Grid.org
Encyclopedia
grid.org was a website and online community established in 2001 that focuses on cluster computing
and grid computing
software for users. For the first 6 years of its history it operated several different volunteer computing
projects that allowed members to donate their spare computer cycles to worthwhile causes. More recently, it has been relaunched as a community for open source
cluster and grid computing software. The website now points to the UniCluster website.
based products offered by Univa.
projects such as the United Devices
Cancer Research Project. It was sponsored philanthropically by United Devices
(UD) and members participated in volunteer computing
by running the UD Agent software (version 3.0).
The United Devices Cancer Research Project, which began in 2001, was seeking possible drugs for the treatment of cancer
using distributed computer
power. There were around 150,000 users in the United States and 170,000 in Europe along with hundreds of thousands more in other parts of the world.
The project is an alliance of several companies and organisations:
United Devices released the cancer research screensaver
under the principle of using spare computing power. The program, which can also be set to run continually, uses "virtual screening" to find possible interactions between molecules and target proteins, i.e. a drug. These molecules (ligand
s) are sent to the host computer's UD Agent. When these molecules dock successfully with a target protein this interaction is scored for further investigation.
The research consisted of two phases:
-sponsored Human Proteome Folding Project ("HPF"), phase 1, was announced on November 16, 2004 and was completed July 3, 2006. The project operated simultaneously on both grid.org and the IBM's World Community Grid
.
It made use of the "Rosetta" software to predict the structure of human proteins in order to help predict the function of proteins. This information may someday be used to help cure a variety of diseases and genetic defects.
According to an announcement on the grid.org forums, after the HPF1 project was completed it was left to continue running on grid.org until August 9, 2006. During that time, members whose computers were configured to run this project got new work and spent computing resources calculating a result, but the result was returned to grid.org for points only—it was not used for scientific research.
The status of the Human Proteome Folding Project caused some discussion on the grid.org forums. Most members wanted to see all available computing power directed toward the still-active Cancer project, but UD representative Robby Brewer asserted that "some [users] like the screensaver". As noted above, in the end the redundant HPF1 work on grid.org was halted.
virus. 35 million potential drug molecules were screened against several smallpox proteins, resulting in 44 strong potential treatments.
The partners of the project included University of Oxford
, the University of Western Ontario
, Memorial Sloan Kettering Cancer Research Center, Essex University, Evotec OAI, Accelrys
, and IBM
.
The World Community Grid
largely began because of the success of this project in shaving years off research time.
bacterial infection.
The project was operated from January 22, 2002 until February 14, 2002 and ended after a total of 3.57 billion molecules had finished screening. The results of the research project were transmitted to biological scientists in order to finish the screening of the computational simulations.
The partners of the project included Oxford University.
project made use of the Hidden Markov model
to search for patterns in genetic DNA sequences.
Cluster Computing
Cluster Computing: the Journal of Networks, Software Tools and Applications is a journal for parallel processing, distributed computing systems, and computer communication networks....
and grid computing
Grid computing
Grid computing is a term referring to the combination of computer resources from multiple administrative domains to reach a common goal. The grid can be thought of as a distributed system with non-interactive workloads that involve a large number of files...
software for users. For the first 6 years of its history it operated several different volunteer computing
Volunteer computing
Volunteer computing is a type of distributed computing in which computer owners donate their computing resources to one or more "projects".-History:...
projects that allowed members to donate their spare computer cycles to worthwhile causes. More recently, it has been relaunched as a community for open source
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
cluster and grid computing software. The website now points to the UniCluster website.
Open Source grid community
Since its relaunch in November 2007, grid.org has been repositioned by Univa as a community to allow users to interact and discuss open source cluster and grid related topics. It also allows users to download, get support for, contribute to, and report issues about the open source Globus ToolkitGlobus Toolkit
The Globus Toolkit, currently at version 5, is an open source toolkit for building computing grids developed and provided by the Globus Alliance.-Standards implementation:The Globus Toolkit is an implementation of the following standards:...
based products offered by Univa.
