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Why does my country have so few members when I know there are more?
Why am I periodically asked to log into World Community Grid again?
How do I view the website in another language?
Why are some areas of the site only available in English?
What happens if I check the box labeled 'Remember Me' when I sign into World Community Grid?
I checked the 'Remember Me' box when I signed in, but now the site is asking me to log in again.
Do you have an XML interface for the statistics?
What is a Project Badge?
I'd like to put something about World Community Grid on my website; is there something that I can use?
What is the World Community Grid widget?
How do I find out the meaning of the messages on the Results Status Page?
Forum Policy for Members
Please remember our collective goal.
What is a Community Advisor?
What do the Member Titles, underneath the Member Name, in the forums mean?
Is World Community Grid a non-profit organization?
How does World Community Grid get new projects?
Are the results produced by World Community Grid part of a commercial venture?
This sounds too good to be true. Am I missing something?
What is different about World Community Grid and other BOINC distributed computing projects?
Will running the World Community Grid Software cost me more in electricity?
What about connection costs?
What energy benefits are realized by performing these computations on World Community Grid?
How can I help reduce the energy usage associated with my computer?
Where are the Help Cure Muscular Dystrophy - Phase 2 FAQs?
Will this project help stop the current H1N1 flu outbreak?
Why can't influenza immunizations solve the problem?
How will my computer make a difference on this project?
How soon is a new influenza drug going to be available?
What is the difference between influenza immunizations and antiviral drugs like Tamiflu and Relenza?
How do I keep from getting H1N1 influenza?
I think I may have H1N1 influenza. What should I do?
What is the first picture on the Influenza Antiviral Drug Search detail page?
What is neuroblastoma?
What is the cause of neuroblastoma?
What are the potential benefits of the Help Fight Childhood Cancer project?
What will our calculations for the Help Fight Childhood Cancer project produce?
What is the benefit of conducting this research on World Community Grid?
Where do the paintings / pictures on the Help Fight Childhood Cancer project research pages and BOINC client come from?
Screen saver/Graphics: When I look at the screen saver image, what is my computer working on?
Screen saver/Graphics: What does the circle of children represent?
Screen saver/Graphics: What does the molecule represent?
Screen saver/Graphics: What does the Progress Bar represent?
Screen saver/Graphics: What do the figures between the Chiba Cancer Center logo and the Chiba University logo represent?
What are the buildings in the slideshow images for Help Fight Childhood Cancer?
Why is solar energy important?
How does an organic solar cell work?
How will The Clean Energy Project help find solar cell materials?
What is the efficiency in a solar cell?
What other technological applications will be relevant to this project?
Screen saver/Graphics: How are The Clean Energy Project plots on the screensaver created?
Screen saver/Graphics: Why are we interested in determining the energy and temperature of a molecular system for The Clean Energy Project?
Screen saver/Graphics: What does "kcal/mole" and "K" mean on these plots for The Clean Energy Project?
Screen saver/Graphics: Why are we interested in investigating alternative sources of energy for The Clean Energy Project?
Screen saver/Graphics: What is the green object in The Clean Energy Project screen saver?
Screen saver/Graphics: What are The Clean Energy Project "Scipplets" all about?
Screen saver/Graphics: The Clean Energy Project Scipplets refer to something called gigajoules (GJ). What is a gigajoule?
Screen saver/Graphics: What does The Clean Energy Project blue plant leaf object represent?
