Search Results for: Minimum + requirements
I registered my agent successfully but it is not running any task.
One possibility is that your device does not meet the minimum resources required for any of our projects. You may check our system requirements here.
If your device does meet our minimum system requirements, please review the Network Connections and Settings FAQs. If this doesn’t apply, please post in our BOINC Support Forum, as a member may be able to quickly assist you with your problem.
Why are my results marked 'too late' or 'server aborted'?
The BOINC software allows us to set limits for each work unit. Below are some examples, but please note that the numbers used below are just examples and not actual:
- Max number of results (example 9)
- Max number of error results ( example 5)
- Max number of success results (example 5)
Please note: number of max successes means that the results are not validating against each other. For example all 5 copies have different results.
What are the recommended minimum system specifications?
In order to participate in World Community Grid, you will need to have at least the following:
- The ability to display graphics (if you wish to see the graphics)
- An Internet connection
In addition, each research project has its own requirement for memory and disk space. These are as follows:
| Research Project | Memory Available | Disk Space | Operating Systems |
| Africa Rainfall Project | 1 GB | 1.5 GB | Windows1,2,6, Mac2,6, Linux1,2,6 |
| Help Stop TB | 200 MB | 200 MB | Windows1,2, Linux1,2 |
| Mapping Cancer Markers | 400 MB | 500 MB | Windows1,2, Mac2, Linux1,2, Android3,4 |
| OpenPandemics - COVID19 | 250 MB | 200 MB | Windows1,2,5, Mac2,5, Linux1,2,3,5,Android3,4 |
| Smash Childhood Cancer | 250 MB | 100 MB | Windows1,2, Mac2, Linux1,2, Android3,4 |
1. Version for x86 processors is available
2. Version for x86-64 processors is available
3. Version for ARM processors is available
4. Android Minimum requirement is Android version 4.4
5. Version for GPU is available (Open CL 1.2)
6. Users who choose to run this project are encouraged to set the 'Leave applications in memory while suspended' option in their device profile
To limit the number of tasks assigned to your device for a specific project, please see the FAQ here.
Was an automatic slide feeder used?
No, scanning TMAs required manual monitoring.
How can I change the screensaver resource limits on my computer?
You will need to modify your Device Profile on the website. On your Settings page, select Device Manager, and then Device Profiles. Under Profile Name, select which Profile you would like to change (Default, School, Home, etc.). Then select the Custom Profile radio button. Under Advanced Options, scroll down to the Graphics section. The defaults are set to 7 frames per second and 5% cpu usage. If you would like the screensavers to refresh quicker, change the frames per second to 30. If the screensavers are taking up too much CPU power, decrease the percentage from 5% down to 2% to keep the screen saver usage to a minimum. Click Save at the bottom of the page to save your changes. The next time your computer communicates with our website, the preferences will be updated.
Are there any specific system requirements for running World Community Grid on Android?
Overall, World Community Grid only requires that the phone be running Android 4.1 or higher, but each research project has its own requirements for storage and memory usage. More details are available here.
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 much hard drive space does the software take on my computer?
The software itself will take less than 50 MB of hard drive space or your computer. The different projects that run on the World Community Grid, however, have different system requirements for running on your computer. To find out if your computer meets those requirements, go here.
Why does this application require zero redundancy, i.e. no comparison of results across devices?
Unlike many of our research projects, FightAIDS@Home – Phase 2 does not require redundancy, where the same research task is sent to two devices and the results are compared for consistency. Instead, this project will be using various processing metrics during the computation of a research task to validate that the task is progressing without errors.
Why are my work units failing with exit code 234 “Error: cl_khr_local_int32_base_atomics extension required by this program is not supported”?
The Help Conquer Cancer graphics card application requires the OpenCL extension cl_khr_local_int32_base_atomics and will not run on cards that do not support this extension. If you see the error above it is because your graphics card does not support the extension.
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 system requirements for devices to participate in OpenPandemics – COVID-19?
Any laptop or desktop can be used. OpenPandemics – COVID-19 runs on Windows, Mac, and Linux systems. Learn more about the system requirements at https://www.worldcommunitygrid.org/help/viewTopic.do?shortName=minimumreq
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.
Will World Community Grid ever run on a game box?
