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Active Distributed Computing Projects - Life Sciences

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Project Information Project % Complete Major Supported Platforms
Life Sciences
Parabon Computation Parabon Computation has research projects (and will have commercial projects) and has a secure Java client like Popular Power's. Version 1.4 is available for Windows 9X/2K/NT as of October, 2002. You can download the full client here. The client automatically upgrades itself, so you don't need to download updates. You can sign up to receive email notification when the Mac and Unix clients are available.

The client currently participates in one or more of the following projects: an exhaustive regression analysis to identify the specific factors that ease the suffering of chemotherapy recipients, a gene expression analysis and a study of the molecular dynamics of protein folding to create greater understanding of the behavior of cancer cells and how they interact with potential new treatments, and an exhaustive regression analysis of clinical trial data for Amarillo Biosciences, Inc. for a treatment of fibromyalgia syndrome.

ongoing Windows 32
grid.org Help find cancer-fighting drugs at United Devices Cancer Research. The project is a partnership among grid.org, the National Foundation for Cancer Research (NFCR), and the Centre for Drug Discovery in the Department of Chemistry at the University of Oxford, England. The first phase of the project, THINK, began in March, 2001 and completed in June, 2002. That phase used over 200,000 hours of CPU time to screen 3.5 billion molecules against a range of cancer protein targets. The second phase, LigandFit, began in June, 2002. This phase will further refine the results from the first phase. Oxford has a detailed website about the science behind the project. grid.org also has the latest news about the project and its results.

On November 16, 2004, the project announced that 400 compounds from the LigandFit phase have been synthesized and tested in a lab. Between 2-4% of them show activity. Typically less than 0.1% of compounds from computer-simulated screening show activity. The next step for the successful compounds "is to persuade pharmaceutical or biotechnology companies to take up these experimentally verified hits and to test them further."

The project uses the grid.org computing platform. See the grid.org platform information for the latest version of the grid.org client. The grid.org client is available for Windows.

Join a discussion group about grid.org's projects.

See grid.org's global stats Windows 32
Folding@home Folding@home is another volunteer project that uses a screensaver or client application based on the Mithral CS-SDK to simulate protein folding in an effort to better understand how proteins self-assemble or fold. Intel supports this project through its Philanthropic Peer-to-Peer Program. You can see what projects are currently running on the current projects page. As of version 3.0, the software client also supports the Genome@Home project. See the project's latest news (last updated August 6, 2004). The site has been translated into many different languages.

On October 21, 2002, the project announced that it achieved its initial goal: to "simulate the folding dynamics of proteins and make quantitative predictions for how [protein folding] works. This has been a 'holy grail' of computational biology." Specifically, the project simulated the folding of a man-made chain of 23 amino acids called BBA5. The simulation's measurements and folding-time matched physical measurements and folding-time of the protein observed in a lab. The achievement was published in the November, 2002, edition of Nature, in an article titled "Absolute comparison of simulated and experimental protein-folding dynamics." In October and November, 2004, the project's lead developer and research scientist, Guha Jayachandran, won the top award at the 2004 Biomedical Computation at Stanford (bcats) conference, and Vijay Pande has been named a 2004 Technovator.

On January 10, 2003, the project broke the 90,000 active CPU mark. On October 10, 2003, it broke the 120,000 active CPU mark. On April 24, 2004, it broke the 150,000 active CPU mark. On September 9, 2004, it broke the 1,000,000 total CPUs and 100 TFLOPs marks.

On November 28, 2001, the project began studies (110 and 5100) on Alzheimer's Disease. On May 8, 2002, the project began studies (503 and 504) on Huntington's Disease, a disease similar to Alzheimer's Disease in that it is caused by protein misfolding. See a list of all of the project's current studies. In June, 2002, the project started using the Gromacs molecular dynamics modeling software. This software allows the project to simulate larger proteins more accurately and much more quickly than the previous software. As of August 12, 2002, the Gromacs software has successfully modeled one of the simpler molecules, project 902, and shows a lot of promise for success with larger molecules. On March 27, 2003, the project began studying several new types or work units, including NTL9 (a protein with both beta and alpha structure) and 1PRB (a three-helix bundle). The project also increased the scope of its trpzip investigation to include a fourth variant trpzip4. On April 23, 2004, it published the first results from its Gromacs core. On August 20, 2004, the project began its P130x projects: these projects have work units much larger than normal, and require users to have hundreds of MB of RAM and be able to transfer 5 MB of data for each result, but the work units have 50% more value in stats. On October 12, 2004, the project released a new AMBER (Assisted Model Building with Energy Refinement) core which will allow it to do things that it can't with its existing Tinker and Gromacs cores. See the AMBER core FAQ.