Screen saver/Graphics: How does The Clean Energy Project benefit humanity?
Why rice?
What is a protein?
What do proteins do?
What does protein structure tell us?
What do proteins look like?
Why do we need to predict protein structure?
How is Protinfo different from other approaches?
Why is protein structure prediction so difficult?
Screen saver/Graphics: What is the rotating shape in the center of the Nutritious Rice for the World graphics?
Screen saver/Graphics: What is the red graph titled RAPDF in the Nutritious Rice for the World graphics?
Screen saver/Graphics: What is in the background of the Nutritious Rice for the World graphic?
Screen saver/Graphics: May I look at the information in the Nutritious Rice for the World graphic a different way?
What are the potential benefits of the "Help Conquer Cancer" project?
What computers can run the "Help Conquer Cancer" Project?
What will World Community Grid's calculations produce?
What will happen with the data generated by all these calculations?
When will this project be completed?
Screen saver/Graphics: When I look at the Help Conquer Cancer graphic, what is my computer working on?
Screen saver/Graphics: What is the moon-crater object in the middle of the Help Conquer Cancer graphic background?
Screen saver/Graphics: In the Help Conquer Cancer graphics: What are the round disks? Each disk has a different color. What does that mean?
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?
What is climate?
What is a General Circulation Model (GCM)?
What is a Regional Circulation Model (RCM)?
What are climate model parameters?
Why was this project just looking at Africa?
Why did this project download and upload so much data?
What are the potential benefits of the "AfricanClimate@Home" project?
What computers can run the "AfricanClimate@Home" Project?
What will World Community Grid's calculations produce?
What will happen with the data generated by all these calculations?
Why were there so many copies of a work unit sent out for AfricanClimate@Home?
Why do I have to opt into AfricanClimate@Home in order to participate?
What version of WRF was being used for the AfricanClimate@Home project?
When will this project be completed?
Screen saver/Graphics: What did the variable Temperature @ 2m on the right graph of the AfricanClimate@Home graphic represent?
Screen saver/Graphics: What did the variable Humidity @ 2m on the right graph of the AfricanClimate@Home graphic represent?
Screen saver/Graphics: What did the variable Precipitation on the right graph of the AfricanClimate@Home graphic indicate?
Screen saver/Graphics: What did the graph on the right side of the AfricanClimate@Home graphic represent?
Screen saver/Graphics: What did the map on the left side of the AfricanClimate@Home graphic represent?
What are the potential benefits of the "Discovering Dengue Drugs - Together" project?
What computers can run the "Discovering Dengue Drugs - Together" Project?
What will World Community Grid's calculations produce?
What will happen with the data generated by all these calculations?
When will the DDD-T project be completed?
What is molecular docking and virtual screening?
What is meant by "binding free energy?"
What are viruses?
What types of viruses belong to the family called Flaviviridae?
How are virus structures determined?
What proteins do these viruses make?
How are protein structures determined?
What antiviral drugs exist?
Why is it so difficult to develop new drugs?
Screen saver/Graphics: Where do the student writings that appear on the Discovering Dengue Drugs - Together graphic come from?
Where are the Help Cure Muscular Dystrophy FAQs?
What is the status of the Help Cure Muscular Dystrophy project?
What is Genome Comparison?
Why did the Genome Comparison project compare protein sequences?
How proteins were compared in the Genome Comparison Project?
What are the potential benefits of the Genome Comparison Project?
What is the status of the Genome Comparison project?
How did the Genome Comparison software work?
Screen saver/Graphics: What did those circles, symbols and letters in the Genome Comparison graphic mean?