Running on game consoles requires specialized technical knowledge, plus the right kind of research project. The technical knowledge can be acquired but the research projects for game consoles must have a very small footprint.
Which World Community Grid research projects can run on GPUs?
For the latest on which World Community Grid research projects run on GPU, please refer to our system requirements.
What energy benefits are realized by performing these computations on World Community Grid?
By utilizing idle capacity on existing computing devices, you arguably avoid the energy associated with manufacturing the additional servers which would be deployed to perform the computations. This realizes energy and resource savings for the materials and processes required to manufacture the servers and components.
By utilizing the power of World Community Grid, simulations can be run which mitigate the need to use materials, equipment, and living systems to perform research activities. While laboratory research will still be required to derive environmental or health benefits in the society at large, the research activities can be more finely focused, minimizing the laboratory research required and thus the materials and energy required to do the work.
The net societal benefit of the use of World Community Grid far outweighs the minimal additional energy which may be drawn from the otherwise idle devices. The power of the grid enables researchers to complete computations in months instead of years and bring new, exciting innovations and solutions to health and environmental issues which affect our communities, our global neighbors and the environment.
Why is the Africa Rainfall Project opt-in only?
The Africa Rainfall Project requires significant computing power from each device: 1 GB of available memory and 1.5 GB of available disk space. Volunteers should make sure that their computers have these resources before opting in to the project.
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 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.
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 review the proposal to ensure that the research is technically correct. After that, it is placed on the schedule for launch.
Why is this project using intermediate uploads and trickle messages?
Unlike many of our research projects, FightAIDS@Home – Phase 2 requires that research tasks within each simulation, and small processing steps within each task, to be carried out in sequence. This means that it would take much longer to get the results to the researchers.
Trickle messaging and intermediate upload capabilities allow us instead to move the same research task from one volunteer to the next, without losing progress along the way. Overall, this assures progress, shortens and stabilizes the processing time required to complete research tasks and speeds up the rate at which valuable results can be returned to the researchers.
While a typical FightAIDS@Home – Phase 2 simulation might take up to a year to complete, using these capabilities means that it can be completed in as little as two months.
How much computing power does this project need, and why?
Based on the molecular dynamics simulations that the researchers have done up to now, using a cluster of 20 nodes (160 CPU cores) for a couple of months at a time, they estimate that to extend the simulations to water-flow velocities typical of practical nanotube filters, they will require another factor of 400 or more in compute time. And to simulate a representative range of membrane pore sizes would require a further factor of 10, for a total of order 106 thousand single-core-CPU-years. Add on to this a wide variety of contaminants they would like to add to the water in the simulations, and the sky is the limit!
Of course, the researchers will have to go one step at a time, and a lot of the computing effort will be to verify previous results at each stage and to make sure the results are reliable.
Why is solar energy important?
It is expected that by the year 2050 the world's energy requirements will be twice today’s demand. Energy is without doubt a prerequisite for economic stability in both the developed and developing world; however, despite its importance, the actual energy system is far from being self-sustainable. Achieving a completely sustainable energy system will require technological breakthroughs that radically change our paradigms on how we produce and use energy. A possible solution to this problem is solar energy. Every hour, enough solar energy reaches Earth to supply our energy need for an entire year. Finding the means to convert the incident solar energy into usable forms to maintain current ways of life represents a main objective of The Clean Energy Project.
Why is Phase 2 of the Clean Energy Project an opt-in project?
These calculations require work units that may run longer, have higher memory, disk space and data transfer requirements. Therefore, we are providing the users the option to opt-in to the project.
In addition, The Clean Energy Project is the first World Community Grid project to use an external server. That is, your result data is directly uploaded to the Harvard research server. Security checks are in place to make certain that uploaded data is transferred correctly and validated by the Harvard research server that is receiving the data. World Community Grid controls which servers the data is sent to and the Harvard servers will not send data files to the member machines.
Therefore, if you're interested in advancing the science of solar cells, please help us out in this great effort!
Will you make GPU processing available for other research projects?
Not all algorithms are suited to general purpose computing on GPUs and may not receive performance improvements. Additionally, general purpose computing on a GPU is a complex process, requiring numerous modifications and optimizations to the underlying algorithms of an application to realize performance increases.
