bbsrc biotechnology and biological sciences research council
1 BASIS is a GRID pilot project to provide a tool for the quantitative study of the biology of...
11
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
-
Upload
jackson-mccall -
Category
Documents
-
view
215 -
download
0
Transcript of 1 BASIS is a GRID pilot project to provide a tool for the quantitative study of the biology of...
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 tissueSkin, gut, brain
Virtual ageing organismNematode worm
basisbiology of ageing e-science
integration and simulation system
Acc
um
ulat
ed p
op
ulat
ion
dou
blin
gs
Days in culture
2
basisbiology of ageing e-science
integration and simulation system
Cellular ageing - Individual mechanismsTelomere shorteningSomatic mutation
Mitochondrial damageOther mechanisms, Sir2, antioxidants, ..Network of mechanisms
Separately coded models replaced with a modelling system
3
basisbiology of ageing e-science
integration and simulation system
4
basisbiology of ageing e-science
integration and simulation system
5
basisbiology of ageing e-science
integration and simulation system
6
basisbiology of ageing e-science
integration and simulation system
7
basisbiology of ageing e-science
integration and simulation system
8
basisbiology 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
basisbiology 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
basisbiology of ageing e-science
integration and simulation system
Architecture
11
basisbiology of ageing e-science
integration and simulation system
Progress 1st year of 4 year project
Model representation, parsing and simulation Several SBML modelsInstallation of Linux beowulf cluster1st 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?
www.basis.ncl.ac.uk
