure prediction will invariably be carried out in parallel with methods including but not limited to: predicting protein-protein interactions, designing proteins and distilling structures from partially assigned experimental data sets. Indeed many of the scoring and search strategies that high-resolution de novo structure refinement methods employ were initially developed in the context of homology modeling and protein design (Kuhlman et al. 2002) (Rohl 2004a). The Rosetta commons is currently developing Rosetta for all these methods and more. The part of Rosetta we use for HPF2 is less than half the code.

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When are points and statistics updated?

World Community Grid points and statistics are updated twice a day. This occurs at 00:00 and 12:00 UTC. This includes all statistics on World Community Grid except for Team Statistics.

Team Statistics are updated once a day at 00:00 UTC.

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How are Team Points and Personal Points Distributed?

Points that you earn are only credited to a team if they are earned while you are a member of that team. Additionally, if you quit a team or join another team, then the points that you earned for your previous team will stay with that team. You cannot transfer credit you previously earned to a new team.

Any points you earn whether you are on a team or not will always show up under your personal statistics.

You can view the points that you have earned for different teams at the bottom of your My Contribution page.

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Why are points not updated even though new work units have been downloaded?

Points are awarded for results when they have been successfully processed on your device. They are awarded after they have been returned to our servers and successfully passed validation. You may learn more about validation here. If you want to check the status of your result(s), you may view your results status page. Additionally, point totals are only updated on the website twice a day, so there can be up to a 12 hour delay between when your result is validated and the points appear on our website.

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What are points?

Your device's contribution is shown in three measures: points, total run time and results returned. The term points is simply used as a way of measuring the amount of computation your device has contributed. For instance, if your device works for three days on one work unit, or in those same three days completes five work units, you will accumulate the same number of points assuming that your device worked at about the same level of effort in each scenario.

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How are points used?

The calculation of Points is the method World Community Grid uses to measure your contribution to individual research projects running on World Community Grid. Points are one method for competitive comparison on the stats pages.

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Why are points on the agent and the web different?

World Community Grid in the past ran two types of agents. A United Devices (UD Windows) agent and a BOINC (Windows/Linux/Mac) agent. Today, World Community Grid only runs the BOINC agent. Points contributed by both of the agents will be part of a member's total on the website. However, only points contributed by BOINC agents will be shown on the BOINC agents. The points previously earned by a UD agent only appear on the website. Additionally, due to differences in how the agents computed points, BOINC points are multiplied by 7 when they are imported into the website. Thus if you earned 5 BOINC points, you will see 35 website points.

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What is validation?

World Community Grid is a volunteer computing grid. This means that work is being sent to computing devices that are outside the control of World Community Grid. Most devices that perform this work are reliable. However, there are a few devices that are not reliable due to things such as users over-clocking their machines, memory errors, disk errors, CPU errors or viruses being present. This means that the results returned need to be validated to make sure that they represent the correct answer.

We perform three different types of validation at World Community Grid:
 

  • Redundant Computations: In this type of validation, two copies of the work unit are sent to members devices. Once both results are returned, they are compared to ensure that the results are identical. If they are, then the result is accepted. If they are not identical, then additional copies are sent until several devices agree on what the result should be. This policy establishes a very high level of confidence in the reliability of the results. Mapping Cancer Markers and Uncovering Genome Mysteries are examples of projects that use this technique.
  • Single Validation - Type 1: In this type of validation, only one copy of a work unit will be sent to a device if the device is "trusted", that is, if it has been participating long enough and returning good results. If the device is not trusted, then it will still be assigned the work unit, but a second copy will be sent to another device and the rules for redundant computation above apply. As a precaution, the research code computes certain items that allow us to quickly check on the server if the computation is likely to have finished correctly. Additionally, trusted devices are randomly sampled to have their results double-checked. These techniques provide a very high level of confidence in the reliability of the results. FightAIDS@Home and Outsmart Ebola Together are examples of projects that have used this technique.
  • Single Validation - Type 2: This is similar to Single Validation - Type 1 except that due to the fact that different results are generated each time the work unit is run (due to the research techniques applied in the application), we send out many copies of each work unit. We currently do not have any research projects utilizing this technique.

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How are points calculated?

Points are calculated in a two-step process which attempts to give a consistent number of points for similar amounts of research computation. First, the computational power/speed of the computer is determined by periodically running a benchmark calculation. Then, based on the central processing unit (CPU) time spent computing the research result for a work unit, the benchmark result is used to convert the time spent on a work unit into points. This adjusts the point value so that a slow computer or a fast computer would produce about the same number of points for calculating the research result for the same work unit. This value is the number of point credits "claimed" by the client. More information about that formula is available here.

Second, research results returned to the servers are validated in a manner which depends on the research project. Then the claimed points for valid results are examined for anomalous (excessively high or low compared to other machines computing the same or equivalent work unit) values and adjusted accordingly. The servers assign the resulting adjusted point values to the member (and team) for each of the returned work units. This process eliminates the ability for malicious users to tamper with results and artificially claim higher points for their work.

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I have completed a result, but I have not yet received credit for it. What is going on?

BOINC does not award credit to users until the work they have performed has been successfully validated. This means that users may experience a delay in being granted credit while BOINC waits for enough results to be returned in order to perform validation.

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How do I calculate my FLOPS (Floating Point Operations Per Second) based off my World Community Grid points?

BOINC provides a reference about credit and its relation to FLOPS here. However, you should know that seven (7) World Community Grid points are equal to one (1) BOINC credit.

Therefore, your total World Community Grid points divided by 700 gives you the number of GigaFLOPs and your World Community Grid points divided by 700,000 gives you the number of TeraFLOPs.