We will work with the research scientists to make projects available on GPU if feasible and applicable to advancing the science application. However, it is up to the research scientists to enable their application to utilize GPU technology.
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 is a World Community Grid team?
Once you register with World Community Grid, you have the option to join an existing team, or create a new team. (Please note: to create a new team you are required to have a username.)
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.
Why can I only get one task at a time for the Africa Rainfall Project?
We have set the default for the Africa Rainfall Project to one task at a time due to the larger than normal system requirements. If any volunteers wish to increase this value, please see the “How do I limit the number of tasks assigned ... for a specific project?” FAQ.
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.
There are other volunteer computing projects related to COVID-19? Does the world really need more than one?
Yes! There other volunteer computing projects right now that are part of the fight against COVID-19, and they are all doing important work. Understanding the molecular structure of the virus that causes COVID-19, searching for treatments, and ultimately finding a vaccine, requires an "all hands on deck" approach from scientists, government agencies, businesses, and the general public.
Why does the screen saver only show a black or blank screen?
This is a known issue with later versions of BOINC. It is caused when you set your screen saver to require a password upon activation. Please upgrade to the latest World Community Grid BOINC agent available here as it will display an alternate screen saver that will show you the agent is working.
I'm having trouble downloading the software
Perhaps your Internet Explorer is configured to block installing downloads. Within Internet Explorer, click on Tools-> Internet Options -> Security -> Custom Level -> Downloads. Check to see that File downloads are enabled. There might be other settings which need to be enabled such as the ability to execute Javascript. Please also check to see if your network requires a proxy, click here for Proxy FAQs.
What operating systems are supported by World Community Grid on BOINC?
World Community Grid currently supports the operating systems listed in our System Requirements FAQ, which you can find here. Although they are not supported by World Community Grid, some of our members have had success using other platforms found here.
Does World Community Grid offer a 64 bit version of the BOINC software?
No. Our recommended BOINC agents are those of the 32 bit variety because even though the client is 32 bit, it will run 64 bit applications. The agent does not do anything that requires 64 bit execution at this time, thus recommending a version that works on both makes life easier. The science applications are available in both 32 bit and 64 bit. A 64 bit science application can run on 32 bit BOINC client. The opposite is also true, a 32 bit science application can run on a 64 bit BOINC client.
What software does the Africa Rainfall Project use?
The Africa Rainfall Project uses the Weather Research & Forecasting (WRF) model for the research application. It is used to simulate weather conditions in a geographical region over a defined time period. The work for this project will be broken into small geographical regions of sub-Saharan Africa, and in the end each region will be simulated for one calendar year.
WRF is a very large, mostly Fortran application, and the simulations being run require more resources than are typically used for a World Community Grid project. For this reason, volunteers will not be automatically opted into this project.
What is trickle messaging?
Trickle messaging is a capability that allows your device to communicate with us while working on a research task to report the progress being made by your device. This allows us to determine whether work should continue on that research task or whether insufficient progress is being made and therefore that task should be handed over to another volunteer for processing.
This capability is particularly useful to a project like FightAIDS@Home – Phase 2 because of the nature of its research tasks, which may require more processing time to complete and can therefore be started by one volunteer and completed by another, without losing the progress made by the first volunteer.
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.
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 is World Community Grid helping with this effort?
While effective, protein folding simulations are resource-intensive and often require more computational power than scientists typically have access to. The Microbiome Immunity Project research team is therefore enlisting the help of World Community Grid volunteers, each of whom runs these simulations on their computers. Each of these simulations is a virtual experiment to predict the structure of a protein.
The massive amount of aggregated computation power World Community Grid brings to this project will greatly advance and accelerate this new area of health research.
Why does the software sometimes display with a piece of the screen missing?
The software requires an 800x600 screen to display properly. If the software's window is opened when the screen is resized (for instance if you begin playing a game that resizes the screen), windows may not properly "re-paint" the windows when the screen is re-sized back to its original setting. To fix this, minimize the software's window by clicking on the downward pointing triangle. Right click on the software's icon in the system tray (the section of the Start bar where the time is displayed) and choose exit. Open the software by clicking on [Start] [Programs] [World Community Grid] [World Community Grid Software].
Why does my firewall keep asking me if I want to contact World Community Grid. Isn't it safe?