What is Tissue Microarray technology?
What does a Tissue Microarray slide look like?
How long does the scanner take to scan in a whole slide?
What is the average number of tissue slices per slide?
Was an automatic slide feeder used?
Where can I find out more on Tissue Microarrays?
Why were there not as many work units for the Help Defeat Cancer project?
How can I find the latest status on the Help Defeat Cancer Project?
Is there a podcast for the Help Defeat Cancer Project?
Screen saver/Graphics: What was the large circle on the Help Defeat Cancer graphic, and what did the Distance and Filter mask graphics mean?
What is FightAIDS@Home?
How do I join the FightAIDS@Home Project?
How does the FightAIDS@Home software work?
Will my computer only be working on the FightAIDS@Home project?
Are there any additional FAQs for FightAIDS@Home?
How can I find the latest status on the FightAIDS@Home Project?
Screen saver/Graphics: FightAIDS@Home - Panel A: Current Dockings
Screen saver/Graphics: FightAIDS@Home - What are the colored spheres in Panel A?
Screen saver/Graphics:FightAIDS@Home - Panel B: Docking Energies
Screen saver/Graphics: FightAIDS@Home - What is electrostatic energy?
Screen saver/Graphics: FightAIDS@Home - What is non-bonded energy?
Screen saver/Graphics: FightAIDS@Home - Panel C: Best Docking Energy
Screen saver/Graphics: FightAIDS@Home - Current Progress Bar
What was the first phase of the Human Proteome Folding project all about?
How long did it take to finish work on a protein?
What is the status of the Human Proteome Folding project?
HPF1 vs. HPF2: Scoring different structures at higher resolutions
HPF1 vs. HPF2: Hydrogen Bonds
HPF1 vs. HPF2: Solvation - modeling the protein in water at higher resolution
HPF1 vs. HPF2: Res-res pair score
Higher resolution is important for other methods as well
When are points and statistics updated?
How are Team Points and Personal Points Distributed?
Why are points not updated even though new work units have been downloaded?
What are points?
How are points used?
Why are points on the agent and the web different?
What is validation?
How are points calculated?
I have completed a result, but I have not yet received credit for it. What is going on?
What is contained in the files I send back to the World Community Grid servers?
May I download and process multiple work units, then return all of the results at one time?
How does the software return results?
What is a Work Unit?
What are teams all about?
May I join more than one team?
How do I join a team?
How do I quit a team?
How do I create a new team?
How may I tell how much my team is contributing?
How do I contact my team members?
How may I change my team name, description, or URL?
My team page contains the words "BOINC Team ID." What does that mean?
Is there an easy way for my friends to join my team?
What is a Team Challenge?
How do I create a Team Challenge?
How do I create a Team Challenge that is open to all teams?
How do I create a Team Challenge that is just limited to certain teams?
How do I invite teams from my team's country?
May I invite more teams to my Team Challenge after I issue it?
How do the Increase in XXXX challenges work?
How will the captains of teams I've invited to my challenge know about it?
Where do I check on the status, statistics, etc. for my Team Challenge (or a challenge my team is participating in)?
Plan Ahead for Team Challenges!
What IBM Software does World Community Grid use?
What is BOINC?
How can I tell which version of the BOINC software I am using?
How do I check if I have the latest supported version of the BOINC software?
How do I upgrade to the latest supported version of the BOINC Software?
How do I know that the BOINC software is running correctly?
I have a platform that isn't supported by World Community Grid. Could I get a copy of the research application code and compile it myself?
Will World Community Grid ever run on a game box?
What was the difference between run time reported by the United Devices version and the BOINC version?

