World Community Grid (WCG) is an effort to create the world's largest public computing grid to tackle scientific research projects that benefit humanity. Launched on November 16, 2004, it is co-ordinated by IBM with client software currently available for Windows, Linux, macOS, and Android operating systems.
Using the idle time of computers around the world, World Community Grid's research projects have analyzed aspects of the human genome, HIV, dengue, muscular dystrophy, cancer, influenza, Ebola, virtual screening, rice crop yields, and clean energy. As of March 2018, the organization has partnered with 449 other companies and organizations to assist in its work, has over 52,000 active registered users, and a combined total run time of over 1.5 million years.
|World Community Grid|
|Initial release||November 16, 2004|
|Operating system||Microsoft Windows, Linux, Android, macOS|
|Average performance||1.1 PFLOPS|
|Active users||52,097 (March 2018) |
In 2003, IBM and other research participants sponsored the Smallpox Research Grid Project to accelerate the discovery of a cure for smallpox. The smallpox study used a massive distributed computing grid to analyze compounds' effectiveness against smallpox. The project allowed scientists to screen 35 million potential drug molecules against several smallpox proteins to identify good candidates for developing into smallpox treatments. In the first 72 hours, 100,000 results were returned. By the end of the project, 44 strong treatment candidates had been identified. Based on the success of the Smallpox study, IBM announced the creation of World Community Grid on November 16, 2004, with the goal of creating a technical environment where other humanitarian research could be processed.
World Community Grid initially only supported Windows, using the proprietary Grid MP software from United Devices which powered the grid.org distributed computing projects. Demand for Linux support led to the addition in November 2005 of open source Berkeley Open Infrastructure for Network Computing (BOINC) grid technology which powers projects such as SETI@home and Climateprediction, and Mac OS X and Linux support was added since the introduction of BOINC. In 2007, the World Community Grid migrated from Grid MP to BOINC for all of its supported platforms.
As of October 2014, World Community Grid had over 65,000 active user accounts, with over 249,000 active devices. Over the course of the project, more than 1,000,000 cumulative years of computing time have been donated, and over 2 billion workunits have been completed.
The World Community Grid software uses the idle time of Internet-connected computers to perform research calculations. Users install WCG client software onto their computers. This software works in the background, using spare system resources to process work for WCG. When a piece of work or workunit is completed, the client software sends it back to WCG over the Internet and downloads a new workunit. To ensure accuracy, the WCG servers send out multiple copies of each workunit. Then, when the results are received, they are collected and validated against each other.
While many public computing grids such as SETI@home and Folding@home are devoted to a single project, World Community Grid offers multiple humanitarian projects under a single umbrella. Users are included in a subset of projects by default, but may opt out of projects as they choose.
When World Community Grid launched, they used the proprietary Grid MP client from United Devices. After adding support for the open source BOINC client in 2005, World Community Grid eventually discontinued the Grid MP client and consolidated on the BOINC platform in 2008.
Even though WCG makes use of open source client software, the actual applications that perform the scientific calculations may not be. However, several of the science applications are available under a free license, although the source is not available directly from WCG.
The World Community Grid software increases CPU usage by consuming unused processing time; in the late 1990s and early 2000s, such calculations were meant to reduce "wasted" CPU cycles. With modern CPUs, where dynamic frequency scaling is prevalent, increased usage makes the processor run at higher frequency, increasing power usage and heating counter to power management. Additionally, because of an increasing focus on power performance, or performance per watt, connecting old/inefficient computers to the grid will increase the total/average power required to complete the same calculations.
The BOINC client avoids slowing the computer by using a variety of limits that suspend computation when there are insufficient free resources. Unlike other BOINC projects, World Community Grid set the BOINC defaults conservatively, making the chances of computer damage extremely small. The default CPU throttle is 60%. The throttle is coarse-grained; for example, if usage is set to 60% it will work at 100% for 3 seconds, then at 0% for 2 seconds, resulting in an average decrease of processor use.
