| Active Distributed Computing Projects - Life Sciences |
|
These links take you to other project categories on this site:
Mathematics Art Puzzles/Games Miscellaneous Distributed Human Projects Collaborative Knowledge Bases Charity See the bottom of this page for a description of the icons on the page. |
| Project Information | Project % Complete | Major Supported Platforms | |
|---|---|---|---|
| Life Sciences | |||
Help
Parabon Computation contribute to
several areas of Life Sciences research. Parabon is currently supporting
the Compute Against Cancer
project, which is supporting the following research projects:
To participate in the project, download and run the project's secure Java client. As of January 15, 2007, the client is available for Windows (NT/2000/XP), Linux (2.4 kernel or higher), and Mac OSX (version 10.2 or later). |
ongoing |
   |
|
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 January 14, 2005, it broke the 170,000 actuve CPU mark. On September 20, 2005, it broke the 200,000 active CPU mark. 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. On January 15, 2005, the project published the results of its p53 tumor suppressor study, part of its cancer research project. These results are "the first peer-reviewed results from a distributed computing project related to cancer." 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 5.04 of the client is available for Windows and Linux for testing as of July 25, 2005. 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 forum about this project. Join a discussion forum about the original project. Join an independent discussion forum about ab-initio protein folding (where the folding is simulated completely in software) |
ongoing |
 PS3 |
|
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
 . The
project published the first volume of its
FightAIDS@Home News
on January 24, 2006.
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 project published Volume 4 of its newsletter on October 16, 2007. On November 19, 2005, the project joined the World Community Grid. The original software client is not supported as of that date. Users of the original client can follow easy migration instructions to move to the World Community Grid client, and World Community Grid participants can follow the directions on the new download page to ensure their client is participating in fightAIDS@home. A BOINC client for Linux should be available soon. |
68,748,135 results returned; experiment 5: 50% |
|
|
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. The Avian Influenza project
began on April 13, 2006.
See a
detailed discussion about the
science behind the project.
The graphical client can run minimized or (on Windows) in the system tray. Version 2.0 of the client does not allow you to select which protein target(s) to work on: future versions will allow this. The client 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 3.0 of the client is available for Windows as of April 16, 2008. See the version 3.0 release notes for new features in 3.0. Version 2.0 of the client is available for Mac OS X, Linux and Solaris as of September 18, 2003. See the version 2.0 release notes for new features in 2.0. Also see a press release about the significant updates in 2.0. Join the D2OL discussion forum. |
ongoing: 678,475,955 conformers tested; 33,923,812 candidates found; Avian Flu Target I: 85.469% complete; SARS Target I / IV: 55.874% / 32.198% complete |
|
|
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 |
|
|
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. It began working on revised PTEN and PI3K
protein targets and new FRAP and EIF4E targets in February, 2003. It began
working on the AKT protein target on November 3, 2003. Phase I of the project
was completed on April 2, 2006. Phase I statistics are available in a
hall of fame.
Phase II began on April 3, 2006. Phase II is finding potential drugs for the protein target Ras homolog enriched in brain (Rheb). "The overexpression of Rheb has been shown to result in unusual overgrowth of various tissues, and is believed to be central to the growth processes underlying tumorgenesis." Phase II is also using new candidate drug libraries. The Phase I targets may be tried with the new libraries in the future. The project published a press release about Phase II on April 13, 2006. 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. For version 2.0, 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 3.0 of the client is available for Windows as of April 16, 2008. See the version 3.0 release notes for new features in 3.0. Version 2.0 of the client is available for Mac OS X, Linux and Solaris as of September 18, 2003 (see a press release about the significant updates in 2.0). Join the TSC discussion forum. |
ongoing: 738,181,511 conformers tested; 36,909,084 candidates generated; TSC Target IV / VI / Ib: 80.059% / 69.933% / 61.652% complete |
|
|
Help
Predictor@home predict
protein structures from protein sequences.
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." The second phase
of the project, charmm, will study protein refinement.
