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Systems Biology Software Infrastructure overview
- 1. TheSystems Biology Software Infrastructure
- 2. ‘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
- 3. Systems Biology Research, CSBE view Network Inference Process Algebras Model analysis Graphical Notation Systems Biology Software Infrastructure™ Existing knowledge Static models Kinetic models New knowledge High-throughput data High-resolution data Kinetic Parameter Facility Her2/ERK signalling Circadian clock RNA metabolism
- 4. Current people involved in SBSI Core developers Biopepa integration Adam Duguid Project management Test Models and Evaluation Requirements & Numerics People previously involved with SBSI Shakir Ali Anatoly Sorokin TreenutSaithong Stuart Moodie Igor Goryanin Nikos Tsorman Neil Hanlon Richard Adams Galina Lebedeva AlexeyGoltsov Circadian clock modellers Azusa Yamaguchi OzgurAkman Carl Troein Stephen Gilmore PI EPCC Andrew Millar Kevin Stratford
- 5. SBSI goals 2008-2009 Parallelized global parameter optimization – for everyone! Develop client application Integrate at least 1 external software package
- 7. Parameter estimation – critical stage in model development
- 8. Multiple data sets for model calibration
- 9. Global optimization needed due to complex cost landscapes
- 10. Genetic /evolutionary techniques perform well.
- 12. Performance scales well with increasing processor cores
- 13. Testing, testing, testing…. Rastrigin ‘abc_1’ VderPol Goldbeter clock Biomodels clock models
- 16. 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-squared 674o – end : Chi-squared
- 24. 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?
- 25. SBSI resources www.sbsi.ed.ac.uk http://sourceforge.net/projects/sbsi/
- 27. Availability SBSI Visual ✔ Desktop application ✔ Upload and edit SBML models ✔ Run simulations ✔ Interact with external repositories ✔ Visualisation of data and results Available for Windows XP/Vista, MacOSX10.5, 64bit Linux . Access to local or remote SBSINumerics
- 29. Submit jobs to HPC✔Retrieve results ✔Provide job status Access to test server, Bluegene
Editor's Notes
- Good morningMy name is Richard Adams & for the last year I’ve project managedthe development of the SBSI.My background is as a cell biologist, but for the last 7 years I’ve been writing software for bioinformatics and systems biology. Today I’ll give a brief introduction to SBSI, and review progress over the last year
- Read out quoteThere is scope for a program that will link models, with experimental data that is perhaps in remote repositories, to the latest analytic tools, in a way that is straightforward for modellers to use.
- SBSI has a broad set of aims, we have initially chosen to focus on a key set that would be of early benefit.Client application easy to useIntegration point for other software projects
- Whyaer we tacklingparmeter estimation first?Predictive models are desirable e.g., for P4 medicineSearch space dimensionality increases with each new parameter to fitLocal minima are a big problem , therefore need global algorithms
- Testing very important to establish legitimacy and encourage user uptake.Important part of 2009’s activities.Developing models, performance benchmarking.Testing is an important part of dvpt process – unit testing, GUI testing, written systems tests as well.
- We’ are now using optimisation framework to fir real datamodelsBlue line is simulation using parameters from published modelGreen line is after fitting. (data is red spots)Fitted parameters reproduce the decaying oscillation in the data
- Screenshot of applicationWorkspace – allows management of project based resourcesViews & editors for simulation, optimisation etc.,Biopepa integration: SBSI benefits – stochastic solvers, Biopepa benefit – can optimise their models, Loosely coupled via SBML filesBased on Eclipse development environment, using SBML as modelRobust plugin model, any developer can add plugin that uses SBML
- Job tracker – hides complexity from userKeeps UI biologically focussedCan track running jobs, download interim results etc.,