An add-on program for Windows computers – TThrottle – can solve the problem of overheating by directly limiting the BOINC project's use of the host computer. It does this by measuring the CPU and/or the GPU temperature and adjusts the run time accordingly. It also uses a shorter switching time of less than one second, resulting in less temperature change during switching.
The contributions of each user are recorded and user contribution statistics are publicly available. Due to the fact that the processing time of each workunit varies from computer to computer, depending on the difficulty of the workunit, the speed of the computer, and the amount of idle resources available, contributions are usually measured in terms of points. Points are awarded for each workunit depending on the effort required to process it.
Upon completing a workunit, the BOINC client will request the number of points it thinks it deserves based on software benchmarks (see BOINC Credit System#Cobblestones). Since multiple computers process the same workunit to ensure accuracy, the World Community Grid servers can look at the points claimed by each of those computers. The WCG servers disregard statistical outliers, average the remaining values and award the resulting number of points to each computer.
Within the grid, users may join teams that have been created by organizations, groups, or individuals. Teams allow for a heightened sense of community identity and can also inspire competition. As teams compete against each other, more work is done for the grid overall.
World Community Grid recognizes companies and organizations as partners if they promote WCG within their company or organization. As of March 2018, WCG had 449 partners.
Also, as part of its commitment to improving human health and welfare, the results of all computations completed on World Community Grid are released into the public domain and made available to the scientific community.
Since its launch, more than twenty projects have run in the World Community Grid. Some of the results include:
FightAIDS@Home (launched November 19, 2005) was World Community Grid's second project and its first to target a single disease. Each individual computer processes one potential drug molecule and tests how well it would dock with HIV protease, acting as a protease inhibitor. Scripps Research Institute published its first peer-reviewed scientific paper about the results of FightAIDS@Home on April 21, 2007. This paper explains that the results up to that point will primarily be used to improve the efficiency of future FightAIDS@Home calculations. FightAIDS@Home project is still ongoing, but there is no computation necessity for the next few months, so tech at WCG changed the project status to completed. According to the tech's words, "If and when more work becomes available, we can quickly open the project again."
Mapping Cancer Markers (launched November 8, 2013). The project aims to identify the markers associated with various types of cancer, and is analyzing millions of data points collected from thousands of healthy and cancerous patient tissue samples. These include tissues with lung, ovarian, prostate, pancreatic and breast cancers. By comparing these different data points, researchers aim to identify patterns of markers for different cancers and correlate them with different outcomes, including responsiveness to various treatment options. The project is focusing on 4 types of cancer, with the first focus being on lung cancer, and will move on to ovarian cancer, prostate cancer and sarcoma.
FightAIDS@Home Phase 2 (launched September 30, 2015) is looking more closely at the results of Phase 1. The project has two goals in the early experiments; the simulation architecture is functioning correctly and giving reliable results, and using BEDAM and AutoDock together provides better results than using just BEDAM or AutoDock.
Help Stop TB was launched in March 2016 to help combat tuberculosis, a disease caused by a bacterium that is evolving resistance to currently available treatments. The computations of this project target mycolic acids in the bacterium's protective coat, simulating the behavior of these molecules in their many configurations to better understand how they offer protection to the bacteria.
OpenZika was launched on May 18, 2016 to help combat the Zika virus. The project targets proteins that is believed the Zika virus uses to survive and spread in the body, based on known results from similar diseases like the dengue virus and yellow fever. These results will help researchers develop an anti-Zika drug.
Starting January 2017, the Smash Childhood Cancer project builds on the work from the Help Fight Childhood Cancer project by looking for drug candidates targeting additional childhood cancers.
Microbiome Immunity Project (launched August 2017) is a study of proteins in bacteria located in and on the human body; the human microbiome, which is made of around 3 million separate bacterial genes. By learning bacteria genes, their individual shapes can be known, and each physical shape determines the function of bacteria. Collaborative institutions includes the University of California San Diego, Broad Institute of MIT and Harvard, and the Simons Foundation's Flatiron Institute.