Note that this project is in its alpha test phase. Credits and results m ay be reset or deleted at any time. Note: The Brooks Research Group [the group that owns this project] will be relocating to the University of Michigan in December, 2007. The project's current website will remain open until December. After that there will be a down time while people and resources for the project are transferred to Ann Arbor, Michigan. The project and website should be up again some time during February, 2008. 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 4 in November, 2004. The project supports BOINC version 4.2x clients as of March 2, 2005. Join a discussion forum about the project. |
ongoing; 485,827,945 total credits |
|
|
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.
As of December 3, 2007, the project is only using computing resources from OpenMacGrid. The public is invited to join OpenMacGrid. 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 the project's goodies section, "where you can download Xgrid-related files and learn more about Xgrid." |
ongoing |
|
|
Help predict protein structures from human genome
sequence data in Human Proteome Folding. The project is a
partnership
among World Community Grid,
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." 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. Phase I of the project was completed in
in June, 2006. Phase II began on June 23, 2006. Also see grid.org's
information about the project.
The project's results database was first accessed by researchers on September 26, 2005. The project uses the BOINC computing platform to run various applications. See the BOINC platform information for the latest version of the BOINC client. If you already have BOINC installed, you can join this and other World Community Grid BOINC-based project by attaching to the project URL www.worldcommunitygrid.org. You can select/de-select World Community Grid projects in your World Community Grid member page, under My Grid --> My Projects. This project is discussed in the World Community Grid forums. |
26,044,374 results returned |
|
|
Help
Rosetta@home "predict and
design protein structures, and protein-protein and protein-ligand
interactions," in order to "develop methods that accurately predict and
design protein structures and complexes, an endeavor that may ultimately help
researchers develop cures for human diseases such as cancer, HIV/AIDS, and
malaria." This project, run by
The Baker Laboratory at the University
of Washington, will help the lab improve its Rosetta software package, which
is used by other projects such as
Human Proteome Folding. The project published its
latest Science News
update on January 27, 2006. On March 20, 2008, the project successfully
created two functional enzymes not found in nature. Designed enzymes could
be used in the future to produce pharmaceuticals and fuel.
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. Version 5.25 of the Rosetta application is available for Windows, Linux and Mac OSX as of June 20, 2006. See a 7 minute YouTube video about the project. The video was created on January 7, 2007. Join a discussion forum about the project. |
ongoing; 3,938,084,837 credits |
|
|
Help
RALPH@home test new application
versions, work unit types, and other updates for
Rosetta@home. This testing improves
Rosetta@home.
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. Join a discussion forum about the project. |
ongoing; 12,074,240 credits |
|
|
Help
SIMAP compute
similarities between all known protein sequences.
"SIMAP is short for
Similarity Matrix of Proteins. SIMAP is a database for the precomputed
homologies of protein sequences and provides specialized retrieval tools for
effective use of that data. The publicly available web based SIMAP
presentation module provides various search tools." See a
more detailed description of the project.
The project had over 10,000 hosts and 5,000 users with credits, and has calculated the similarities for more than 1 million protein sequences, as of March 22, 2006. The project uses the BOINC computing platform. See the BOINC platform information for the latest version of the BOINC client. Version 5.11 of the SIMAP application is available for Linux as of July 17, 2006. Version 5.10 is available for Windows and Mac OSX as of July 12, 2006. Versions 5.6 and later reduce the calculation time per work unit to 1/10th that of previous versions. Dialup users should be aware that work units are about 1.5 MB and results are about 1.3 MB. Join a discussion forum about this project. |
ongoing; 368,916,553 credits |
|
|
Help
malariacontrol.net simulate
the ways that the malaria parasite (Plasmodium falciparum malaria)
spreads in Africa, and its effects on human health. The models it creates
will help scientists and doctors "determine optimal strategies for
delivering mosquito nets, chemotherapy, or new vaccines which are currently
under development and testing." This project is part of the
Africa@home project.