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.

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.

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.

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.

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 computer. This means that you do not have to sign in again in order to access your My Grid pages or post in the forums. You can have World Community Grid 'remember me' on as many computers 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 computer for more than two weeks. Additionally, if you change your password, then World Community Grid will continue to remember you only on the computer 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 computer.

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).

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.

What is a Project Badge?
What is a Project Badge?
A Project Badge is an acknowledgement of the contribution that a member has made to one of the research projects running at World Community Grid. All available badges may be viewed here.
A badge appears as a image for a member on their My Grid page, the Member Information page and next to their name in the forums. A badge is awarded to a member based upon how much computer processing time they have contributed to the project.
There are 6 levels of badges for run time donated to each research project and each is denoted by a different color background:
- Bronze - 14 days
- Silver - 45 days
- Gold - 90 days
- Ruby - 180 days
- Emerald - 1 year
- Sapphire - 2 years
No badge will appear until members contribute a minimum 14 days of run time to a research project. World Community Grid may occasionally change these rules for certain projects. This was done for the AfricanClimate@Home project, which required only 1 days worth of run time for a Bronze badge, 7 days for a Silver badge, and 30 days for a Gold badge, 45 days for Ruby, 60 days for Emerald, and 75 days for Sapphire.

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.

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 My Grid tab, 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!

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.

Forum Policy for Members
The Forum Policy for Members can be found here.

Please remember our collective goal.
World Community Grid's mission is to create the largest public computing grid benefiting humanity. You have joined in order to donate the idle cycle time from your computer to accelerate the research projects running on World Community Grid and in that way, help to improve human conditions 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 computer run time available for the humanitarian research projects we run. This web site is not a place to promote any other cause or issue.

What is a Community Advisor?
World Community Grid has a great group of Community Advisors ready to help answer any question you might have. A Community Advisor is a member who has been identified by World Community Grid as someone who has provided significant assistance to other members in the forums. The title "Community Advisor" has been given to distinguish them in the forums. The role of the Community Advisors is to provide guidance to and answer questions for other World Community Grid members, and to bring any issues or problems that arise in the forums to the attention of the World Community Grid support team. Community Advisors also have the ability to post in the Start Here: Community-Maintained FAQs. Community Advisors are not employees of World Community Grid but have volunteered to help in this role and also have to follow the forum rules.
The members who are Community Advisors include:
- Dave Bell
- lawrencehardin
- retsof
- Sekerob
- stares
- JmBoullier
- Jean Pierre.
World Community Grid sincerely appreciates the invaluable help that these members provide and asks that you respect the requests and opinions of the Community Advisors.

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

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

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.

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.

This sounds too good to be true. Am I missing something?
Everything is on the level. Members who volunteer their unused computer cycles benefit by not only making their computers more productive, but also by helping make scientific inroads on humanitarian problems. Research organizations benefit by having Grid computing available to them at no cost, enabling them to make more effective use of critical funds. The people of the world benefit because humanitarian research is advanced, and the results are shared because they are made available in the public domain.

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

Will running the World Community Grid Software cost me more in electricity?
The amount of electrical energy consumed by your computer 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 computer and simultaneously using more programs causes the computer to consume more power. The World Community Grid software runs during times at which your computer would otherwise be idle. This will cause the computer 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 “My Grid” page or on your computer.
The default processor usage rate for World Community Grid is set to 60% of the processor time. 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 “My Grid” 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.

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.

What energy benefits are realized by performing these computations on World Community Grid?
By utilizing idle capacity on existing workstations, you arguably avoid the energy associated with manufacturing the servers which would be deployed to perform the computations. This realizes energy and resource savings for the materials and processes required to manufacture the computer and its 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 idle workstations. The power of the grid enables researchers to complete computations in weeks 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.

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.

Where are the Help Cure Muscular Dystrophy - Phase 2 FAQs?
FAQs about the project are in the Resesarch section under Project FAQs.

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.

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.

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.

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.

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.

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.

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:

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.

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.

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.

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.

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.

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.

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.

Screen saver/Graphics: When I look at the screen saver image, what is my computer working on?
It means that your computer is processing one of the 3 million 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 computer.

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 computer at the time you are looking at the screen saver. The children are hopeful that a cure for neuroblastoma will be found using your computer.

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 computer, 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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!

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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.

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:
| M | toggle member info (show/hide) |
| I | toggle progress graph size and position (large/small) |
Protein visualization:
| B | toggle backbone shape (show/hide) |
| S | toggle structure atoms (show/hide) |
| C | carbon (C and Cα) |
| A | carbon (Cα) |
| N | nitrogen |
| O | oxygen |

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.

What computers can run the "Help Conquer Cancer" Project?
Due to the inherent granularity of our image analysis problem, there are very modest memory and CPU requirements for the compute nodes. However, without access to thousands of CPUs, researchers would not be able to process 80 million images in a reasonable amount of time. Multiple platforms will be able to run the project; World Community Grid is launching Linux and Windows compiled code first, with Macintosh OS to follow.

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.

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.