Version 5.02 of some of the Windows, Linux and Mac OS X clients is available as of August 20, 2004. Version 4.00 of the other clients is available as of December 19, 2003. Note the 2.x clients have a compatibility problem, and you should upgrade to the latest client if you are using an old version. Beta version 5.03 pre 9 is available for Windows.

Students and teachers should see the Education@Home section of the site.

See the research papers and articles published from the results of this project.

See Professor Pande's February 19, 2004, talk at Xerox PARC: Folding@Home: Can a grid of 100,000 CPUs tackle fundamental barriers in molecular simulation? Windows Media Player is required to view the video.

See independently-maintained hourly team and user stats for this project at statsman.org.

See an independent support site for helpful hints about participating in this project.

See the original Folding@Home project.

Join a discussion group about this project.

Join a discussion group about the original project.

Join an independent discussion group about ab-initio protein folding (where the folding is simulated completely in software)

ongoing Windows 32
fightAIDS@home Help design new drugs to fight AIDS at fightAIDS@home. The project is sponsored by the non-profit Scripps Research Institute. The project website site is also available in Chinese Chinese.

The project completed Phase I on May 21, 2003 (in this phase, almost 60,000 computers completed 1,400 years of computing to process over 9 million tasks).

"[Phase I] has ably demonstrated that with such massive computational abilities, researchers can utilize intensive approaches to identify drug candidates that succumb to resistance mutations and those that are more resilient to such mutations. An early lead developed during Phase I, TL-3, has been shown to be promising against the drug resistant strains that have arisen from the currently approved HIV Protease inhibitors. The characteristics of TL-3 have been born out by the FAAH computational work."

The project began Phase II on May 21, 2003. Note that for Phase II, the project transfered completely to The Scripps Research Institute (and became a completely non-profit project) and Entropia is no longer involved. You will need to reregister and download a new client to participate in Phase II. You can learn more about the project through articles it published on January 19 and January 26, 2004:
The Resistance Part I: From Petri Dishes to Population Dynamics
The Resistance Part II: Fighting HIV Resistance At Home and in the Laboratory

The client is currently available for Windows. It is best for users with permanent Internet connections. The client will eventually be available for Mac OS X and Linux.

waiting for Phase II stats to become available Windows 32
Ubero Übero's Java-based client allows you to participate in for-pay projects similar to other current and upcoming for-pay projects. The current Beta version of the client runs "genetic alignment algorithms" which "look for similar amino acid strings in various organisms." This volunteer project is being done for the Institute of Genomics and Bioinformatics at the University of California, Irvine. Future volunteer projects may include protein folding and radiation research. Note: this project was completed in November, 2001, so no new results are being discovered. However, the project data is being used to test new features for the client application. Your contribution will help to test the new features and improve the client.

The Beta version 0.7.1 of the client is available as of January 8, 2002. This version of the client has support for users behind proxy-based firewalls, uses your CPU and network bandwidth more efficiently, and has many other new features. The client will run on any platform that will run Java 2. This project is better suited for users with full-time Internet connections because a work unit completes in only a few minutes on my Pentium II 350 and the client doesn't buffer work units. Note: as of November 8, 2004, the project is moving to a new data center environment. Users should edit their agent.cfg files and change the "Coordinator-Address" field to the new value of dctp.ubero.net.

View the project's discussion forum.

ongoing Windows 32
D2OL Help find oral drugs which can fight Anthrax, Smallpox, Ebola, SARS, deadly diseases for which there is currently no cure, and Malaria, a life-threatenting disease for which 40% of the world's population is at risk, in the Drug Design Optimization Lab (D2OL)TM. This project, sponsored by The Rothberg Institute for childhood diseases, uses volunteer resources to screen Anthrax, Smallpox, Ebola, SARS, and Malaria proteins against a database of 2 million potential drugs. The SARS project began on April 17, 2003. The Malaria project began on November 7, 2003. See a detailed discussion about the science behind the project.