On or soon after September 17, 2007, the project will begin testing a third science application called optimizer. This application will be run as a test application, "meaning that only users who have 'run test applications' and 'run optimizer application' checked in their account settings (under malariacontrol.net preferences) will get work, and only Windows users will get work. Results from the optimizer application will help the project team "to improve the main malariacontrol application in the future." The project uses the BOINC computing platform to run various applications. See the BOINC platform information for the latest version of the BOINC client. Version 5.51 of the project's malariacontrol.net software application is available for Windows, Linux and Mac OSX as of August 30, 2007. Version 5.2 of the project's Prediction of Malaria Prevalence application is available for Windows as of September 17, 2007. Join a discussion forum about this project. |
ongoing; 258,838,823 credits |
|
|
 Help
TANPAKU predict
protein structures. "The project name 'TANPAKU' is taken from the Japanese
word tanpaku-shitsu, meaning protein." See a
more detailed description
of the project. The project website is also available in
Japanese
.
The project uses a BOINC-based client. See the BOINC platform information for the latest version of the BOINC client. Version 5.99 of the BD client is available for Windows, Linux and Mac OSX as of October 1, 2007. |
ongoing |
|
|
Help
Docking@Home find better ways to
discover disease-fighting drugs and to study ways to adapt the discovery
process based on iterative results from the project. The project "aims to
accomplish both bioscience and computer science goals. From the bioscience
point of view, the project aims to further knowledge of the atomic details
of protein-ligand interactions and, by doing so, will search for insights
into the discovery of novel pharmaceuticals. From the computer science point
of view, this project aims to extend volunteer computing to enable adaptive
multi-scale modeling of the docking applications: different models that
represent the same phenomena in nature with different level of accuracy and
resource requirements will be chosen at run-time based on results collected
so far and characteristics of the protein-ligand complex." See
more information
about the project.
The project uses a BOINC-based client. See the BOINC platform information for the latest version of the BOINC client. The project is currently in Alpha testing. Version 5.03 of the Charmm client is available for Windows as of September 18, 2006. Version 5.02 of the client is available for Linux as of October 2, 2006. Version 5.02 of the client is available for Mac OSX as of September 18, 2006. Join a discussion forum about this project. |
ongoing; 10,315,529 credits |
|
|
Help
proteins@home
solve the "inverse protein folding problem" (enumerating the allowed
sequences for a given fold) for a large number of known protein folds.
The project is studying a representative subset of about 1,500 folds. See
more information
about the project.
The project team published its first paper, "Computational protein design: Software implementation, parameter optimization, and performance of a simple model," on December 10, 2007. The project uses a BOINC-based client. See the BOINC platform information for the latest version of the BOINC client. The project is currently in Alpha testing. Version 7.41 of the Xplor client is available for Windows as of February 1, 2008. Join a discussion forum about this project. |
ongoing; 69,620,654 credits |
|
|
Help the World Community Grid and
Décrypthon
find better treatments for muscular dystrophy and other neuromuscular
diseases. The project is "investigating protein-protein interactions for
40,000 proteins whose structures are known, with particular focus on those
proteins that play a role in neuromuscular diseases. The database of
information produced will help researchers design molecules to inhibit or
enhance binding of particular macromolecules, hopefully leading to better
treatments for [these] diseases." There is currently no cure for people
affected by these diseases. See more information
about the project. See a progress page
(written in French) for the project.
Phase 1 of the project performed cross-docking calculations on over 150 proteins, to see how well each protein iteracts with each of the other proteins. This phase ended on June 11, 2007. In the 7 months that Phase 1 ran, "106,000 members will have donated more than 8,000 years of computer time on 154,000 different computers," and computed 5,416,082 results. Phase 2 should begin in 2008. Participants can view progress toward Phase 2 in Dr. Alessandra Carbone's and Dr. Sophie Sacquin-Mora's posts in the project forums. See the project's FAQ. The project uses the World Community Grid computing platform. Participants are encouraged to participate through World Community Grid. See World Community Grid platform information for the latest version of these platform clients. The clients are currently available for Windows, Linux and Mac OSX. Please review the clients' system requirements. Join a discussion forum about World Community Grid's projects. |
5,416,082 results returned for Phase 1; waiting for Phase 2 to begin |
|
|
Help
Discovering Dengue Drugs - Together,
a World Community Grid project,
"identify promising drug leads to combat the related dengue, hepatitis C, West
Nile, and Yellow fever viruses." See more information
about the project and the project's FAQ.