The first project launched on World Community Grid was the Human Proteome Folding Project, or HPF1, which aims to predict the structure of human proteins. The project was launched on November 16, 2004, and completed on July 18, 2006. This project was unique in that computation was done in tandem with the grid.org distributed computing project. Devised by Richard Bonneau at the Institute for Systems Biology, the project used grid computing to produce the likely structures for each of the proteins using a Rosetta Score. From these predictions, researchers hope to predict the function of the myriad proteins. This increased understanding of the human proteins could prove vital in the search for cures to human diseases. Computing for this project was officially completed on July 18, 2006. Research results for the yeast portion of HPF1 have been published.
Human Proteome Folding - Phase 2 (HPF2) (launched June 23, 2006) was the third project to run on World Community Grid, and completed in 2013. This project, following on from HPF1, focused on human-secreted proteins, with special focus on biomarkers and the proteins on the surface of cells as well as Plasmodium, the organism that causes malaria. HPF2 generates higher-resolution protein models than HPF1. Though these higher-resolution models are more useful, they also require more processing power to generate.
In a July 2012 status report, the project scientists reported that the results generated by the WCG calculations are being used by Dr. Markus Landthaler of the Max Delbruch Center for Molecular Medicine (MDC) in Berlin. The HPF2 results helped Dr. Markus Landthaler and his collaborators in writing up a new paper on "The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts"
The Help Defeat Cancer project seeks to improve the ability of medical professionals to determine the best treatment options for patients with breast, head, or neck cancer. The project was launched on July 20, 2006, and completed in April 2007. The project worked by identifying visual patterns in large numbers of tissue microarrays taken from archived tissue samples. By correlating the pattern data with information about treatment and patient outcome, the results of this project could help provide better targeted treatment options.
The Genome Comparison project is sponsored by the Brazilian research institution Fiocruz. The project was launched on November 21, 2006, and completed on July 21, 2007. The project seeks to compare gene sequences of different organisms against each other in order to find similarities between them. Scientists hope to discover what purpose a particular gene sequence serves in a particular function of one organism, via comparing it to a similar gene sequence of known function in another organism.
Help Cure Muscular Dystrophy is run by Décrypthon, a collaboration between French Muscular Dystrophy Association, French National Center for Scientific Research and IBM. Phase 1 was launched on December 19, 2006, and completed on June 11, 2007. The project investigated 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 muscular dystrophy and other neuromuscular diseases. This project was available only to agents running the Grid MP client, making it unavailable to users running BOINC.
Discovering Dengue Drugs – Together was sponsored by scientists at the University of Texas and the University of Chicago and will run in two phases. Phase 1, launched August 21, 2007, used AutoDock 2007 (the same software used for FightAIDS@Home) to test potential antiviral drugs (through NS3 protease inhibition) against viruses from the family flaviviridae and completed on August 11, 2009. Phase 2 "[uses] a more computationally intensive program to screen the candidates that make it through Phase 1." The drug candidates that make it through Phase 2 will then be lab-tested.
The mission of AfricanClimate@Home was to develop more accurate climate models of specific regions in Africa. It was intended to serve as a basis for understanding how the climate will change in the future so that measures designed to alleviate the adverse effects of climate change could be implemented. World Community Grid's tremendous computing power was used to understand and reduce the uncertainty with which climate processes were simulated over Africa. Phase 1 of African Climate@Home launched on September 3, 2007, and ended in July 2008.
Help Conquer Cancer project (launched November 1, 2007) is sponsored by the Ontario Cancer Institute (OCI), Princess Margaret Hospital and University Health Network of Toronto, Canada. The project involves X-ray crystallography. The mission of Help Conquer Cancer is to 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.
The HCC project was the first WCG project benefiting from graphics processing units (GPU)s which helped finish it a lot earlier than initially projected due to the massive power of GPUs. In the April 2013 status report the scientists report there is still a lot of data to analyze but that they are preparing a new project that will search for prognostic and predictive signatures (sets of genes, proteins, microRNAs, etc.) that help predict patient survival and response to treatment. The project finished in May 2013.