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What is contained in the files I send back to the World Community Grid servers?

When the software has completed processing a work unit, it will create a file containing the results which will be sent back to the World Community Grid servers. If a work unit was aborted due to an error, a report of the occurrence may be submitted in place of the result file.

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May I download and process multiple work units, then return all of the results at one time?

The software used by World Community Grid does allow you to download multiple work units. It is unlikely that you will return all the work units together unless your device is disconnected from the internet while it completes the work units. For more information on cacheing workunits, please refer to this FAQ.

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How does the software return results?

The software returns a result to the World Community Grid servers in two phases. The first phase begins as soon as the workunit has finished processing. The first phase involves uploading the result files to the World Community Grid servers. The second phase consist of the software contacting the World Community Grid scheduler and notifying it that all the result files have been uploaded and the result is ready for validation. The second phase might not occur for several hours after a workunit has finished processing. This delay is because the software tries to minimize the number of scheduler communications that are made in order to minimize the load on the World Community Grid servers. By delaying the request, the software may be able to combine two communications into one.

If you have a ‘always on connection’ or if your machine is configured to automatically dial-up when an internet connection is needed, then the software will perform all of these activities automatically without any member intervention required.

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What is a Work Unit?

A work unit consists of data that represents a small part of an overall problem that the research project is trying to solve. Work Units are also referred to as Results.

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What are teams all about?

Once you become a member, you may participate in a team by going to your My Contribution page and then selecting My Team. You may either join a team or Create a New Team. When you are on a team, you may compete with other teams for total run time, points, and results returned. Joining a team does not affect your individual member statistics.

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May I join more than one team?

No. A member may join only one team at a time but may leave a team and join another team at any time. The statistics that you accrue while on a team, remain with that team.

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How do I join a team?

Go to the home page and log in. From the My Contribution page, select My Team from the left navigation menu. From the Find a Team page, under Keyword Search, Next to "Team" select the "Name" drop down and in the text box next to "Contains:", enter all or portions of the team name of the team that you wish to join, Then press search. If there is more than one team name returned, find the one that you wish to join. Then click on the team name and the system will return the team information. Press "join this team" to become a member of the team.

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How do I quit a team?

Go to the home page and sign in. From the My Contribution page, select My Team from the left navigation menu, the system will return the team information for the team of which you are a member. Press "quit this team" and you will no longer be a member of that team. The statistics that you have contributed to this team will stay with that team.

If you are not currently a member of any team, "quit this team" will not be an option.

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How do I create a new team?

Go to the home page and sign in. From the My Contribution page, select My Team from the left navigation menu, then select Create a New Team from the left navigation menu. Follow the instructions on the page for adding a team and then select save.

Please familiarize yourself with what the World Community Grid considers objectionable before creating a new team.

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How may I tell how much my team is contributing?

There are two ways to do this:

  1. Go to the home page and sign in. On the My Contribution page, the team that you are a member of will be shown in the center of the page next to My Team. Select that link to view the team statistics.
  2. Click Here to search for a team. This section is listed under "Find a Team" in the My Contribution section, but will allow you to search through all the teams that have been created at World Community Grid.

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How do I contact my team members?

Team captains may e-mail (email) the members of their team and team members may send e-mails to their team captain. To use this feature, just go to your team page and click the "e-mail team" or "e-mail captain" button.

To respect our members privacy, World Community Grid did not opt anyone in to receive team e-mails automatically if they were already a member when this feature was added to our website.

New members may opt-in to receive team e-mails if they select a team on the registration page. There is also a link to the My Profile page to opt-in when a member joins a team or becomes a captain. Team e-mails will be sent to any member of the team who has opted-in to receive the e-mails. If there are no members opted-in, there is a warning message for the captain, and there is no button to send the e-mail. The same applies in reverse if the captain has not opted-in.

To opt-in to team e-mails, you may go to My Profile and select the option to receive team e-mails. You will also see that you can enter in an alternate email address that is used only for team emails.

Some teams have a URL pointing to their site where they have created a special forum for team members to chat. As an alternative, you might go to the
World Community Grid forums by selecting Forums from the global navigation bar. The forums contain Team forums expressly for team activity. You might consider reaching out to other members from your team in one of these forums.

We recommend that you do not divulge any private information in the forums as they are public forums.

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How may I change my team name, description, or URL?

Team name, description, and URL may only be changed by the team captain. To change this information, sign in to My Contribution, select My Team from the left menu. From the My Team page, select Edit. On the Edit Your Team page, make the changes and select Save.

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My team page contains the words "BOINC Team ID." What does that mean?

World Community Grid has members who participate through BOINC. On BOINC, these members have a layer of team statistics as they are able to participate in multiple distributed computing projects. BOINC Team ID" refers to an identifier found on the BOINC site for this purpose (http://www.boincstats.com/). For more information about BOINC, please go to the Help facility and search on BOINC.

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Is there an easy way for my friends to join my team?

Yes. At the bottom of your My Team page are two web addresses that provide an easy way for your friends to join your team.

The first web address may be sent in an email to your friends that are already members of World Community Grid and they may just click on the web address and then click on the join now button on the page that appears.

The second web address may be sent in an email to your friends that are not currently members of World Community Grid. When they register, the team will be automatically selected for them. Let them know that they will still need to download and install the World Community Grid software.

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How do you change team captains?

If you are the current team captain, you may appoint a new team captain by following these steps:

1. Log in to your World Community Grid account.
2. Click on My Contribution, then click on My Team on the left side of the page.
3. Click on the 'Appoint New Captain' link, next to your Member Name listed as Captain.
4. Choose the team member who you would like to become captain, and click the 'Appoint as Captain' link next to their name.

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How is my team rank calculated?