The graphical client can run minimized or (on Windows) in the system tray. Currently it does not allow you to select which protein target(s) to work on: future versions will allow this. It does not require a continuous Internet connection: it allows you to set the number of work units it will cache so that you can cache more work if you connect to the Internet infrequently. Note that if you pause or restart the client, you will lose all of the conformers you've generated for the current work unit. The client supports users behind firewalls. Version 2.0 of the client is available for Windows, Mac OS X, Linux and Solaris as of September 18, 2003. See a press release about the significant updates in this version.

Join the D2OL discussion forum.

ongoing: 1,743,271,049 conformers tested; 46,857,946 candidates found;
Anthrax Lethal Factor: 38.217% complete;
Smallpox Target 1: 37.412% complete;
Ebola Target 1: 37.778% complete;
SARS Target 1 / 2 / 3 / 4: 72.257% / 38.038% / 35.208% / 37.962% complete

Windows 32

Virtual Lab Help screen molecules to design drugs to fight diseases in The Virtual Laboratory Project. This project does not work in the way that traditional projects do. Instead of downloading a software client and having it get work assignments, you set up Globus grid computing software on your system and then make your system available to the World Wide Grid (WWG), a global computing grid. Then the Virtual Lab project coordinators can schedule computations on your system at their convenience. Because of this setup, this project is best for users with permanent Internet connections. For this project, the coordinators use their grid scheduler, called Nimrod-G, to deploy their Nimrod-G agents on your machine to do the molecule screening. Their view of the project looks like this.

See a white paper about this process: The Virtual Laboratory: Enabling Molecular Modeling, and a PhD thesis. The biology collaborator working on this project has already designed a drug to counteract an ECE enzyme involved in heart stroke, and is currently using the Virtual Laboratory to study liver cancer.

See another white paper by the project coordinators: Grids and Grid Technologies for Wide-Area Distributed Computing.

Note: this project is currently only for Linux/Unix users. Windows is not supported yet.

ongoing Linux
CommunityTSC Join the CommunityTSC project and help find drugs to fight Tuberous Sclerosis Complex (TSC), "a genetic disorder that leads to benign tumors in multiple organs, including the brain, kidneys, heart, eyes, lungs and other organs. The project is sponsored by The Rothberg Institute for childhood diseases. The project began work on its second protein target, PI3K, on June 17, 2002. The project began working on revised PTEN and PI3K protein targets and new FRAP and EIF4E targets in February, 2003. The project began working on the AKT protein target on November 3, 2003.

The project tested its 1 billionth conformer in July, 2004.

The project uses the D2OL software client. On Windows the client runs in the system tray, but in all versions it also has a graphical interface and a command-line interface to allow you to watch what it's doing. It does not require a continuous Internet connection: it allows you to set the number of work units it will cache so that you can cache more work if you connect to the Internet infrequently. Note that if you pause or restart the client, you will lose all of the conformers you've generated for the current work unit. The client supports users behind firewalls. Version 2.0 of the client is available for Windows, Mac OS X, Linux and Solaris as of September 18, 2003 (see a press release about the significant updates in this version).

Join the TSC discussion forum.

1,209,568,837 conformers tested;
60,118,877 candidates generated;
PTEN 48.773%;
P13K 54.164%
EIF4E 49.845%
FRAP 54.392%

Windows 32

Find-a-Drug Help researchers find new drugs for major diseases at Find-a-Drug, a non-profit project run by Treweren Consultants, creators of the THINK screensaver. Find-a-Drug runs one or more projects, although some projects may not be active at any given time. Project newsletter #4 was published July 9, 2003.

On June 30, 2003, the project announced that it successfully found some potential cancer-inhibiting drugs. After testing over 500 million molecules, it produced a set of candidates. 39 candidates were tested in a laboratory, and 7 of those (20%) showed the desired anti-cancer properties. Only 2-3% were expected to show the desired properties. On November 12, 2003, the project announced that it has found growth inhibitors for 5 anti-cancer protein targets. "42 of the 200 molecules tested [so far] showed the desired anti-cancer properties." On March 22, 2004, the project announced that it "has found more molecules which inhibit the growth of cancer cells," and has now discovered "growth inhibitors for 7 anti-cancer protein targets." On April 16, 2004, the project announced that it has found 18 molecules which inhibit the growth of HIV protease, an AIDS protein. More of its cancer-fighting drugs were confirmed to be effective in laboratory tests as of July 2, 2004.