The Nutritious Rice for the World project is carried out by Ram Samudrala's Computational Biology Research Group at the University of Washington. The project was launched on May 12, 2008, and completed on April 6, 2010. The purpose of this project is to predict the structure of proteins of major strains of rice, in order to help farmers breed better rice strains with higher crop yields, promote greater disease and pest resistance, and utilize a full range of bioavailable nutrients that can benefit people around the world, especially in regions where malnutrition is a critical concern. The project has been covered by more than 200 media outlets since its inception. On April 13, 2010, World Community Grid officially announced that the Nutritious Rice for the World project finished on April 6, 2010.
In April 2014, an update was posted stating that the research team was able to publish structural information about thousands of proteins, and advance the field of computational protein modeling. These results – which were only possible because of the massive amount of donated computing power they had available – are expected to guide future research and plant science efforts.
The Clean Energy project is sponsored by the scientists of Harvard University's Department of Chemistry and Chemical Biology. The mission of the Clean Energy Project is to find new materials for the next generation of solar cells and later, energy storage devices. Researchers are employing molecular mechanics and electronic structure calculations to predict the optical and transport properties of molecules that could become the next generation of solar cell materials.
Phase 1 was launched on December 5, 2008, and completed on October 13, 2009. By harnessing the computing power of the World Community Grid, researchers were able to calculate the electronic properties of tens of thousands of organic materials – many more than could ever be tested in a lab – and determine which candidates are most promising for developing affordable solar energy technology.
Phase 2 was launched June 28, 2010, sponsored by the scientists of Harvard University's Department of Chemistry and Chemical Biology. Further calculations about optical, electronic and other physical properties of the candidate materials are being conducted with the Q-Chem quantum chemistry software. Their findings have been submitted to the Energy & Environmental Science journal.
Help Fight Childhood Cancer project (launched March 13, 2009) is sponsored by the scientists at Chiba Cancer Center Research Institute and Chiba University. The mission of the Help Fight Childhood Cancer project is to find drugs that can disable three particular proteins associated with neuroblastoma, one of the most frequently occurring solid tumors in children. Identifying these drugs could potentially make the disease much more curable when combined with chemotherapy treatment.
Influenza Antiviral Drug Search project is sponsored by Dr. Stan Watowich and his research team at The University of Texas Medical Branch (Galveston, Texas, USA). The project was launched on May 5, 2009, and completed on October 22, 2009. The mission of the Influenza Antiviral Drug Search project is to find new drugs that can stop the spread of an influenza infection in the body. The research will specifically address the influenza strains that have become drug resistant as well as new strains that are appearing. Identifying the chemical compounds that are the best candidates will accelerate the efforts to develop treatments that would be useful in managing seasonal influenza outbreaks, and future influenza epidemics and even pandemics. Phase 1 of The Influenza Antiviral Drug Search project has already finished on October 22, 2009. Now the researchers are performing post-processing on the results from Phase 1 and are preparing for Phase 2.
In November 2012, the project's scientists stated that, given the fact that there is no immediate danger of an influenza outbreak, all of the project's results would be posted online and their resources would be refocused on the Dengue Project.
World Community Grid and researchers supported by Decrypthon, a partnership between AFM (French Muscular Dystrophy Association), CNRS (French National Center for Scientific Research), Universite Pierre et Marie Curie, and IBM were investigating protein–protein interactions for more than 2,200 proteins whose structures are known, with particular focus on those proteins that play a role in neuromuscular diseases. Phase 2 was launched on May 12, 2009, and completed on September 26, 2012. The database of information produced will help researchers design molecules to inhibit or enhance binding of particular macromolecules, hopefully leading to better treatments for muscular dystrophy and other neuromuscular diseases.
Discovering Dengue Drugs – Together – Phase 2 (launched February 17, 2010) is sponsored by The University of Texas Medical Branch (UTMB) in Galveston, Texas, United States and the University of Chicago in Illinois, USA. The mission is to identify promising drug candidates to combat the Dengue, Hepatitis C, West Nile, Yellow Fever, and other related viruses. The extensive computing power of World Community Grid will be used to complete the structure-based drug discovery calculations required to identify these drug candidates.