A member may see their team stats on their My Team page for run time, points, and results returned. Your team rank is based on the total number of teams that have returned a result. You may see how many teams there currently are on the Team Statistics page.

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What is a Team Challenge?

A Team Challenge is essentially a competition between teams to see which team can return the most results, or generate the most points or run time in a given time period. A Team Challenge can be open to all teams on World Community Grid, or limited to only teams invited by the challenge creator.

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How do I create a Team Challenge?

As the captain of a team, you may create as many Team Challenges as you want; the only requirement is that they have different names so members can tell them apart from other Team Challenges.

To create a Team Challenge, go to My Contribution and click on My Team in the lefthand navigation. Just under the Team Information, you'll see the Team Control Panel with an Issue Team Challenge button. Click the button to be taken to the Issue Team Challenge page.

Once on the Issue Team Challenge page, you start by picking a name for your Team Challenge. After that, decide if you want your Team Challenge to be open to all teams, or if you want to choose which teams to invite. If you want an Open Challenge, check the box next to "Open Challenge?"

Next up, pick the dates for your Team Challenge. The Start Date must be at least one day in the future, but not more than 30 days away. The End Date must be at least one day after the Start Date, but not more than 180 days after the Start Date.

Once you've chosen the dates, select what type of Team Challenge you'd like. The choices are Points, Run Time, and Results Returned, or an Increase in one of Points, Run Time, or Results Returned. For more in the "increase" challenges, read this FAQ.

Next choose whether or not you want to allow Late Joiners; that is, allow teams to join the challenge after the Start Date. This applies to teams that are invited as well as for Open challenges. Teams that join a challenge after the Start Date will only receive credit for statistics after they join the challenge.

Last but not least, you may invite other teams to participate in your Team Challenge. You may invite teams even if your are issuing an Open Challenge. If you are issuing a Closed Challenge you must invite at least one team.

To invite teams, just search for the name of the team you want to invite, and click the link to "Invite This Team." For more general searches (for example: "IBM"), only the first 25 teams are returned. If this happens, try being a little more specific in your search ("IBM New York").

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How do I create a Team Challenge that is open to all teams?

When on the Issue Team Challenge page, just give your Team Challenge a name, check the box labeled "Open Challenge?", enter dates for your Team Challenge, select a type of challenge, and click the submit button. Done!

You can invite teams to an Open Challenge if you'd like. This will insure that your challenge invitation shows up in the team captains Pending Challenges under the Challenge Control Panel. If the team captain has chosen to receive Team E-mails (via the My Profile page) they will also receive an e-mail informing them of your newly created Team Challenge.

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How do I create a Team Challenge that is just limited to certain teams?

When on the Issue Team Challenge page, just give your Team Challenge a name, enter dates for your Team Challenge, select a type of challenge, and invite at least one other team. Inviting teams is as simple as searching for a team name, and clicking the link to "Invite This Team." You may do a search, invite some teams, and then do another search to get a broad array of teams to invite to your challenge.

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How do I invite teams from my team's country?

Unfortunately, the Issue Team Challenge team search doesn't filter by country. To invite teams from your country to your Team Challenge, you can filter by country on the Find A Team page, and then do a search by name on the Issue Team Challenge search for the teams that come up in the country-filtered Find A Team search. The best way to do this is to open two browser windows so that you can have each page open at the same time. The Issue Team Challenge page will not save the teams you've invited if you go to a different page before clicking the submit button.

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May I invite more teams to my Team Challenge after I issue it?

Once a Team Challenge has been issued (by pressing the submit button on the Issue Team Challenge page), no more teams may be invited. If you have issued an Open Challenge, other teams may still join the challenge up to the Start Date, or until the end of the challenge if you have chosen to allow Late Joiners (Late Joiners only get credit for statistics accumulated after joining the challenge).

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How do the Increase in XXXX challenges work?

The Increase in XXXX challenges, can also be viewed as "percent increase" challenges. In these challenges, a baseline is calculated based on the recent daily average production for each team in the challenge. During the challenge, the daily team statistics are averaged for the current duration of the challenge and then the baseline average is subtracted to yield and average increase (or decrease). That average increase/decrease is divided by the baseline average to determine the percent increase/decrease. For example, if a team averages 3 days of Run Time per day leading up to the challenge, and then averages 4 days of Run Time during the period of the challenge, the percent increase would be 33%. The math would be: (4-3)/3.

The final winner of the challenge will be the team with the largest percent increase over their baseline average.

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How will the captains of teams I've invited to my challenge know about it?

There are two ways that World Community Grid informs captains about challenge invitations:

  1. If a captain has chosen to receive Team E-mails (on the My Profile page), they will receive an email for each challenge to which they are invited.
  2. On the My Team page, there is a Challenge Control Panel. Team captains will see challenges to which they've been invited under a section called Pending Challenges. Captains can accept challenges directly from the Challenge Control Panel, or they can click the name of the Team Challenge to view the full details of the Team Challenge before accepting or declining the invitation.

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Where do I check on the status, statistics, etc. for my Team Challenge (or a challenge my team is participating in)?

Just go to your My Team page, and scroll down to the Challenge Control Panel. All team members will see up to five Current and Upcoming Team Challenges (team captains will see Pending Team Challenges as well). If your team has more than five Current Team Challenges or more than five Upcoming Team Challenges, you may click the link at the bottom of the Challenge Control Panel to view your team's entire Team Challenge History. In the Challenge Control Panel or Team Challenge History View you may click on the name of the challenge to view more details about the challenge; for example: scores for all teams in the challenge, the names of the other teams participating in the challenge, and whether the challenge is open or not. The Team Challenge History page is where you may view your team's past challenges.

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Plan Ahead for Team Challenges!