Past volunteer computing projects
From its establishment in April 2001 until April 27, 2007, grid.org was the website and organization that ran distributed computingDistributed computing
Distributed computing is a field of computer science that studies distributed systems. A distributed system consists of multiple autonomous computers that communicate through a computer network. The computers interact with each other in order to achieve a common goal...
projects such as the United Devices
United Devices
United Devices, Inc. was a privately held, commercial distributed computing company that focused on the use of grid computing to manage HPC infrastructures and enterprise cluster management...
Cancer Research Project. It was sponsored philanthropically by United Devices
United Devices
United Devices, Inc. was a privately held, commercial distributed computing company that focused on the use of grid computing to manage HPC infrastructures and enterprise cluster management...
(UD) and members participated in volunteer computing
Volunteer computing
Volunteer computing is a type of distributed computing in which computer owners donate their computing resources to one or more "projects".-History:...
by running the UD Agent software (version 3.0).
| Timeline of projects hosted by grid.org |
|---|
Cancer Research Project
Cancer
Cancer , known medically as a malignant neoplasm, is a large group of different diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the...
using distributed computer
Distributed computing
Distributed computing is a field of computer science that studies distributed systems. A distributed system consists of multiple autonomous computers that communicate through a computer network. The computers interact with each other in order to achieve a common goal...
power. There were around 150,000 users in the United States and 170,000 in Europe along with hundreds of thousands more in other parts of the world.
The project is an alliance of several companies and organisations:
- United Devices Inc.United DevicesUnited Devices, Inc. was a privately held, commercial distributed computing company that focused on the use of grid computing to manage HPC infrastructures and enterprise cluster management...
- National Foundation for Cancer ResearchNational Foundation for Cancer ResearchThe National Foundation for Cancer Research was founded in 1973 on the initiative of Albert Szent-Györgyi and Franklin Salisbury as a non-profit organization under U.S. tax code 501. Over the past 30 years, NFCR has provided more than $200 million in support of discovery-oriented basic science...
- University of Oxford Department of Chemistry
- Donors of molecular research
United Devices released the cancer research screensaver
Screensaver
A screensaver is a type of computer program initially designed to prevent phosphor burn-in on CRT and plasma computer monitors by blanking the screen or filling it with moving images or patterns when the computer is not in use...
under the principle of using spare computing power. The program, which can also be set to run continually, uses "virtual screening" to find possible interactions between molecules and target proteins, i.e. a drug. These molecules (ligand
Ligand
In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...
s) are sent to the host computer's UD Agent. When these molecules dock successfully with a target protein this interaction is scored for further investigation.
The research consisted of two phases:
- Phase 1 tested over 3 billion drug-like molecules against 12 proteins which were known to be suitable targets for anti-cancer drugs. It used the "THINK" software for the simulation of the molecular interactions.
- Phase 2, using the "LigandFit" software developed by AccelrysAccelrysAccelrys is a software company headquartered in the US, with representation in Europe and Japan. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries.Accelrys started in 2001...
to model interactions, sought to refine the Phase 1 data to produce a more manageable list of drug candidates for testing that would require experimental collaborators, including some from industry.
Human Proteome Folding Project, phase 1
The IBMIBM
International Business Machines Corporation or IBM is an American multinational technology and consulting corporation headquartered in Armonk, New York, United States. IBM manufactures and sells computer hardware and software, and it offers infrastructure, hosting and consulting services in areas...
-sponsored Human Proteome Folding Project ("HPF"), phase 1, was announced on November 16, 2004 and was completed July 3, 2006. The project operated simultaneously on both grid.org and the IBM's World Community Grid
World Community Grid
World Community Grid is an effort to create the world's largest public computing grid to tackle scientific research projects that benefit humanity...
.
It made use of the "Rosetta" software to predict the structure of human proteins in order to help predict the function of proteins. This information may someday be used to help cure a variety of diseases and genetic defects.