Computing for Clean Water (launched September 20, 2010) is sponsored by the Center for Nano and Micro Mechanics of Tsinghua University in Beijing. The project's mission is to provide deeper insight on the molecular scale into the origins of the efficient flow of water through a novel class of filter materials. This insight will in turn guide future development of low-cost and more efficient water filters. It is estimated that 1.2 billion people lack access to safe drinking water, and 2.6 billion have little or no sanitation. As a result, millions of people die annually – an estimated 3,900 children a day due to a lack of clean water. On April 25, 2014, the project scientists released an update stating that they had exciting results to report when the paper is submitted and that the project on WCG was finished.
Drug Search for Leishmaniasis (launched September 7, 2011) is spearheaded by the University of Antioquia in Medellín, Colombia, with assistance from researchers at the University of Texas Medical Branch in Galveston, Texas. The mission is to identify potential molecule candidates that could possibly be developed into treatments for Leishmaniasis. The extensive computing power of World Community Grid will be used to perform computer simulations of the interactions between millions of chemical compounds and certain target proteins. This will help find the most promising compounds that may lead to effective treatments for the disease.
The mission of the GO Fight Against Malaria project (launched November 16, 2011) is to discover promising drug candidates that could be developed into new drugs that cure drug resistant forms of malaria. The computing power of World Community Grid will be used to perform computer simulations of the interactions between millions of chemical compounds and certain target proteins, to predict their ability to eliminate malaria. The best compounds will be tested by scientists at The Scripps Research Institute of La Jolla, California, U.S.A. and further developed into possible treatments for the disease.
Say No to Schistosoma (launched February 22, 2012) was the 20th research project to be launched on World Community Grid. The researchers at Infórium University in Belo Horizonte and FIOCRUZ-Minas, Brazil, ran this project on World Community Grid to perform computer simulations of the interactions between millions of chemical compounds and certain target proteins in the hope of finding effective treatments for schistosomiasis. As of April 2015, subsequent analysis had been performed, and the three most promising candidate substances had been identified for in-vitro testing.
Computing for Sustainable Water was the 21st research project to be launched on World Community Grid. The researchers at the University of Virginia were running this project on World Community Grid to study the effects of human activity on a large watershed and gain deeper insights into what actions can support the restoration, health and sustainability of this important water resource. The project was launched on April 17, 2012, and completed on October 17, 2012.
Uncovering Genome Mysteries project launched on October 16, 2014 and is a joint collaboration between Australian and Brazilian scientists. The project aims to examine close to 200 million genes from many life forms and compare them with known genes in order to find out what their function is. The results could have an effect in fields such as medicine and environmental research.
Outsmart Ebola Together was a collaboration with the Scripps Research Institute to help find chemical compounds to fight Ebola Virus Disease. It was launched on 3 December 2014. The aim is to block crucial steps in the life cycle of the virus, by finding drugs with high binding affinity with certain of its proteins. There are two targets: a surface protein used by the virus to infect human cells, and "transformer" proteins which change shape to carry out different functions. The project officially completed December 6, 2018.
The first experiments of FightAIDS@Home Phase 2 seek to achieve two goals: first, to confirm that the new simulation schema is working as intended and gives sufficiently reliable results compared to traditionally run simulations; second, to demonstrate that using BEDAM in conjunction with AutoDock results in better predictions than using AutoDock or BEDAM alone.
We have completed OET. Thank you for your help and contribution towards this project.
AutoDock is a molecular modeling simulation software. It is especially effective for protein-ligand docking. AutoDock 4 is available under the GNU General Public License. AutoDock is one of the most cited docking software in the research community. It is a base for the FightAIDS@Home project run by World Community Grid. In February 2007, a search of the ISI Citation Index showed more than 1,100 publications have been cited using the primary AutoDock method papers. As of 2009, this number surpassed 1,200.
AutoDock Vina is a successor of AutoDock, significantly improved in terms of accuracy and performance. It is available under the Apache license.