It's a good idea to make the Start Date of your Team Challenge at least a week in the future so that other teams will have a chance to join your challenge before it starts. Remember, after the Start Date, no teams may join your challenge, unless you opt to allow Late Joiners, so try to give the other team captains adequate time to get in!

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What are the goals of the Help Stop TB project?

The tuberculosis (TB) bacterium has an outer coat that protects it from treatments and a patient’s immune system. The Help Stop TB project is aimed at helping scientists to better understand that coat and its role in protecting the bacteria. This understanding can help us and other scientists to design better drugs against TB in the future.

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How are you going to meet those goals?

The outer protective coat of the TB bacteria contains a class of waxy or fatty molecules called mycolic acids. These are long, chain-like molecules of varying length and structure, and although they can be classified into three main groups, there are many variations within these groups that have not been modeled before.

By using World Community Grid to simulate the interactions of these molecules and their variations along with other molecules present in the coat, scientists will be able to understand for the first time how these variations affect molecule behavior. The simulation results will provide a realistic representation of the outer coat of the TB bacterium for the first time. The researchers will use these results to build a database of mycolic acid molecules that occur in the outer coat of the TB bacteria, allowing scientists to better understand how this outer coat protects the bacteria from drugs and the host immune system.

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What would be the long-term anticipated outcomes as a result of this research?

The results will provide a detailed understanding of the conformational behavior of mycolic acids, which can shed light into their biological role and how it is linked to their folding pattern. With these details, we will have a greater understanding of how mycolic acids help the TB bacterium to survive and spread.

Additionally, we will be able to create a database of structures that will be used to build a detailed model of the bacterium’s outer layer. This model will be used to investigate the bacterium's biological properties further, and to assess how this knowledge can aid in TB drug development.

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What is tuberculosis? How is it transmitted?

Tuberculosis is a disease caused by Mycobacterium tuberculosis (M. tb). The disease mostly affects the lungs, but if left untreated, can also spread to other organs and ultimately lead to death. TB is transmitted by small, airborne droplets resulting from coughing or sneezing from an infected person.

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Why is TB still a major global health problem?

One factor in the increase of TB infection is related to an increase in HIV infection. People with HIV/AIDS have a weakened immune system and are therefore more susceptible to TB. Once healthy people come into contact with the TB bacteria, the bacteria can usually be fought off effectively by their immune system without developing TB. However, a person with HIV is about 30 times more likely to develop TB disease, due to their weakened immune system. It is more difficult to detect and treat TB in an HIV-infected individual, and therefore those co-infected with TB and HIV often remain reservoirs of TB for extended times, with the potential of infecting more people.

Another factor in the increased TB infection is the TB bacteria becoming increasingly resistant to TB drugs. As drug resistance has increased, it has become more difficult to treat TB successfully, requiring much longer treatment times with combinations of drugs. Often, patients fail to continue treatments to the full term which can take up to two years. When treatment stops part-way, the bacteria evolve resistance to the drugs because it lets the bacteria that survived the initial portion of treatment live and infect others. This also results in people carrying TB for a longer time, potentially infecting more people with drug resistant strains of TB that are more difficult to treat. The World Health Organization recently ranked tuberculosis as nearly tied with HIV as the deadliest infectious disease in the world, mostly due to TB building its resistance to drugs.

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Is TB a serious problem compared to other diseases?

HIV, TB and malaria represent three major infectious diseases. TB is second only to HIV and the combination of HIV and TB is particularly serious since one infection promotes the other. TB and HIV each accounted for about 1.1 to 1.2 million deaths in 2014. Malaria accounted for over 500,000 deaths in 2013.

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Who does TB affect?

Most people who come into contact with TB do not become ill with the disease, but those who are malnourished or have weakened immune systems, such as HIV patients, are more susceptible to developing the disease once they have been exposed to the bacteria. In addition, poor living conditions and overcrowded places are the ideal conditions for TB to spread through coughing or sneezing of infected individuals.

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How can I help stop TB?

You can help stop TB by joining World Community Grid and donating your computer’s spare computing time to this project.

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What are the broader social and economic impacts of TB?

It is quite common for TB patients to suffer from discrimination. Fear of infection is the most common cause of TB stigma. TB stigma has serious socioeconomic consequences and it is thought to increase diagnostic delay and treatment noncompliance. The disease is also associated with factors that can themselves create stigma, such as poverty and HIV. TB patients who are discriminated against may be isolated socially, especially in small communities. TB also has a serious economic impact, especially in developing countries. The growing cost of TB medical care is a constant drain on health systems, rendering developing countries unable to provide proper medical care for their patients.

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What is tuberculosis, or consumption?

Tuberculosis, or TB (short for tubercle bacillus), is an infectious disease caused by a bacterium called Mycobacterium tuberculosis. In the past, the disease was also called phthisis, from the Greek 'φΘίσις' which means 'decay', or consumption, because of the extreme weight loss TB patients suffered. TB is an airborne disease, which means that it spreads through the air when people with an active TB infection sneeze or cough.

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What is the history of TB?

Tuberculosis has plagued humankind throughout history and prehistory. Mycobaterium tuberculosis may have killed more people than any other microbial pathogen. It has existed for over 20,000 years and has been discovered even among Egyptian mummies. Evidence of TB is also found in the Middle Ages, when it was known as the “king’s evil” and was believed to be curable by the touch of a king. In the 18th century, TB reached epidemic proportions in Western Europe and North America, earning the nickname “White Plague.” In 1882, Robert Koch discovered that the causative agent of the disease was Mycobacterium tuberculosis. Around 1921, Albert Calmette and Camille Guérin developed a vaccine (BCG) against it and in 1944, streptomycin was the first antibiotic successfully used against the disease. The first oral mycobacterial drugs, rifampicin and isoniazid, followed.