According to an announcement on the grid.org forums, after the HPF1 project was completed it was left to continue running on grid.org until August 9, 2006. During that time, members whose computers were configured to run this project got new work and spent computing resources calculating a result, but the result was returned to grid.org for points only—it was not used for scientific research.
The status of the Human Proteome Folding Project caused some discussion on the grid.org forums. Most members wanted to see all available computing power directed toward the still-active Cancer project, but UD representative Robby Brewer asserted that "some [users] like the screensaver". As noted above, in the end the redundant HPF1 work on grid.org was halted.
Smallpox Project
The Smallpox Research Grid was a part of United Devices "Patriot Grid" initiative to fight biological terrorism. This project helped analyze potential drug candidates for a medical therapy in the fight against smallpox virus. It made use of the "LigandFit" software (that had already been used by phase 2 of the Cancer Research project), but with a specialized set of target molecules that targeted the smallpoxSmallpox
Smallpox was an infectious disease unique to humans, caused by either of two virus variants, Variola major and Variola minor. The disease is also known by the Latin names Variola or Variola vera, which is a derivative of the Latin varius, meaning "spotted", or varus, meaning "pimple"...
virus. 35 million potential drug molecules were screened against several smallpox proteins, resulting in 44 strong potential treatments.
The partners of the project included University of Oxford
University of Oxford
The University of Oxford is a university located in Oxford, United Kingdom. It is the second-oldest surviving university in the world and the oldest in the English-speaking world. Although its exact date of foundation is unclear, there is evidence of teaching as far back as 1096...
, the University of Western Ontario
University of Western Ontario
The University of Western Ontario is a public research university located in London, Ontario, Canada. The university's main campus covers of land, with the Thames River cutting through the eastern portion of the main campus. Western administers its programs through 12 different faculties and...
, Memorial Sloan Kettering Cancer Research Center, Essex University, Evotec OAI, Accelrys
Accelrys
Accelrys is a software company headquartered in the US, with representation in Europe and Japan. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries.Accelrys started in 2001...
, and IBM
IBM
International Business Machines Corporation or IBM is an American multinational technology and consulting corporation headquartered in Armonk, New York, United States. IBM manufactures and sells computer hardware and software, and it offers infrastructure, hosting and consulting services in areas...
.
The World Community Grid
World Community Grid
World Community Grid is an effort to create the world's largest public computing grid to tackle scientific research projects that benefit humanity...
largely began because of the success of this project in shaving years off research time.
Anthrax Project
The Anthrax Research Project was a part of the United Devices "Patriot Grid" initiative to fight biological terrorism. It made use of the "LigandFit" software (that had already been used by phase 2 of the Cancer Research project), but with a specialized set of target molecules that targeted the advanced stages of anthraxAnthrax
Anthrax is an acute disease caused by the bacterium Bacillus anthracis. Most forms of the disease are lethal, and it affects both humans and other animals...
bacterial infection.
The project was operated from January 22, 2002 until February 14, 2002 and ended after a total of 3.57 billion molecules had finished screening. The results of the research project were transmitted to biological scientists in order to finish the screening of the computational simulations.
The partners of the project included Oxford University.
HMMER Project
The HMMER Genetic ResearchHMMER
HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences. It does this by comparing a profile-HMM to either a single sequence or a database of sequences...
project made use of the Hidden Markov model
Hidden Markov model
A hidden Markov model is a statistical Markov model in which the system being modeled is assumed to be a Markov process with unobserved states. An HMM can be considered as the simplest dynamic Bayesian network. The mathematics behind the HMM was developed by L. E...
to search for patterns in genetic DNA sequences.
Webload Project
The Web Performance Testing project was operated as a commercial opportunity with select web hosting providers in order to help them test the scalability of their server infrastructures under periods of high-demand.External links
- Grid.org (redirects to the UniCluster website).
- The National Foundation for Cancer Research
- United Devices Inc.
- Department of Chemistry at the University of Oxford
- Evotec OAI - drug R&D company