Systems Biology Software Infrastructure overview
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The Systems Biology Software Infrastructure
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‘A new infrastructure to streamline the
connection between data, models, and
analysis,
allowing the updating of large scale
data, models
and analytic tools with greatly reduced
overhead’
SBSI objective
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Graphical
Notation
Network Inference
Process Algebras
Model analysis
Existing knowledge
High-resolution data
High-throughput
data
New knowledge
Static models
Kinetic models
Systems Biology Software Infrastructure™
Kinetic Parameter Facility
RNA metabolism
Her2/ERK signalling
Systems Biology Research, CSBE view
Circadian clock
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Current people involved in SBSICore developers
EPCC
Test Models and Evaluation
Project management
Circadian clock modellers
Stephen Gilmore PI
Nikos Tsorman Neil Hanlon
Galina Lebedeva
Alexey Goltsov
Azusa Yamaguchi
Kevin Stratford
People previously involved with SBSI
Shakir AliAnatoly Sorokin
Treenut SaithongStuart Moodie
Igor Goryanin
Ozgur Akman
Carl Troein
Biopepa integration
Adam Duguid
Richard Adams
Requirements & Numerics
Andrew Millar
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Parallelized global parameter optimization – for everyone!
Develop client application
Integrate at least 1 external software package
SBSI goals 2008-2009
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Parameter Estimation Problem
• Building predictive models –challenging problem in Systems Biology
• Parameter estimation – critical stage in model development
• Multiple data sets for model calibration
• Global optimization needed due to complex cost landscapes • Genetic /evolutionary techniques perform well.
• Circadian clock modellers have existing high-quality time-series data to fit.
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Global parameter optimisation is compute intensive !
MacBook Pro2.2 GHz, intel Core 2 Duo
IBM BlueGene L32 node, 64 proc
Total optimization time for 100 generations
> 25 h Approx. 20 min;(BG is >75 times faster!)
Weimann mammalian circadian core oscillator 7 ODEs, 24 parametersUsing synthetic dataParallelized genetic algorithm
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Performance scales well with increasing processor cores
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Testing, testing, testing….
Rastrigin
‘abc_1’
VderPol
Goldbeter clock
Biomodels clock models
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Multi-objective optimisation
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Optimizing Circadian Clock models with experimental data
Locke 2 loop model from Biomodels (57 params, 13 species)
Using BG/L 128 nodes, it finished at 63140th generation by non-improvement criteria.Run-time 46 hours. 0-6740 :FFT +Chi-squared674o – end : Chi-squared
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Integration of other CSBEprojects
BioPepa ✔ EPE
Outline of SBSI design
✔Command line
SBSI Web Interface
SBSI Dispatcher
(Task Manager)✔ Compile C codes✔Submit jobs to HPC
✔Retrieve results✔Provide job status
SBSI Numerics
Numerical algorithms and Frameworks for
- Global optimisation ✔-Sensitivity analysis
- Bifurcation analysis
core
SBSI Visual
✔ Desktop application✔ Upload and edit SBML models✔ Run simulations✔ Interact with external repositories✔ Visualisation of data and results
SBSI clients
Eddie (ECDF)
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Integration of other CSBEprojects
BioPepa ✔ EPE
Outline of SBSI design
SBSI repository
Models (SBML)
Data ( SBSI standard format):-experimental data-simulation results
Command line
SBSI Web Interface
SBSI Dispatcher
(Task Manager)✔ Compile C codes✔Submit jobs to HPC
✔Retrieve results✔Provide job status
SBSI Numerics
Numerical algorithms and Frameworks for
- Global optimsation ✔-Sensitivity analysis
- Bifurcation analysis
core
SBSI Visual
✔ Desktop application✔ Upload and edit SBML models✔ Run local and remote simulations✔ Interact with external repositories✔ Visualisation of data and results
SBSI clients
Eddie (ECDF)
Plasmo, Robust
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Aims early 2010
Move all code to SourceForge, encourage open-source access
Publish SBSI paper
Integrate Edinburgh Pathway Editor
Develop plugin mechanism for SBSI Dispatcher to connect to other HPCs, Grid?
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SBSI resourceswww.sbsi.ed.ac.uk
http://sourceforge.net/projects/sbsi/
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Availability
SBSI Numerics
Numerical algorithms and Frameworks for
- Global optimsation ✔-Sensitivity analysis
- Bifurcation analysis
Command line on local machine,Bluegene, or ECDF
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Availability
Available for Windows XP/Vista, MacOSX10.5, 64bit Linux .
SBSI Visual
✔ Desktop application✔ Upload and edit SBML models✔ Run simulations✔ Interact with external repositories✔ Visualisation of data and results
Access to local or remote SBSINumerics
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Availability
Deployed on SBSI server.
Access to test server, Bluegene
SBSI Dispatcher
(Task Manager)✔ Compile C codes✔Submit jobs to HPC
✔Retrieve results✔Provide job status
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