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What are the symptoms of TB?

TB symptoms include chronic cough with blood-tinged sputum, fever, breathlessness, chest pain, night sweats, fatigue and weight loss.

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Does TB only attack the lungs?

Tuberculosis typically attacks the lungs (pulmonary TB) but it can also develop in areas outside the lungs (extrapulmonary TB), such as the bones and joints, the digestive system, the bladder and reproductive system, the nervous system and the lymph nodes. Extrapulmonary TB is more common in people with a weakened immune system, such as HIV patients

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Why is TB hard to treat?

TB diagnosis and treatment are very complex. Diagnosis is long, with several tests usually needed to diagnose active TB, including chest X-rays, sputum samples, microscopy and culture, CT scans and biopsies. Treatment is also long, with regimens consisting of six to nine months or more of multidrug therapy. Patients can also fall ill with what is known as latent TB infection (LTBI), which means that they are infected with TB but they don’t manifest the clinical symptoms of the disease. It is estimated that one third of the world’s population has LTBI and although they don’t have active TB they may develop it in the future. The available diagnostic tools for LTBI have serious limitations in terms of both accuracy and effectiveness, thus leaving many cases undiagnosed.

Mycobacteria are naturally resistant to antibiotics due to being surrounded by a waxy coat of lipids, called mycolic acids. This waxy coat protects the bacterium and makes it impermeable to most antibiotics. This means that even after the lengthy process of diagnosis, it is still very difficult to establish which combination of antibiotics might be successful against the bacterium.

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What treatments options exist today for TB?

The usual course of treatment for pulmonary TB is two antibiotics (isoniazid and rifampicin) every day for six months and two additional antibiotics (pyrazinamide and ethambutol) every day for the first two months. It may be several weeks or even months before the patient starts feeling better. Such long treatments cause implications such as increased relapse risk, serious side effects from the drugs (such as loss of appetite, nausea, dizziness, abdominal pain and blurred vision), increased risk of clinical hepatitis, especially in cases of underlying liver disease, and, crucially, treatment noncompliance. Additionally, there are strains of TB which are resistant to nearly all antibiotics used to treat TB. Patients with drug-resistant TB need to receive special medical treatment that can potentially cause more side effects, such as depression or psychosis, hearing loss, hepatitis, and kidney impairment. These patients will also be under greater risk of dying from the disease. Resistant TB treatment is extremely challenging as it is very expensive, lengthy and disruptive for the patients’ lives

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When and how were the existing treatments for TB found?

Streptomycin, isolated from the bacterium Streptomyces griseus, was discovered in 1944 as the first antibiotic with proven activity against TB. The development of isoniazid followed in 1952, as the first oral mycobactericidal drug. This breakthrough would introduce combination therapy which reduced the typical therapy duration which up until then lasted for more than 18 months. The Medical Research Council (MRC) TB unit in the United Kingdom, in collaboration with the United States Public Health Service (USPHS), spent the next forty years developing the current treatment scheme consisting of isoniazid, rifampicin, pyrazinamide and ethambutol. The introduction of rifampicin in the therapeutic course in 1968 allowed treatment times to be shortened to 6 months when used in combination with pyrazinamide.

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Is there a TB vaccine?

Currently there is one approved vaccine for TB, the Bacille Calmette Guérin (BCG) vaccine, developed in 1921. However, it is 70-80% effective against the most severe forms of TB, such as TB meningitis in children, and it is less effective in protecting from respiratory TB which is the most common form of the disease in adults. Also, it is not possible to receive booster BCG shots later in life. While several new vaccines are in development, none are yet approved for use. The data that we will produce with your help will shed light on the biological role of the bacterium’s defense to antibiotics, thus contributing to the efforts of developing new vaccines.

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Where are resistant strains of TB coming from?

Resistant TB strains occur for a combination of reasons. The cell wall of the bacterium has a natural permeability barrier formed by mycolic acids (a class of waxy compounds) that protects the bacterium from drugs. Gene mutations in the bacterium can also lead to the development of resistant strains. Completion of antibiotic treatment in diagnosed TB cases is crucial. The long treatment times often discourage patients from completing their treatment, thus paving the way for resistance to develop. Finally, especially in developing countries, antibiotics often are scarce and of poor quality, thus contributing to the rise of resistant strains.

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Where can I learn more about TB?

World Health Organization
UK National Health Service
National Institute for Care and Health Excellence

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What does the screen saver look like when Help Stop TB is running?

Here is a video of the Help Stop TB project graphics:

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What does the screen saver show?

The right portion of the screen saver shows both the cell wall molecules and surrounding molecules, depicted as a collection of small spheres that represent the atoms of each molecule. These are the specific molecules that your device is currently working on.

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What does the progress bar in the screen saver represent?

The progress bar, towards the bottom of the screen saver, represents approximately how much of the current task your device has processed. When it reaches 100%, the computation is complete and the results will then be sent back to World Community Grid, where they will be packaged and delivered to the Help Stop TB researchers.

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What do the small spheres in the screen saver represent?

The small spheres represent the atoms in both the cell wall molecules and surrounding molecules currently being processed by your device.

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What does The University of Nottingham logo in the screen saver represent?

The University of Nottingham, in the United Kingdom, was rated No. 8 for research power in the 2014 Research Excellence Framework and is the home of the research team behind the Help Stop TB project.

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Where may I download pictures of the Help Stop TB graphics?

A screenshot of the project graphics is available for download in the following resolutions:

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What are the goals of OpenZika and how are these goals being met?