When will this project be completed?
Once the project starts, we will have a better idea about the time required to process the images on World Community Grid. This will be determined by the number of suitable computers and the number of projects being concurrently executed on World Community Grid. However, researchers have several interesting subsets of images, which will be analyzed first, thus enabling preliminary results to be available after a few weeks. These images comprise a set previously analyzed by an earlier version of CrystalVision, as well as by multiple human experts.

Screen saver/Graphics: When I look at the Help Conquer Cancer graphic, what is my computer 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.

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.

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.


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.

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

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

When will this project be completed?
The first phase of the project ran through July, 2008.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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."

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.

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.

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.

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.

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.

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.

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.

Where are the Help Cure Muscular Dystrophy FAQs?
FAQs about the project are in the Resesarch section under Project FAQs.

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.

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.

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.

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.

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

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.

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.

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.

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. TMAs hold tremendous promise for improved accuracy in prognosis, therapy planning and drug discovery.

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).


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.

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.

Was an automatic slide feeder used?
No, scanning TMAs required manual monitoring.

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.

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.

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.

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.

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.


What is FightAIDS@Home?
FightAIDS@Home is a project of the Olson laboratory that uses distributed computing to contribute your computer's idle resources to accelerate research into new drug therapies for HIV, the virus that causes AIDS.

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 computer is then automatically put to work and you continue using your computer as usual.

How does the FightAIDS@Home software work?
We use software that automatically downloads small pieces of data and performs calculations that model how drugs interact with various HIV virus mutations. After your computer processes the information, the results are sent by World Community Grid 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 The World Community Grid needs you (and your friends!) to participate in FightAIDS@Home.

Will my computer only be working on the FightAIDS@Home project?
Your computer will work on whatever projects you want. 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.

Are there any additional FAQs for FightAIDS@Home?
Yes, there are more FAQs on the FightAIDS@Home website.

How can I find the latest status on the FightAIDS@Home Project?
You may find the latest status on the FightAIDS@Home Project here.

Screen saver/Graphics: FightAIDS@Home - Panel A: 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:

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.

Screen saver/Graphics: FightAIDS@Home - 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.

Screen saver/Graphics:FightAIDS@Home - Panel B: 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.

Screen saver/Graphics: FightAIDS@Home - 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.

Screen saver/Graphics: FightAIDS@Home - 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.

Screen saver/Graphics: FightAIDS@Home - Panel C: 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.

Screen saver/Graphics: FightAIDS@Home - 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 computer 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.

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.

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.

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.

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.

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 wont 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:


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.

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).

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.

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.

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 a 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 Grid page.

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 computer. 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

What are points?
Your computer 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 computer has contributed. If your computer works for three days on one work unit, or in those same three days completes 5 work units, you will accumulate the same number of points assuming that your computer worked at about the same level of effort in each scenario.

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.

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 members 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.

What is validation?
World Community Grid is a volunteer computing grid. This means that work is being sent to computers that are outside the control of World Community Grid. Most computers that perform this work are reliable. However, there are a few computers that are not reliable due to things such as users over-clocking their machines, memory errors, disk errors, CPU errors or viruses being present on the machine. 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 workunit are sent to members computers. 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 computers agree on what the result should be. This policy establishes a very high level of confidence in the reliability of the results. Help Conquer Cancer is an example of a project which has used this policy.
- Single Validation – Type 1: In this type of validation, only one copy of a workunit will be sent to a computer if the computer has been participating long enough and returning good results so that the computer is trusted. If the computer is not trusted, then they will still be assigned the workunit, but a second copy will be sent to another computer 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 computers 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 Discovering Dengue Drugs – Together are examples of projects which use 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 workunit is run (due to the research techniques applied in the application), we send out many copies of each workunit. Human Proteome Folding – Phase 2 and Nutritious Rice for the World are projects which use this technique.

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.

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.

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.

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 computer is disconnected from the internet while it completes the work units. For more information on cacheing workunits, please refer to this FAQ

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.

