1 BASIS is a GRID pilot project to provide a tool for the quantitative study of the biology of ageing (MRC, BBSRC and the DTI) Virtual ageing cell ~200.

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Presentation transcript:

1 BASIS is a GRID pilot project to provide a tool for the quantitative study of the biology of ageing (MRC, BBSRC and the DTI) Virtual ageing cell ~200 cell types Virtual ageing tissue Skin, gut, brain Virtual ageing organism Nematode worm basis biology of ageing e-science integration and simulation system Accumulated population doublings Days in culture

2 basis biology of ageing e-science integration and simulation system Cellular ageing - Individual mechanisms Telomere shortening Somatic mutation Mitochondrial damage Other mechanisms, Sir2, antioxidants,.. Network of mechanisms Separately coded models replaced with a modelling system

3 basis biology of ageing e-science integration and simulation system

4 basis biology of ageing e-science integration and simulation system

5 basis biology of ageing e-science integration and simulation system

6 basis biology of ageing e-science integration and simulation system

7 basis biology of ageing e-science integration and simulation system

8 basis biology of ageing e-science integration and simulation system Modelling SBML development: e-cell, virtual cell, JigCell, BioSpice, Gepasi, SBW,… Model Representation (SBML) Parser (libxml, libxerces,libsbml) Stochastic and Deterministic Simulation (libm, libgsl) Results and visualisation GRID/Web services

9 basis biology of ageing e-science integration and simulation system External Services Search for a model based on a keyword returns a list of model Ids and descriptions Get a model with a given ID returns a model as SBML Add a model using given SBML returns a model ID Replace model with given ID by given SBML success/fail Submit a request for a simulation run given a model ID and some additional parameters returns a job ID Request status info for a given job ID returns info Request summary of results for a completed run with given job ID returns summary Request full raw results of a simulation run with given job ID returns very large database table extract

10 basis biology of ageing e-science integration and simulation system Architecture

11 basis biology of ageing e-science integration and simulation system Progress 1st year of 4 year project Model representation, parsing and simulation Several SBML models Installation of Linux beowulf cluster 1st workshop with groups from Germany, France, Italy and Unilever Current issues What GRID tools are available to help us? Would OGSA-DAI be useful to us? Python or Java? How do we make our services available to non-Grid aware people?