The main goal of the OpenZika project is to identify promising drug candidates to treat a Zika virus infection. In order to help scientists reach this goal, World Community Grid volunteers are donating their unused computing power to conduct virtual experiments, called “docking calculations.” Based on the results of the docking calculations, the researchers will be able to predict which drug candidates are most likely to show promising results in laboratory tests.

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How might the data generated on this project be useful to Zika researchers?

World Community Grid volunteers’ computers and Android devices will complete virtual screenings of chemical compounds that may be effective against the Zika virus. These virtual screenings will generate data about the potential effectiveness of chemical compounds that could be used as antiviral medicines. Once the virtual screenings are complete, researchers will use the data to test promising compounds in laboratories.

In compliance with World Community Grid policy, the researchers will make their data openly accessible, thereby allowing other scientists to apply their own methods and approaches to further study promising compounds. The open data component of this project (and all other World Community Grid projects) means that the likelihood of finding effective drug treatments for Zika may be higher than if the researchers worked in isolation.

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What is Zika?

The Zika virus (ZIKV) is a flavivirus (a family of mosquito-borne or tick-borne viruses), which is similar to dengue virus, yellow fever and West Nile virus. The virus has been found to be transmitted by bites from infected Aedes mosquitoes, from mother to fetus, through blood transfusion, urine, saliva, and sexual transmission.

Zika usually only causes relatively mild symptoms, such as fever, joint pains, rash, conjunctivitis (red eyes), headache and/or swollen lymph nodes. However, Zika has been recently associated with serious neurological conditions, such as Guillain-Barré syndrome, in adults and children. Additionally, scientists have linked cases of severe brain under-development in some fetuses and infants to mothers being infected with Zika during pregnancy.

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Why is Zika a major global health problem?

Zika virus is a global health issue, because it spreads rapidly and is related to severe neurological diseases (in adults and children), such as microcephaly, Guillain-Barré syndrome, acute myelitis, and meningoencephalitis. While the Zika virus itself was first identified in the late 1940s, the connection to widespread neurological issues is relatively new, because the Zika virus is spreading rapidly to populations that do not have immunity to it.

In February 2016, the World Health Organization (WHO) Director-General declared that the cluster of microcephaly cases and other neurological disorders reported in Brazil constitutes a Public Health Emergency of International Concern. There is currently no effective antiviral medication for Zika virus, and no vaccine. Therefore, the disease can continue to spread rapidly if left unchecked.

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Which geographic areas and populations are most impacted by Zika?

Since it was first identified in the Zika forest of Uganda, Africa, the Zika virus has spread across Asia, the Pacific, and more recently to the Americas. Serious concerns about the virus have been raised since 2015, due to a rapid rise in infections in the Americas coinciding with an increase in cases of microcephaly and other neurological disorders.

Between 2007 and April 2016, 62 countries reported cases of the Zika virus. Most of these cases occurred in the Americas (Central, North and South), Oceania, Pacific Islands, and Africa. Any areas with active Aedes mosquito populations—particularly tropical and subtropical regions—are vulnerable to the introduction and spread of the Zika virus. Recent estimates from an international group of university researchers suggest that more than two billion people could potentially be at risk.

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What are the broader community and public health impacts of Zika?

Without a vaccine or effective antiviral treatments, the Zika virus will continue to spread rapidly. And until scientists have more information about the links between the Zika virus and potential neurological complications, it will be difficult to know the full impact of the virus.

In Brazil alone, the Zika virus has affected millions of people. This caused drops in productivity, and an increased need for healthcare (especially for patients with complications and for infants born with microcephaly).

Additionally, people are less likely to travel to countries with high rates of Zika virus infections, which impacts local economies. Potentially, Zika outbreaks could increase pressure on healthcare systems and destabilize governments.

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What measures are being taken in countries where Zika has spread or could potentially spread? What can individuals do to protect themselves from the Zika virus?

Because there is no treatment and no vaccine for the Zika virus, prevention and containment efforts are largely focused on controlling the mosquito population. However, many mosquitoes have become increasingly resistant to insecticides, and the mosquitoes that harbor the Zika virus tend to hide inside homes, which makes eradication difficult. In addition, unlike most other types of mosquitoes, the female Aedes mosquito tends to feed on humans during the day, which makes insecticide-treated bed nets an impractical solution for impeding the spread of this virus.

Some countries with large populations of Aedes mosquitoes have advised women to avoid pregnancy until the Zika outbreak subsides.

Individuals who want to minimize their risk can take actions to avoid mosquito bites, such as wearing long-sleeved shirts and long pants, and staying in places with air conditioning and window/door screens to keep mosquitoes outside.

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How can I help stop Zika?

You can help stop this virus by joining World Community Grid and contributing to the OpenZika project. When you join, you donate your computer or Android device’s unused computing power to run virtual experiments to help researchers identify promising candidates for anti-viral drugs to combat Zika.

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What kind of mosquitoes transmit Zika?

The Aedes aegypti mosquito is known to transmit the Zika virus, and researchers believe the Aedes albopictus mosquito may also spread the virus.

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What is microcephaly? How is it linked to the Zika virus?

Microcephaly is a condition in which a child’s brain fails to develop properly in the womb, often leading to diminished brain size, impaired cognitive ability, motor control problems, seizures and related symptoms. The condition has been found in some infants whose mothers were infected with the Zika virus during pregnancy. In April 2016, a link between the Zika virus and microcephaly was confirmed by the Center for Disease Control.

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What are other potential complications that might be linked to the Zika virus?

In addition to microcephaly, conditions suspected of being associated with Zika include:

  • Guillain–Barré syndrome, which causes sudden muscle weakness and even paralysis in adults.
  • Myelitis, which is an infection of the spinal cord.
  • Meningoencephalitis, an inflammation of the brain and surrounding tissues, usually caused by infection.
These neurological effects have caused great concern and prompted the World Health Organization to form a Zika Emergency Committee to address the problem.