Both AutoDock and Vina are currently maintained by The Scripps Research Institute, specifically The Molecular Graphics Laboratory (Dr. Arthur J. Olson).Berkeley Open Infrastructure for Network Computing
The Berkeley Open Infrastructure for Network Computing (BOINC, pronounced – rhymes with "oink"), an open-source middleware system, supports volunteer and grid computing. Originally developed to support the SETI@home project, it became generalized as a platform for other distributed applications in areas as diverse as mathematics, linguistics, medicine, molecular biology, climatology, environmental science, and astrophysics, among others. BOINC aims to enable researchers to tap into the enormous processing resources of multiple personal computers around the world.
BOINC development originated with a team based at the Space Sciences Laboratory (SSL) at the University of California, Berkeley and led by David Anderson, who also leads SETI@home. As a high-performance distributed computing platform, BOINC brings together about 311,742 active participants and 834,343 active computers (hosts) worldwide processing on average 26.431 PetaFLOPS as of 9 June 2018. (it would be the fourth largest processing capability in the world compared with an individual supercomputer Supercomputer TOP500 list) The National Science Foundation (NSF) funds BOINC through awards SCI/0221529, SCI/0438443 and SCI/0721124. Guinness World Records ranks BOINC as the largest computing grid in the world.BOINC code runs on various operating systems, including Microsoft Windows, macOS, Android, Linux and FreeBSD. BOINC is free software released under the terms of the GNU Lesser General Public License (LGPL).Clean Energy Project
The Clean Energy Project (CEP) is a virtual high-throughput discovery and design effort for the next generation of plastic solar cell materials. It studies millions of candidate structures to identify suitable compounds for the harvesting of renewable energy from the sun and for other organic electronic applications. It runs on the BOINC platform.Discovering Dengue Drugs – Together
Discovering Dengue Drugs – Together (DDDT) is a World Community Grid project sponsored by scientists at the University of Texas Medical Branch at Galveston and the University of Chicago. Its goal is to identify new antiviral drugs effective against viruses from the family flaviviridae. The specific targets are:
Hepatitis C virus
West Nile virus
Yellow fever virusDiscovering Dengue Drugs – Together is divided into two phases. Phase 1, launched August 21, 2007, used AutoDock 2007 (the same software used for FightAIDS@Home) to test how well antiviral drug candidates are predicted to bind to the target virus's proteases. Compounds predicted to bind strongly (protease inhibitors) are potential antiviral drug candidates. This phase ended in August 2009.Phase 2 "will use a more computationally intensive program to screen the candidates that make it through Phase 1." The drug candidates that make it through Phase 2 will then be lab-tested.Like all World Community Grid projects, Discovering Dengue Drugs – Together uses a computational grid made up of thousands of client (computing) computers belonging to independent volunteers, in conjunction with servers that distribute portions of the work to the clients.In 2008, the project was temporarily suspended because of Hurricane Ike. Processing resumed in January 2009, with the server function transferred from the University of Texas Medical Branch in Galveston to the Texas Advanced Computing Center in Austin.Décrypthon
Décrypthon is a project which uses grid computing resources to contribute to medical research. The word is a portmanteau of the French word "décrypter" (to decipher) and "telethon".FightAIDS@Home
FightAIDS@Home ("Fight AIDS at home") is a distributed computing project operated by the Olson Laboratory at The Scripps Research Institute. It runs on internet-connected home computers, and since July 2013 also runs on Android smartphones and tablets. It aims to use biomedical software simulation techniques to search for ways to cure or prevent the spread of HIV/AIDS.Fiocruz Genome Comparison Project
The Fiocruz Genome Comparison Project is a collaborative effort involving Brazil's Oswaldo Cruz Institute and IBM's World Community Grid, designed to produce a database comparing the genes from many genomes with each other using SSEARCH. The program SSEARCH performs a rigorous Smith–Waterman alignment between a protein sequence and another protein sequence, a protein database, a DNA or a DNA library.