Firewalls are not familiar with World Community Grid. Even though World Community Grid is safe, firewalls are designed to ask you to make the decision. Many firewalls will ask you to allow the World Community Grid software to communicate with the World Community Grid servers soon after the software is installed. Although firewalls differ, you should be able to click on your firewall icon in your system tray and set permissions to allow communications.
Also please note, sometimes when firewall software is updated by the manufacturer, you may be required to re-approve your permissions for the World Community Grid software to communicate with the World Community Grid servers. The same is true if you install a new version of the World Community Grid software.
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 treatments exist for Leishmaniasis?
Although pentavalent antimonials (commercially known as Pentostam or Glucantime) have been the drugs of choice to treat this disease, there have been frequent reports of treatment failure due to resistance by the parasite. In addition, these drugs can cause mild to severe adverse effects, including death. Second-choice drugs, such as amphotericin B, pentamidine and paromomycin, also have toxic effects, sometimes requiring hospital management. Miltefosine, an oral drug, is one of the compounds used recently in the treatment of Leishmaniasis, but its effectiveness has only been tested with some species of the Leishmania protozoans. Although its administration is oral and effective against some species of Leishmania, its prescription is contraindicated in pregnant women because of the potential of causing birth defects.
How does ultrafiltration work?
Ultrafiltration refers to the process of reducing or eliminating very small particles from water by passing water under very high pressure through a membrane containing very fine pores. The unwanted particles have a harder time getting through the membrane than the water molecules, so fewer of them appear on the other side. The high pressure needed for ultrafiltration requires expensive equipment and much energy.
Any way to reduce the pressure needed in ultrafiltration can make water purification a cheaper and more accessible process. This is precisely what the Computing for Clean Water Project is ultimately aiming to achieve, by first studying in detail how the water molecules flow through filters.
Why is COVID-19 considered to be so dangerous?
COVID-19 is considered to be highly infectious disease, since the virus is usually spread through droplets generated when an infected person coughs or sneezes, or through droplets of saliva or discharge from the nose. The World Health Organization has stated that COVID-19 may be able to spread in all types of weather and may not necessarily require direct contact with an infected person. The virus can affect people of all ages, although the elderly, immunocompromised, and anyone with existing health problems are believed to be more susceptible.
As of the launch of this project, there is no effective treatment, cure, or vaccine for COVID-19.
Is there a work unit limit set per core?
Yes. The current limit is 70 per core.
The reason for this limit is that in the past, we have had results with wild estimations which could cause a machine to download more days worth of work than what the deadline allowed for, which was causing many results to go into a too late state and required reliable hosts to pick those up after the fact. This also caused many reliable hosts to become unreliable.
With multiple projects, the estimations to BOINC can vary even though we try our best to prevent this event from happening. This work unit limit has helped to prevent this type of event from happening again.
Am I required to add a username to my profile?
No. Adding a username to your profile is optional, after you have completed the registration process. However, you will not be able to do any of the following if you have not added a username to your profile:
- post in the forums
- create a team
- become a team captain
- make your World Community Grid data public
- recover the email address associated with your member account
Once you have added a username, you will not be able to revert back to having no username associated with your account. You can change your username at any time. If you do change your username, your previous username will become available to other members.
How do I set up my device so that it will download enough work to keep my device working for several days?
You may set up the BOINC agent so that it will keep a cache of work units to keep your device busy. You can do this on the website by going to your Settings page, and then selecting Device Manager. This screen will show you a list of your active devices. Associated with each device is a device profile. Click on the device profile associated with the device you want to cache additional work units on. On the Device Profile screen select 'Custom Profile' and then find the field labeled 'Work Unit Cache Settings', change the fields to meet your requirements and save the profile. Please do not use values longer then 4 days, as the scheduling algorithm in the client may prevent you from getting as much work as you would like.
What is the Verification Code and what is it used for?
The Verification Code is a private, personal code that you can use to verify your team membership and team stats. There are teams that provide incentives and/or rewards to members for being a part of their team. World Community Grid is providing the Verification Code as a way for these teams to verify their members' statistics and team membership without requiring members to give the team their password.
Note that your Verification Code will change if you change your member name and/or password. If your team is relying on your verification code to verify your membership and statistics, be sure they have your current Verification Code.