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Why should pregnant women be concerned?

Pregnant women infected with the Zika virus can transmit the virus to the fetus. Additionally, infants of women who are infected with Zika during pregnancy have a higher risk than normal of microcephaly, which is a condition where the brain does not develop properly in the womb. A link between a Zika infection during pregnancy and microcephaly was confirmed in April 2016. Due to this risk, some countries have advised women to delay pregnancy until the Zika outbreak is over.

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What is a flavivirus?

The flavivirus genus, which includes Zika, dengue, yellow fever, West Nile viruses and others – are viruses which are transmitted to humans by a mosquito or tick bite. The Zika virus is transmitted primarily by two kinds of mosquitos: the yellow fever mosquito (Aedes aegypti) and the Asian tiger mosquito (Aedes albopictus).

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Can work on related diseases help fight Zika?

Closely related viruses may give clues that could help researchers fight Zika. This is one of the reasons why OpenZika includes “template” crystal structures of targets from related viruses in our virtual screening experiments against the Zika models. However, although Zika may look like dengue, subtle changes on the virus surface and in the viral enzymes could impact how antivirals or even vaccines may work. The mechanism for these viruses getting into cells and their effects can vary dramatically. The top computational results from OpenZika will thus be tested in “wet lab” experiments with the actual Zika virus, to verify which compounds can help fight Zika.

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What is the history of the Zika virus?

The original description of the virus was published in 1952, although it was originally isolated in 1947 in Uganda, Africa. It was subsequently isolated from mosquitos in 1948 and from humans in 1952. Zika is a re-emerging, mosquito-transmitted virus that was relatively unknown until 2007, when it caused a major epidemic on Yap Island in Micronesia, followed by outbreaks in Oceania in 2013-2014. Following its introduction into Brazil in 2015, the virus has spread rapidly across the Americas.

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What are the symptoms of Zika?

The symptoms of Zika are usually relatively mild, including fever, joint pains, rash, conjunctivitis (red eyes), headache, and/or swollen lymph nodes.

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How is Zika diagnosed?

Zika virus can be diagnosed by performing specific blood serum tests during the first week after onset of symptoms. Additional antibody testing can be performed to confirm an initial diagnosis.

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How is Zika transmitted?

Scientists have confirmed a number of different means of transmission, including:

  • Bite from an infected mosquito
  • Blood transfusion
  • Sexual transmission
  • Transmission from mother to fetus

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Are there any existing treatments for the Zika virus?

There are currently no treatments for the Zika virus, and there is no vaccine. Because the disease’s symptoms are usually mild, it has not been widely researched until the most recent outbreak began in the Americas. Therefore, scientists are just beginning to understand the molecular structure of the viral components and the full implications of the disease.

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Is there a Zika vaccine?

Because the Zika virus usually only has mild symptoms, and because it was not widespread until recently, there has been little research on a vaccine until the outbreak in Brazil began in 2015. Currently, there are several groups researching vaccines in India, Brazil and the United States, but no vaccine has been approved as of May 2016.

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What is the difference between a vaccine and an antiviral drug?

A vaccine is administered before a person becomes infected. Vaccination usually consists of one or several shots which stimulate the immune system to protect against subsequent exposure to the virus.

Antiviral drugs are used when a patient is currently infected with the virus. They generally work by blocking the activity of the proteins that the virus uses to replicate itself or to infect other cells. These drugs must be taken by an infected patient multiple times, until the virus is destroyed.

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Are there other research efforts to fight Zika?

There are other efforts to fight the Zika virus throughout the world, most involving research into the atomic structure of the virus itself (or its individual components) and work on potential vaccines, based on viruses that are thought to be similar in structure to Zika. Organizations such as the World Health Organization, the Ministry of Health in Brazil, the Oswaldo Cruz Foundation (Fiocruz), and the Centers for Disease Control (U.S. CDC) are heavily involved in publicizing and supporting these efforts, and in encouraging researchers to share their data. Limited funding makes many research efforts difficult.

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How is this project different from other Zika research efforts?

The OpenZika project is searching for potential antiviral drugs to combat the virus, whereas many other projects are looking for a vaccine or are studying the structure of the Zika virus itself. The exact, atomic scale structures of most of the proteins that play a key role in the Zika virus lifecycle have yet to be determined (by experiments called “X-ray crystallography”). Until then, scientists will use approximate structures derived from a process called “homology modeling.” This involves using the genetic information for the Zika proteins and looking for very similar target proteins from other organisms, such as the dengue virus, for which some of the protein structures are known at atomic detail. These known structures (called “templates”) are then used as the basis to develop models of the targets that likely resemble the Zika proteins. As scientists learn more about the structure of the Zika virus, we and they will be able to focus on the target proteins that are most crucial to finding antiviral drugs.

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What efforts are there to control the mosquitos that transmit the Zika virus?

Countries in South America and Central America have launched plans to contain and eliminate mosquitos through widespread use of insecticides, mosquito traps, bedding nets, window screens, and other measures. In the United States, similar measures are being planned under the direction of the Centers for Disease Control. These measures are helpful, but can be limited by the fact that Aedes mosquitoes tend to hide in homes, they generally feed on humans during the day, and most types of mosquitoes are becoming increasingly resistant to many insecticides.

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Where can I learn more about Zika?

World Health Organization:

Wikipedia: Centers for Disease Control and Prevention: National Institute of Allergy and Infectious Diseases: U.S. Food and Drug Administration: USAID:

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What does the screen saver look like when OpenZika is running?