The nature of the computation in the project allows it to easily take advantage of distributed computing. This, along with the likely humanitarian benefits of the research, has led the World Community Grid (a distributed computing grid that uses idle computer clock time) to run the Fiocruz project. All products are in the public domain by contract with WCG.Help Conquer Cancer
Help Conquer Cancer is a distributed computing project that runs on the BOINC platform. It is a joint project of the Ontario Cancer Institute and the Hauptman-Woodward Medical Research Institute. It is also the first project under World Community Grid to run with a GPU counterpart.Help Defeat Cancer
The Help Defeat Cancer project ran on World Community Grid from July 20, 2006 to April 2007. It seeks to improve the ability of medical professionals to determine the best treatment options for patients with cancers of the breast, head, or neck. The project worked by identifying visual patterns in large numbers of tissue microarrays taken from archived tissue samples. By correlating the pattern data with information about treatment and patient outcome, the results of this project could help provide better targeted treatment options.Help Fight Childhood Cancer
Help Fight Childhood Cancer was a distributed computing project that runs on the BOINC platform. It is a joint effort of Chiba University and the Chiba Cancer CenterHuman Proteome Folding Project
The Human Proteome Folding Project (HPF) is a collaborative effort between New York University (Bonneau Lab), the Institute for Systems Biology (ISB) and the University of Washington (Baker Lab), using the Rosetta software developed by the Rosetta Commons.
HPF Phase 1 applied Rosetta v4.2x software on the human genome and 89 others, starting in November 2004. Phase 1 ended in July 2006. HPF Phase 2 (HPF2) applies the Rosetta v4.8x software in higher resolution, "full atom refinement" mode, concentrating on cancer biomarkers (proteins found at dramatically increased levels in cancer tissues), human secreted proteins and malaria.
Phase 1 ran on two distributed computing grids: on United Devices' grid.org, and on the World Community Grid, an IBM philanthropic initiative. Phase 2 of the project ran exclusively on the World Community Grid; it terminated in 2013 after more than 9 years of IBM involvement.The Institute for Systems Biology will use the results of the computations within its larger research efforts.IBM Research – Africa
IBM Research – Africa is one of twelve research laboratories comprising IBM Research. Located at the Catholic University of Eastern Africa in Nairobi, it opened on November 7, 2013. It is the first commercial technology research facility on the African continent conducting both applied and far-reaching exploratory research.The lab is directed by Chief Scientist Osamuyimen Stewart, who oversees a research staff of 25.IBM Research – Australia
IBM Research – Australia is a research and development laboratory established by IBM Research in 2009 in Melbourne. It is involved in social media, interactive content, healthcare analytics and services research, multimedia analytics, and genomics. The lab is headed by Vice President and Lab Director Joanna Batstone. It was to be the company’s first laboratory combining research and development in a single organisation.The opening of the Melbourne lab in 2011 received an injection of $22 million in Australian Federal Government funding and an undisclosed amount provided by the government of the state of Victoria.IBM Research – Ireland
IBM Research – Ireland is one of IBM Research's twelve worldwide research laboratories, a first for the European Union and the only one which focuses on smarter technology for cities.
Opened in 2011 in Damastown Industrial Park, in the north-west of Dublin, Ireland, it conducts research on such critical resources as water, energy, and marine environments, as well transportation, city fabric, risk, and exascale computing.The Smarter Cities Technology Centre at IBM Research – Ireland represents an IDA Ireland - supported investment of up to EUR 66 million. As many as 200 new jobs are hoped to be created.Nutritious Rice for the World
Nutritious Rice for the World is a World Community Grid research project in the field of agronomy led by the Samudrala Computational Biology Research Group at the University of Washington. It was launched on May 12, 2008. The objective of this project is to predict the structure of proteins of major strains of rice. The intent is to help farmers breed better rice strains with higher crop yields, promote greater disease and pest resistance, and utilize a full range of bioavailable nutrients that can benefit people around the world, especially in regions where malnutrition is a critical concern.
Determining the structure of proteins is an extremely difficult and expensive process. Though it is possible to computationally predict a protein's structure from its corresponding DNA sequence, there are thousands of distinct proteins found in rice. This presents a computational challenge that a single computer cannot solve within a reasonable timeframe.Once that the entire rice genome had been sequenced, the effort shifted to identifying genes that are involved in increased yield, disease resistance and nutritional value. This problem is made more difficult because very few cereal plants have been sequenced, and therefore, many of the rice genes do not resemble any genes of known function. The Computational Biology Research Group at the University of Washington developed the Protinfo software, which can produce protein structures at a fraction of the cost and time.