To verify the team membership and statistics for a member, use the API:
http://www.worldcommunitygrid.org/verifyMember.do?name=MEMBERNAME&code=VERIFICATIONCODE
You must set your data sharing preferences to "Display my data" for this API to return data for your account.
You will get a response in XML containing the membership information for that member. If there is an error, it will be reported back in the XML response.
How does a molecular dynamics simulation work?
Newton wrote down simple equations of motion to describe how balls fly through the air or apples fall. The world of atoms and molecules is subject to quantum mechanics, which is a good deal more complex than classical Newtonian mechanics. Yet it turns out that by making certain approximations and simplifications, it is possible to simulate the molecular world by letting large numbers of atoms or molecules interact according to Newton’s laws.
So the idea of a molecular dynamics simulation is to let things evolve using a computer program which can track every detail of what happens to each molecule over time as it is buffeted by all the surrounding ones. But to get a statistically meaningful picture from such simulations it usually requires repeating the simulations thousands or even millions of times with slightly different starting conditions. It is this computational challenge that this project addresses, by getting volunteers to provide more than a thousand times the computing power that a typical research group would have access.
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.
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.
How does understanding protein structure help scientists understand the role of bacteria in human health?
Different proteins can have many different structures (shapes). They can have sticky portions which like to attach to certain chemical compounds, or repel them. They can sometimes be flexible. For example, enzymes are proteins which can enhance certain chemical reactions or even cut proteins or other compounds apart. Their structures and the patterns of electrical charges on their surface determine which other compounds they may interact with and how they may alter the other compounds.
Since cells use proteins for most of their basic life processes, their functions, determined by their structure, are very important. If these functions are disturbed, diseases can result. Since the human microbiome has over 1,000 times more different kinds of proteins than the human body, many of those have the potential for affecting human cells' operations. Some of these proteins can be beneficial or even necessary, while others may be harmful. This is an area which still needs a lot of exploration. One of the early steps in understanding the role of the microbiome is to discover the functions of its proteins. That requires discovering the structure of those proteins.
I have received the error message "Suspending computation - CPU usage is too high" in my Message Log. What action can be taken to fix this?
This message means that other applications on your device are using your processor to do work. In order to allow those applications to run as fast as possible, the World Community Grid software is suspending the research until your device is once again idle.
If you wish to change the level of processor use that is required before World Community Grid stops running the research application, then please take the following steps:
What will World Community Grid's calculations produce?
The calculations done on World Community Grid will predict which small molecule compounds, out of the millions contained in a library database, should be tested for their ability to inhibit the flavivirus protease. This is a major step towards the ultimate goal of discovering new drugs to stop flavivirus infections.
Phase 1 of this project predicted how each small drug molecule might bind to the active site of the viral protease. This phase also produced preliminary "energies" that coarsely rank the strength of the intermolecular interactions between the compounds and viral protease.
Phase 2 will accurately predict free energies of binding between each drug compound and the viral protease. This calculation utilizes the binding orientations calculated in Phase 1. Due to computation time required for each free energy of binding calculation, only compounds with "good" scores from Phase 1 will be selected for Phase 2 calculations.
As an analogy, Phase 1 will tell us how two people might hold hands, whereas Phase 2 will tell us whether or not they want to hold hands.
Phase 2 of our project is designed to reduce the number of Phase 1 false positives (i.e., dead ends) that are tested in our laboratory. Phase 2 will take several thousand Phase 1 hits, run each hit through computationally demanding free energy calculations, and remove many of the false positives from the hit list. Phase 2 is expected to produce an updated list of hits that contains ~80% true positives. Testing Phase 2 hits in the laboratory will be much more productive, efficient, and rewarding than testing Phase 1 hits. For instance, to find 25 small molecules that stop dengue virus replication in the laboratory, we would need to synthesize and test either 250-500 Phase 1 hits or ~30 Phase 2 hits.