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.

What are teams all about?
Once you become a member, you may participate in a team by going to your My Grid 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.

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.

How do I join a team?
Go to the home page and sign in. From the My Grid page, select My Team from the left navigation menu or select "Find a Team to Join" in the middle of the page, 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.

How do I quit a team?
Go to the home page and sign in. From the My Grid 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.

How do I create a new team?
Go to the home page and sign in. From the My Grid 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.

How may I tell how much my team is contributing?
There are two ways to do this:
- Go to the home page and sign in. On the My Grid 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.
- Click Here to search for a team. This section is listed under "Find a Team" in the My Grid section, but will allow you to search through all the teams that have been created at World Community Grid.

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.

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 Grid, 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.

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.

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.

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.

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 Grid 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").

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.

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.

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.

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).

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.

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:
- 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.
- 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.

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.

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!

What IBM Software does World Community Grid use?
World Community Grid runs on IBM WebSphere Application Server Network Deployment 6.1, IBM DB2 Enterprise 9.5 with the Performance Optimization, pure XML, and the Storage Optimization Features, and IBM WebSphere MQ 7.0.

What is BOINC?
BOINC is an open source grid software package. BOINC stands for Berkeley Open Infrastructure for Network Computing. It has been developed under a National Science Foundation grant. The software provides server side components that allow the management of a science project. It also includes client software that runs on a variety of platforms, including Linux. More information about BOINC may be found at http://boinc.berkeley.edu/.

How can I tell which version of the BOINC software I am using?
Right click on the World Community Grid, or BOINC, icon in the bottom right corner of your display (by the date and time). Click on “About World Community Grid – BOINC Client” or “About BOINC” and the current version of the software will be displayed.

How do I check if I have the latest supported version of the BOINC software?
You may check which version of the software that World Community Grid is currently supporting by visiting this page: https://secure.worldcommunitygrid.org/ms/viewDownloadAgain.do . The version number is displayed below the name of the agent for each operating system. If this number is the same as the version number that you have installed then you have the latest supported version.

How do I upgrade to the latest supported version of the BOINC Software?
You may upgrade to the latest version of the World Community Grid software by visiting https://secure.worldcommunitygrid.org/ms/viewDownloadAgain.do and following the directions on that page.

How do I know that the BOINC software is running correctly?
One way to check is to double-click on the World Community Grid, or BOINC, icon in the system tray in the lower right of your display. An information panel will pop up that should reflect that the application is running and the panel will also display the “elapsed time” and “time remaining”.

I have a platform that isn't supported by World Community Grid. Could I get a copy of the research application code and compile it myself?
No. The code has to remain in the control of the World Community Grid support team. Even the slightest change in the code, including using a different compiler, could render the research results useless. In addition, the license agreement that we have with the researchers for their code stipulate that only the World Community Grid support team can touch the source code. The source code usually differs slightly from potential public versions of the same code due to changes made for use with the specific grid project. Furthermore, we typically run many tests to make certain there are no problems on a given platform.

Will World Community Grid ever run on a game box?
Running on game boxes requires specialized technical knowledge, plus the right kind of research project. The technical knowledge can be acquired but the research projects for game boxes must have a very small footprint. World Community Grid is investigating the feasibility of providing a client for gamers but we don't have a specific project scheduled at this time given our current priorities to launch new research projects. Going forward, we will re-evaluate the feasibility, cost and timing of making the client available to gamers and update the member community.

What was the difference between run time reported by the United Devices version and the BOINC version?
It is important to note, that the time reported to the server doesn't mean that the UD version was doing more work then the BOINC version. The UD version simply overcounted the actual time that was contributed to the project. In fact, the BOINC version actually contributes more time to the project because it is able to take advantage of multi-core processors or multi-processory systems. The UD version could only use one core or processor. The BOINC version will start up a science application on each core or processor and thus be able to get two or more times the work done.
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