SIMAP@Home Project

From Unofficial BOINC Wiki

Contents 1 General 2 Status of the Project 3 Reading List for Protein Folding Related Projects 4 More About SIMAP@Home 5 Also See 6 Active BOINC Projects

[edit] General

The SIMAP@Home Project, a BOINC Powered Project is in its last testing stage (Beta Test) at the moment.

The SIMAP@Home Project computes the Similarity Matrix of Proteins SIMAP, a publicly available resource to investigate and to utilize similarities between protein sequences. Similarities between two protein sequences imply a common evolutionary origin, also called homology. If two proteins are probably homologs, it is quite likely that they share a similar three-dimensional fold and, importantly, might have the same or similar functionality. The SIMAP@Home Project uses a Science Application called the "SIMAP Computation Application" which is used to precompute these similarities in an all-against-all approach using the Fasta algorithm. SIMAP allows convenient access by different interfaces as the web-interface and web-services for researchers all around the world.

SIMAP speeds up analysis wherever homology detection plays a role. It is therefore a valuable resource for many different kinds of biological/bioinformatical analysis and may give additional insights since it allows to investigate the whole 'protein space' at once or in user-defined parts.

The SIMAP system itself is maintained by the Chair of Comparative Genome Research at the Technical University of Munich (TUM) and developed in cooperation with MIPS/IBI, the Munich Institute for Protein Sequences (MIPS/IBI) at the GSF research center for environment and health.

[edit] Status of the Project

Currently, the first Work Units have been computed. Some problems still remain and have to be solved, for example: the stability of the Linux-client. The generation process of the Work Units has been changed in order to generate Results of moderate size.

[edit] Reading List for Protein Folding Related Projects

Regrettably, there is somewhat confusing vocabulary necessary to begin a discussion of the Rosetta@Home method of protein folding, as well as comparisons of this approach with other related BOINC Powered Projects: Poem@Home, Folding@Home, Predictor@Home, Rosetta@Home, SIMAP@Home, and World Community Grid.

• Proteins
• Protein Structure
• Protein Folding

[edit] More About SIMAP@Home

• Getting started with SIMAP@Home
• SIMAP@Home FAQ
• The Science Behind SIMAP@Home
• What Is The Difference Between The Different Protein Projects; Including Folding@Home, Predictor@Home, Rosetta@Home, SIMAP, and World Community Grid?
• How much resource share should I give to SIMAP@Home?
• More about the SIMAP@Home Science
• In-built Visualization/Screensaver
• Problems Running - How-To Test Machine Stability

[edit] Also See

The SIMAP web-interface at MIPS.

[edit] Active BOINC Projects

These BOINC Powered Projects are in the production phase. They are considered reasonably stable and are doing valid science. Alpha and Beta Projects are less stable and not recommended for general Participation.

Wiki Project Page	Project Web Site	Project Goal or Comments
ABC@Home	ABC@Home Web Site	This project will try to find abc triples related to the ABC conjecture.
BBC Climate Change Experiment	BBC Climate Change Experiment Web Site	Study of transient climate change model predictions. As of 10.12.2006, this project is closed for new users. New users should join the main Climateprediction.net (CPDN) project instead.
Climateprediction.net (CPDN)	Climateprediction.net Web Site	Study of Climate Models to answer some of the important Climate Change Questions. Note: Only works with Version 5.x.x or later of the BOINC Client Software.
Seasonal Attribution Project	Seasonal Attribution Project Web Site	High resolution variant of CPDN, taking a more in depth look at certain regional areas. As of December 2007, out of work again with no current plans of a 3rd. extension.
Einstein@Home	Einstein@Home Web Site	Search for gravitational waves to reveal the presence of neutron stars (pulsars).
Leiden Classical	Leiden Classical Web Site	Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student.
LHC@Home	LHC@Home Web Site	Model and improve the design of the CERN, LHC particle accelerator. Has work infrequently.
MalariaControl.net	MalariaControl.net Project Web Site	The MalariaControl.net project is an application that makes use of network computing for stochastic modelling of the clinical epidemiology and natural history of Plasmodium falciparum malaria. Also see: Africa@Home
Predictor@Home	Predictor@Home Web Site	Investigate protein behavior. As of February 2007 is beta-testing a new application.
Rosetta@Home	Rosetta@Home Web Site	Predict and design protein structures, and protein-protein and protein-ligand interactions using the Rosetta program.
SETI@Home	SETI@Home Web Site	Look for radio evidence of extraterrestrial life.
SIMAP@Home	SIMAP@Home Web Site	Study of protein similarities. Has work infrequently, check home page for more info.
SZTAKI Desktop Grid	SZTAKI Web Site	Hungarian project. This project is exploring a mathematical domain looking for solutions to a particular problem space.
World Community Grid	World Community Grid Web Site	Runs multiple sub-projects, users can choose which project(s) to run. Note: Only works with Version 5.x.x or later of the BOINC Client Software.