The project uses the BOINC computing platform to run various applications. See the BOINC platform information for the latest version of the BOINC client. If you already have BOINC installed, you can join this and other World Community Grid BOINC-based project by attaching to the project URL www.worldcommunitygrid.org. You can select/de-select World Community Grid projects in your World Community Grid member page, under My Grid --> My Projects. This project is discussed in the World Community Grid forums. |
17,026,896 results returned |
|
|
Help
The Lattice Project study
various problems in bioinformatics. This project is the first to combine
private computing grids (based on the
Globus platform) and a public distributed
computing infrastructure (based on the
BOINC platform). Note that the BOINC
client is part of a general-purpose computing grid and may be supporting
one of several different
projects at any
given time. See
more information about
the project and the project FAQ.
The project uses a BOINC-based client. See the BOINC platform information for the latest version of the BOINC client. Versions 5.09, 5.10, 5.11 and 5.12 of the GARLI client are available for Windows, Linux and Mac OSX as of December 18, 2007. Version 5.05, 5.06 and 5.10 of the HMMPfam client are available for Windows, Linux and Mac OSX as of December 18, 2007. Version 5.02 of the MARXAN client is available for Windows as of December 18, 2007. Join a discussion forum about this project. |
ongoing; 15,864,397 credits |
|
|
Help
POEM@HOME research and predict
protein structure. The project uses a computational approach to:
The project uses a BOINC-based client. See the BOINC platform information for the latest version of the BOINC client. Versions 0.07 of the POEM Protein Folding application is available for Windows as of November 29, 2007. Version 0.08 is available for Linux and Mac OS X as of January 11, 2008. Join a discussion forum about this project. |
ongoing; 84,859,818 credits |
|
|
Help
Help Conquer Cancer,
a World Community Grid project, "improve the
results of protein X-ray crystallography, which helps researchers not only
annotate unknown parts of the human proteome, but importantly improves their
understanding of cancer initiation, progression and treatment." See
more information
about the project and the project's FAQ.
The project uses the BOINC computing platform to run various applications. See the BOINC platform information for the latest version of the BOINC client. If you already have BOINC installed, you can join this and other World Community Grid BOINC-based project by attaching to the project URL www.worldcommunitygrid.org. You can select/de-select World Community Grid projects in your World Community Grid member page, under My Grid --> My Projects. This project is discussed in the World Community Grid forums. |
13,160,454 results returned |
|
|
 Help Cels@Home "do research in cell adhesion. One of the many applications of this is in cancer research, as the point at which cancerous cells quit staying in place, and instead break free to move throughout the body, is a critical event that makes the disease much harder to treat." The project uses a BOINC-based client. See the BOINC platform information for the latest version of the BOINC client. Versions 1.00 of the Cels@Home application is available for Windows as of February 25, 2008. Join a discussion forum about this project. |
ongoing; 1,996,620 credits |
|
|
Help
MindModeling@Home use
"computational cognitive process modeling to better understand the human mind."
The project hopes to "improve on the scientific foundations that explain the
mechanisms and processes that enable and moderate human performance and
learning." The project is not yet active as of April 2, 2008, but participants
can help beta test it.
The project uses a BOINC-based client. See the BOINC platform information for the latest version of the BOINC client. Versions 3.00 of the project's client application is available for Windows, Linux and Max OS X as of March 5, 2008. Join a discussion forum about this project. Join a discussion forum about the beta test project. |
ongoing; 4,028,671 credits |
|
|
| The following icons may appear in the Supported Platforms section of the table: | |||||||||||||
|
| Top... |