Protinfo is being used to create three-dimensional models of the tens of thousands of rice proteins. These models are then used to predict the function of each protein and to understand the role of the gene that encodes it. The models, and any analysis resulting from examining them, will be housed at the Bioverse database and webserver, which is a comprehensive framework to relate molecules such as proteins and DNA to an organism's pathways and systems.
Volunteers' computers on World Community Grid will run the Protinfo software to create models of all proteins encoded by the rice genome whose structure can be predicted reliably. These models will be analyzed to choose the best ones. From the resulting structures, prediction tools will determine the function of each protein and the role of the gene that encodes it. Using the power of Protinfo, World Community Grid will initially examine over 10,000 genes, and produce 100,000 models per gene.
Eventually, the structures of 30,000 to 60,000 proteins will be studied. Generating one billion models on the 320 CPU cluster at the Computational Biology Research Group was anticipated to take about 30 years to accomplish; however, using World Community Grid took only about two years working at 167 TFLOPS. The distributed computing function was suspended in April 2010 while in-house analysis of results continues. The DC function will resume when funding is secured for further phases.
The resulting knowledge base will hopefully lead to the development of improved hybrids of rice strains with higher yield, greater disease and pest resistance, and a full range of bioavailable nutrients. This knowledge can also be extended to other food crops such as wheat and maize.Rosetta@home
Rosetta@home is a distributed computing project for protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC) platform, run by the Baker laboratory at the University of Washington. Rosetta@home aims to predict protein–protein docking and design new proteins with the help of about sixty thousand active volunteered computers processing at over 210 teraFLOPS on average as of July 29, 2016. Foldit, a Rosetta@Home videogame, aims to reach these goals with a crowdsourcing approach. Though much of the project is oriented toward basic research to improve the accuracy and robustness of proteomics methods, Rosetta@home also does applied research on malaria, Alzheimer's disease, and other pathologies.Like all BOINC projects, Rosetta@home uses idle computer processing resources from volunteers' computers to perform calculations on individual workunits. Completed results are sent to a central project server where they are validated and assimilated into project databases. The project is cross-platform, and runs on a wide variety of hardware configurations. Users can view the progress of their individual protein structure prediction on the Rosetta@home screensaver.
In addition to disease-related research, the Rosetta@home network serves as a testing framework for new methods in structural bioinformatics. Such methods are then used in other Rosetta-based applications, like RosettaDock and the Human Proteome Folding Project, after being sufficiently developed and proven stable on Rosetta@home's large and diverse set of volunteer computers. Two especially important tests for the new methods developed in Rosetta@home are the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and Critical Assessment of Prediction of Interactions (CAPRI) experiments, biennial experiments which evaluate the state of the art in protein structure prediction and protein–protein docking prediction, respectively. Rosetta@home consistently ranks among the foremost docking predictors, and is one of the best tertiary structure predictors available.The Weather Company
The Weather Company is a weather forecasting and information technology company that owns and operates weather.com and Weather Underground. The Weather Company is a subsidiary of the Watson & Cloud Platform business unit of IBM.United Devices
United Devices, Inc. was a privately held, commercial distributed computing company that focused on the use of grid computing to manage high-performance computing systems and enterprise cluster management. Its products and services allowed users to "allocate workloads to computers and devices throughout enterprises, aggregating computing power that would normally go unused." It operated under the name Univa UD for a time, after merging with Univa on September 17, 2007.Volunteer computing
Volunteer computing is a type of distributed computing, "an arrangement in which people, so-called volunteers, provide computing resources to projects, which use the resources to do distributed computing and/or storage". Thus, computer owners or users donate their computing resources (such as processing power and storage) to one or more "projects".
Volunteers are frequently members of the general public in the possession of their own personal computers with an Internet connection, but also organizations can act as volunteers and provide their computing resources.
Projects in this context are mostly science-related projects executed by universities or academia in general.
Berkeley Open Infrastructure for Network Computing (BOINC) Projects
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