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Name of Collaboratory :

 

BioSimGrid

 
 

URL :

  http://biosimgrid.org/default.aspx  
 

Collaboratory Status :

 
Completed   Start Date : End Date : Info Last Updated : Fri, Dec 3 2010 10:01am PST
 
 

Primary Collaboratory Function :

  Community Infrastructure Development  
 

Secondary Collaboratory Functions :

  Community Data Systems  
 

Domain(s) :

  BIOLOGICAL/AGRICULTURAL SCIENCES >Biological Sciences >Molecular Biology  
 

Brief Description of the Collaboratory :

 

BioSimGrid is a project that seeks to exploit the potential of the Grid on biomolecular simulation data and tries to solve some of the problems that hamper comparative analysis. It provides a platform for the biochemists for conveniently storing, retrieving and analysing biomolecular simulation data.

BioSimGrid currently has multiple data resources spread across six different university research labs in the UK. It deals with simulation data that exists in the form of trajectories (sets of coordinates corresponding to the positions of atoms for a series of time steps) which can go up to the size of 10 GB per trajectory.

Users of BioSimGrid are able to deposit their simulation data, which exists in multiple data formats, into this repository. These data can then be made available to the whole community. The BioSimGrid data retrieval component enables a user to retrieve data transparently without knowledge of the database mechanisms behind the scenes. The flexibility of the retrieval tools allows users to access different slices of a trajectory seamlessly. BioSimGrid also provides a set of custom-built analysis tools which can be used to study the functional dynamics of a simulation, e.g. root mean square deviations, volume and average structure, interatomic distance and surface area. Alternatively, users can write their own analysis tools by utilising the retrieval components to access different slices of a trajectory as their analysis requires.

 
 

Access to Instruments :

   
 

Access to Information Resources :

  Users of BioSimGrid are able to deposit their simulation data, which exists in multiple data formats, into the distributed BioSimGrid repository. These data can then be made available to the whole community. The BioSimGrid data retrieval component enables a user to retrieve data transparently without knowledge of the database mechanisms behind the scenes.  
 

Access to People as Resources :

   
 

Funding Agency or Sponsor :

 
Biotechnology and Biological Sciences Research Council (BBSRC)
Department for Business Innovation and Skills (BIS)
 
 
 

Notes on Funding Agencies/Sponsors:

 
 
 
Organizations with Funded Participants:
 
Organization name:
Approx # of participants:
Description of organization's role(s):
University of Oxford
   Department of Biochemistry (University of Oxford)
5
Collaborator
Birkbeck University of London
   Department of Biological Sciences (Birkbeck University of London)
1
Collaborator
University of York
   Department of Biology (University of York)
1
Collaborator
University of California, San Diego (UCSD)
   Department of Chemistry and Biochemistry (UCSD)
1
Collaborator
University of Notre Dame
   Interdisciplinary Center for Network Science and Applications (Notre Dame)
1
Collaborator
Pacific Northwest National Laboratory (PNNL)
1
Collaborator
Bristol University
   School of Chemistry (Bristol University)
1
Collaborator
University of Southampton
   School of Chemistry (University of Southampton)
7
Collaborator
University of Nottingham
   School of Pharmacy (University of Nottingham)
1
Collaborator
 
TOTAL PARTICIPANTS:
19
 

Notes on Participants/Organizations:

   
     
 
 

Communications Technology Used :

   
 

Technical Capabilities :

   
  Key Articles :    
 

Project-reported performance data :

  BioSimGrid (as of 2006, the date of its last publication) is still at its prototype stage with over 20 users. It has over 200 trajectories contributing to 450 MB of metadata and approximately 1 TB of flat files. The system has storage space for 24 TB of data distributed over six sites. The available storage space can be increased by adding further machines.  
 
         
    
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