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. 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. This low-resolution method first reduces strands to vectors (ignoring helical secondary structure fragments) and then scores strand arrangement (and the correct hydrogen bonding implicit in this arrangement) via functions dependent on the angular and distance relationships between the two vectors. Thus, the scoring function is robust to a rather large amount of error in the coordinates of individual atoms participating in backbone hydrogen bonds (as large numbers of residues are reduced to the angle and distance between the two vectors representing the strands). In the high-resolution, refinement, mode of Rosetta an empirical hydrogen bond terms with angle and distance dependence between individual electro-positive and electro-negative atoms is used (Rohl, 2005). This more detailed hydrogen bond term has a higher fidelity and a more straightforward connection to the calculation of physically realistic energies (meaningful units, physicists won't make as much fun of us for using this one) but requires more sampling, as small changes in the backbone can cause large fluctuations in computed energy. Here is a small protein with the chain colored from N-terminus/start/blue to C-terminus/red.
Why is TB still a major global health problem?
One factor in the increase of TB infection is related to an increase in HIV infection. People with HIV/AIDS have a weakened immune system and are therefore more susceptible to TB. Once healthy people come into contact with the TB bacteria, the bacteria can usually be fought off effectively by their immune system without developing TB. However, a person with HIV is about 30 times more likely to develop TB disease, due to their weakened immune system. It is more difficult to detect and treat TB in an HIV-infected individual, and therefore those co-infected with TB and HIV often remain reservoirs of TB for extended times, with the potential of infecting more people.
Another factor in the increased TB infection is the TB bacteria becoming increasingly resistant to TB drugs. As drug resistance has increased, it has become more difficult to treat TB successfully, requiring much longer treatment times with combinations of drugs. Often, patients fail to continue treatments to the full term which can take up to two years. When treatment stops part-way, the bacteria evolve resistance to the drugs because it lets the bacteria that survived the initial portion of treatment live and infect others. This also results in people carrying TB for a longer time, potentially infecting more people with drug resistant strains of TB that are more difficult to treat. The World Health Organization recently ranked tuberculosis as nearly tied with HIV as the deadliest infectious disease in the world, mostly due to TB building its resistance to drugs.
Why does my device show high CPU use?
The CPU in computers and other computing devices is actually highly utilized no matter what is going on, except when it is powered off, or stopped. There is a hidden "idle" task running in the background that runs at lower priority than everything else in the device, even lower than the World Community Grid software. The idle task counts up the percentage of the time it runs and calls this "idle time" and reduces the reported CPU utilization figure accordingly. Neither the World Community Software software nor the idle task will run if your device has other work to do. However, since our software runs at a slightly higher priority than the idle task, the idle task won't run at all and thus report that your computer will be 100% utilized*. Having our software run in the background along with other applications is usually not a problem unless you have a system with relatively little memory. For such systems you may want to change your preferences to meet your requirements.
An overview of the various performance settings may be found here.
* Note: If you set the throttle in the BOINC agent (called: Use no more than: % of processor time) to 60%, the agent will run at 100% for three seconds, and then at 0% for two seconds.
How do I create a Team Challenge?
As the captain of a team, you may create as many Team Challenges as you want; the only requirement is that they have different names so members can tell them apart from other Team Challenges.
To create a Team Challenge, go to My Contribution and click on My Team in the lefthand navigation. Just under the Team Information, you'll see the Team Control Panel with an Issue Team Challenge button. Click the button to be taken to the Issue Team Challenge page.
Once on the Issue Team Challenge page, you start by picking a name for your Team Challenge. After that, decide if you want your Team Challenge to be open to all teams, or if you want to choose which teams to invite. If you want an Open Challenge, check the box next to "Open Challenge?"
Next up, pick the dates for your Team Challenge. The Start Date must be at least one day in the future, but not more than 30 days away. The End Date must be at least one day after the Start Date, but not more than 180 days after the Start Date.
Once you've chosen the dates, select what type of Team Challenge you'd like. The choices are Points, Run Time, and Results Returned, or an Increase in one of Points, Run Time, or Results Returned. For more in the "increase" challenges, read this FAQ.
Next choose whether or not you want to allow Late Joiners; that is, allow teams to join the challenge after the Start Date. This applies to teams that are invited as well as for Open challenges. Teams that join a challenge after the Start Date will only receive credit for statistics after they join the challenge.
Last but not least, you may invite other teams to participate in your Team Challenge. You may invite teams even if your are issuing an Open Challenge. If you are issuing a Closed Challenge you must invite at least one team.
To invite teams, just search for the name of the team you want to invite, and click the link to "Invite This Team." For more general searches, only the first 25 teams are returned. If this happens, try being a little more specific in your search.
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.