Ti met may10
-
Upload
guest18af32 -
Category
Documents
-
view
393 -
download
2
Transcript of Ti met may10
The Systems Biology Software Infrastructure
TiMet Workshop
May 7th 2010, Edinburgh
Richard Adams
www.sbsi.ed.ac.uk
http://sourceforge.net/projects/sbsi/
‘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 - Overall objective
SBSI Contributors
Core 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
Ozgur Akman
Igor GoryaninCarl Troein
Biopepa integration
Adam Duguid
Richard Adams
Requirements & Numerics
Andrew Millar
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
Circadian clock
RNA metabolismInterferon signalling
Systems Biology Research, CSBE view
ERB-b signalling
Initial use case :Parameter Estimation Problem
• Building predictive models – challenging problem in Systems Biology
• Parameter estimation – critical stage in model development
• Multiple data sets needed for model calibration
• Optimization of large scale models –computationally challenging
• Circadian clock modelling project requires model optimization.
SBSI Numerics optimization
SBML model, Parameter constraints,Experimental Data
filesConfiguration file
Model.cpp,Datafiles,Parameter constraints
SBML->C++ conversion
-Best parameters-Cost function behaviour-Time course with best parameters
Eddie (ECDF)
Output
Using command line client
Run on HPC
retrieve results
Input
Integration of other CSBEprojects
BioPepa ✔
Outline of SBSI design
External model & experimentaldata sources
BioModels ✔
SBSI Dispatcher
(Task Manager)Compile C codes
Submit jobs to HPC ✔Retrieve results
✔Provide job status
SBSI Numerics
core
SBSI Visual
✔Desktop application✔Upload and edit SBML models Run simulations Configure and run optimisations✔Interact with external repositories✔Visualisation of data and results
Eddie (ECDF)
SBSI Numerics SBSI Numerics
SBSI serversSBSI Numerics
SBSI - complete system
Integration of other CSBE projects
BioPepa ✔ EPE
External model & experimentaldata sources
SBSI Visual
✔Desktop application✔Upload and edit SBML models Run simulations Configure and run optimisations✔Interact with external repositories✔Visualisation of data and results
SBSI Numerics
SBSI - local mode
SBSI Dispatcher
(Task Manager)Compile C codes
Submit jobs to HPC ✔Retrieve results
✔Provide job status
SBSI Numerics
CellDesigner
Eddie (ECDF)
SBSI Numerics SBSI Numerics
SBSI serversSBSI Numerics
A plugin for CellDesigner
CellDesigner –SBSI plugin
Nactem
CellDesigner
Dunnart
InSilicoIDESBSI
PathText Kleio
Panther Pathwaysdatabase
autolayouts
visualizes
annotates
Provides SBML models
Optimizes?
Sabio-RKdatabaseKinetic
parameters
Copasi
Ananiadou/Tsujii/Kemper
Mi (SRI) Funahashi/Ghosh
Nomura (Osaka)
updates
EHMN
Goryanin (Edinburgh)
Boyd (Melbourne)
4-6 July Manchester, 8-9 October Edinburgh (ICSB), OIST early March 2011
Existing organisations/interactions
Planned collaborations
Gilmore (Edinburgh)
GARUDA partners
Proposed collaborations
Multiple Cost Function
Optimizing Circadian Clock models with experimental data
BIOMD055: “Extension of a genetic network model by iterative experimentation and mathematical analysis.” by J. C. W. Locke, M. M. Southern, L. Kozma-Bognar, V. Hibberd, P. E. Brown, M. S. Turner, A. J. Millar (2005b). Molecular Systems Biology. 1:13The model has 57 parameters and 13 states( equations). Fitting data is 2 of those states obtained by experiment.
Using BG/L 128 nodes, it finished at 63140th generation by non-improvement criteria.The run time is 46 hours. Multiple Cost Function is used up to 6740 generation, after 6740th, only X2Cost is applied
Release code base on Sourceforge
Establish SBSI Numerics on Hector
Provide access to SBSI through CellDesigner
Develop user base /community
Publish!
SBSI goals 2010
In the workspace you can store models, data, objective functions and results
Editor view allows access to files
Data visualization panel
Step 1 – create a new SBSI project
Running parameter optimisations…
Running parameter optimisations…
Step 2 – choose models,data and algorithm type-multiple datasets can be selected
Step 3: choose parameters, constraints and initial values
Running parameter optimisations…
Running parameter optimisations…
Step 4: configure optimization algorithm
Step 5: Compare simulation using best parameters, with experimental data.