Here is a video of the OpenZika screen saver:

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What does the screen saver show?

The right portion of the screen saver shows both the target protein and drug candidate molecules, depicted as a collection of small spheres that represent the atoms of each molecule. These are the specific molecules that your device is currently working on. The left portion of the screen saver shows a rendering of the Zika virus.

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What does the progress bar in the screen saver represent?

The progress bar, towards the bottom of the screen saver, represents approximately how much of the current task your device has processed. When it reaches 100%, the computation is complete and the results will then be sent back to World Community Grid, where they will be packaged and delivered to the OpenZika researchers.

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What do the small spheres in the screen saver represent?

The small spheres represent the atoms in both the target protein molecule and candidate molecule currently being processed by your device.

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What does the UFG logo in the screen saver represent?

The logo represents Universidade Federal de Goiás which is a public federal institution of higher education for teaching and research, associated with the Ministry of Education, in Brazil.

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Where may I download pictures of the OpenZika graphics?

A screenshot of the project graphics is available for download in the following resolutions:

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What are the goals of the project and how are they being met?

The project’s primary goal is to identify drug candidates to control or cure certain types of childhood cancers. To meet this goal, the Smash Childhood Cancer research team is using World Community Grid to determine which of millions of chemical compounds may bind to certain target proteins or molecules involved with childhood cancers. These compounds would then be candidates for further testing and drug development, hopefully leading to treatments against these cancers.

To help achieve these goals, the research team plans to make the data from this project available to other scientists.

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What kinds of childhood cancers will this project focus on?

The initial childhood cancers being addressed are: neuroblastoma (nerve cancer), brain tumors, Wilms' tumor (kidney tumor), germ cell tumors, hepatoblastoma (liver cancer), and osteosarcoma (bone cancer).

The project is focusing on these particular childhood cancers because the researchers have discovered target molecules related to these diseases. The molecular structures of these targets have already been determined through previous research, and scientists believe these targets can be used to control the cancer. The research team aims to find drug candidates which can disable or enhance the activity of these target molecules, in order to control or cure the cancer.

Some of these target molecules are also involved with a number of adult cancers (colorectal cancer, lung cancer, gastric cancer, pancreatic cancer, renal cancer, liver cancer, nasopharyngeal cancer, prostate cancer and others) and may therefore help with treatments for those diseases, too. 

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How common is childhood cancer?

Worldwide, approximately 300,000 children are diagnosed with cancer every year, according to World Child Cancer. In the United States, the American Childhood Cancer Organization reports that more children are killed by cancer than any other disease, with over 15,000 children being diagnosed each year.  Learn more

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What current treatments are available for those types of cancers? What are the current survival rates?

A combination of surgery, chemotherapy, radiation therapy (including proton beam cancer therapy), and immunotherapy is applied to treat the patients with pediatric solid tumors. The survival rates of neuroblastoma, hepatoblastoma, brain tumors, and osteosarcoma depend on the tumor stages; the prognosis for those in advanced stages are usually very poor. Among those cancers, the survival rates for children with high-risk neuroblastoma or brain tumors are particularly low.

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How have treatment options and cure rates improved, or not, in the recent past? Why is this research important?

In general, the cure rates of pediatric cancers have largely improved; overall, the five-year survival rate has increased to approximately 80% for the last 50 years, due to progress in comprehensive therapies. However, the five-year survival rates for children with advanced stage tumors, metastatic cancer, and those with high-risk neuroblastoma and brain tumors are still very poor.

In the past 20 years, only a small number of new drugs designed to treat childhood cancer have been approved by the U.S. Food and Drug Administration. Half of all the chemotherapy treatments used for children with cancer have been in existence for 25 years or longer. (Learn more about these statistics at http://curechildhoodcancer.org/facts/.)

Therefore, discovering new drugs to eventually substitute for radiation would be a very important advancement in the field of pediatric oncology.

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How is this different from the team's previous project, Help Fight Childhood Cancer? Why is neuroblastoma being targeted again?

Help Fight Childhood Cancer, which ran on World Community Grid from 2009 to 2013,  found several potential new drugs candidates for neuroblastoma, a childhood cancer with poor prognosis when not diagnosed in the earliest stages. Further testing of these drug candidates continues.

The Smash Childhood Cancer project expands the scope to address not only neuroblastoma, but also additional pediatric solid tumors with poor outcomes.

The drug discovery targeting the TrkB protein, which was a neuroblastoma target during Help Fight Childhood Cancer, will be continued in this study. The research team will also study additional proteins which may be important in the development of cancer cells.

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What does the screen saver look like when Smash Childhood Cancer is running?

Here is a video of the Smash Childhood Cancer screen saver:

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What does the screen saver show?

The right portion of the screen saver shows both the target protein and drug candidate molecules, depicted as a collection of small spheres that represent the atoms of each molecule. These are the specific molecules that your device is currently working on.

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What does the progress bar in the screen saver represent?

The progress bar, towards the bottom of the screen saver, represents approximately how much of the current task your device has processed. When it reaches 100%, the computation is complete and the results will then be sent back to World Community Grid, where they will be packaged and delivered to the Smash Childhood Cancer researchers.

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What do the small spheres in the screen saver represent?

The small spheres represent the atoms in both the target protein molecule and candidate molecule currently being processed by your device.

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What does the double cross logo in the screen saver represent?

This the logo for the Saga Medical Center Koseikan, in Saga, Japan. The medical center was established 182 years ago, and is the oldest hospital in Japan. The logo was created to commemorate an International Red Cross activity that took place at the hospital 140 years ago.

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Where may I download pictures of the Smash Childhood Cancer graphics?

A screenshot of the project graphics is available for download in the following resolutions:

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