The Cancer and Proteome projects are active as of August 8, 2002. The Bioterrorism Antidotes project is active as of October 15, 2002. A new methodology project is active as of October 26, 2002 (methodology projects improve the performance and accuracy of the Think software). A new protein, Tyrosine phosphatase (PTP1B) was added to the methodology project on February 19, 2003. The Respiratory Disease (starting with SARS) and Multiple Sclerosis projects are active as of May 7, 2003. A second SARS target was begun on May 29, 2003. The HIV project is active as of July 1, 2003. The Malaria project is active as of May 10, 2004.

The client supports users behind firewalls. It allows you to easily opt in and out of any of the drug-finding projects, so you can participate in only the projects that interest you. And it allows you to buffer work units so that you can work off-line. Note that if you have work units for a protein query which has been closed, those work units will not be used or counted if you return them more than 30 days after the query has ended. Version 1.25g of the client for Windows and Linux is available as of November 12, 2004.

Join a discussion forum about the project.

ongoing dialup-friendly

Windows 32

Predictor@home Help Predictor@home predict protein structures from protein sequences. The project is sponsored by the non-profit Scripps Research Institute. The first phase of the project, mfold, tests and evaluates "new algorithms and methods of protein structure prediction in the context of the Sixth Biannual CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiment" to help answer "critical biomedical questions of protein-related diseases." mfold's current targets are T0196 through T0205. The second phase of the project, charmm, will study protein refinement.

Note that this project is in its alpha test phase. Credits and results may be reset or deleted at any time. Note also that the project is on hold as of November 1, 2004, while it submits a grant for more funding, installs a new project server, and migrates its applications to BOINC 4.x.

The top 5 predictions for targets T0196 and T0197 are available as of July 1, 2004. You can see them in the project's gallery.

The project uses the BOINC computing platform. See the BOINC platform information for the latest version of the BOINC client. The BOINC client is available for Windows, Linux and Mac OSX. Note that the client needs 150 MB of disk space and 50 MB of RAM to run. You may need to adjust your available disk and memory percentages to allow the client to use these amounts. The project server was upgraded to BOINC 3.19 on June 27, 2004.

Join a discussion forum about the project.

ongoing; 20,152,279 total credits dialup-friendly

Windows 32

XGrid@Stanford Help XGrid@Stanford to "modelize the conformational changes of the beta 2 adrenergic receptor, and have a better understanding of its pharmacology." This project is run by Charles Parnot, a postdoctoral fellow in Brian Kobilka's lab in the Molecular and Cellular Physiology department of Stanford University. Note that this project is not designed to be a complete, public distributed computing research project: it is designed for Apple OSX users running Apple's XGrid software to help a university researcher complete his research. This site is also available in French French.

The project was presented at the 2004 Biomedical Computation at Stanford (bcats) conference on October 16, 2004.

To participate in the project, follow the installation instructions (text-only version) and send email to charles.parnot@stanford.edu so that he can contact you with project updates.

see a realtime gauge of the cluster's current speed
World Community Grid grid.org Help predict protein structures from human genome sequence data in Human Proteome Folding. The project is a partnership among World Community Grid, the grid.org, the Institute for Systems Biology, the University of Washington at Seattle, and IBM. The project uses the Rosetta software package, developed by The Baker Laboratory at the University of Washington, to predict protein structures for proteins in the human genome. "Understanding the complete set of human proteins, what their structures are and how they interact in the human body is a hugely important scientific problem that could lead to treatments for a myriad of human diseases." See a more detailed description of how Rosetta is used in the project. Rosetta could require up to 1,000,000 years of computation on a current (as of November, 2004) PC to examine the entire human genome. The project plans to be completed by December, 2005. Also see grid.org's information about the project.

The project uses the World Community Grid or grid.org computing platforms. Volunteers who are not already registered with grid.org are encouraged to participate through World Community Grid. See World Community Grid and grid.org platform information for the latest version of these platform clients. The clients are currently available for Windows. Work units for the project time out after 4 weeks. Client systems must have a minimum of 256 MB of RAM in order to participate in the project. The latest version of the Rosetta core was released on November 29, 2004.

Join a discussion forum about World Community Grid's projects.

Join a discussion forum about grid.org's projects.

224,056 results returned Windows 32

The following icons may appear in the Supported Platforms section of the table:
dialup-friendlythis project is good for users with dialup Internet access
paid projectthis is a for-pay project
Windows 32this project runs on the Windows 32-bit platform
Linuxthis project runs on the Linux platform
MacOSthis project runs on the Mac OS platform
Solaristhis project runs on the Solaris platform