TheSystems Biology Software Infrastructure<br />
‘A new infrastructure to streamline the<br /> connection between data, models, and analysis,<br /> allowing the updating o...
Systems Biology Research, CSBE view<br />Network Inference<br />Process Algebras<br />Model analysis<br />Graphical Notati...
Current people involved in SBSI<br />Core developers<br />Biopepa integration<br />     Adam Duguid<br />Project managemen...
SBSI goals 2008-2009<br />Parallelized global parameter optimization – for everyone!<br />Develop client application  <br ...
Parameter Estimation Problem<br /><ul><li>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.</li></li></ul><li>Global parameter optimisat...
Performance scales well with increasing processor cores<br />
Testing, testing, testing….<br />Rastrigin<br />‘abc_1’<br />VderPol<br />Goldbeter clock<br />Biomodels clock<br /> model...
Multi-objective optimisation<br />
Optimizing Circadian Clock models  with experimental data<br />Locke 2 loop model from Biomodels (57 params, 13 species)<b...
Outline of SBSI design<br />SBSI <br />clients<br />Integration of other CSBE<br />projects<br />BioPepa✔<br /> EPE<br />S...
Submit jobs to HPC</li></ul>✔Retrieve results<br />✔Provide job status<br />SBSI Numerics<br />Numerical algorithms and <b...
Outline of SBSI design<br />SBSI <br />clients<br />Integration of other CSBE<br />projects<br />BioPepa✔<br /> EPE<br />S...
Submit jobs to HPC</li></ul>✔Retrieve results<br />✔Provide job status<br />SBSI Numerics<br />Numerical algorithms and <b...
Aims early 2010<br />Move  all code to SourceForge, encourage open-source access<br />Publish SBSI paper <br />Integrate E...
SBSI resources<br />www.sbsi.ed.ac.uk<br />http://sourceforge.net/projects/sbsi/ <br />
Availability<br />SBSI Numerics<br />Numerical algorithms and <br />Frameworks for <br /><ul><li>Global optimsation✔</li><...
Availability<br />SBSI Visual <br />✔ Desktop application<br />✔ Upload and edit SBML models<br />✔ Run simulations<br />✔...
Availability<br />Deployed on SBSI server.<br />SBSI <br />Dispatcher<br />(Task Manager)<br /><ul><li>Compile C codes
Submit jobs to HPC</li></ul>✔Retrieve results<br />✔Provide job status<br />Access to test server, Bluegene<br />
Systems Biology Software Infrastructure overview
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Systems Biology Software Infrastructure overview

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Overview presentation of the Systems Biology Software Infrastructure

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  • Good morningMy name is Richard Adams &amp; 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 &amp; 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.,
  • Systems Biology Software Infrastructure overview

    1. 1. TheSystems Biology Software Infrastructure<br />
    2. 2. ‘A new infrastructure to streamline the<br /> connection between data, models, and analysis,<br /> allowing the updating of large scale data, models <br />and analytic tools with greatly reduced overhead’<br />SBSI objective<br />
    3. 3. Systems Biology Research, CSBE view<br />Network Inference<br />Process Algebras<br />Model analysis<br />Graphical Notation<br />Systems Biology Software Infrastructure™<br />Existing knowledge<br />Static models<br />Kinetic models<br />New knowledge<br />High-throughput data<br />High-resolution data<br />Kinetic Parameter Facility<br />Her2/ERK signalling<br />Circadian clock<br />RNA metabolism<br />
    4. 4. Current people involved in SBSI<br />Core developers<br />Biopepa integration<br /> Adam Duguid<br />Project management<br />Test Models and <br />Evaluation <br />Requirements &<br />Numerics<br />People previously involved with SBSI<br />Shakir Ali<br />Anatoly Sorokin<br />TreenutSaithong<br />Stuart Moodie<br />Igor Goryanin<br />Nikos Tsorman<br />Neil Hanlon<br />Richard Adams<br />Galina Lebedeva<br />AlexeyGoltsov<br />Circadian clock modellers<br />Azusa Yamaguchi<br />OzgurAkman<br />Carl Troein<br />Stephen Gilmore<br /> PI<br />EPCC<br />Andrew Millar<br />Kevin Stratford <br />
    5. 5. SBSI goals 2008-2009<br />Parallelized global parameter optimization – for everyone!<br />Develop client application <br />Integrate at least 1 external software package <br />
    6. 6. Parameter Estimation Problem<br /><ul><li>Building predictive models –challenging problem in Systems Biology
    7. 7. Parameter estimation – critical stage in model development
    8. 8. Multiple data sets for model calibration
    9. 9. Global optimization needed due to complex cost landscapes
    10. 10. Genetic /evolutionary techniques perform well.
    11. 11. Circadian clock modellers have existing high-quality time-series data to fit.</li></li></ul><li>Global parameter optimisation is compute intensive !<br />Weimann mammalian circadian core oscillator <br />7 ODEs, 24 parameters<br />Using synthetic data<br />Parallelized genetic algorithm <br />
    12. 12. Performance scales well with increasing processor cores<br />
    13. 13. Testing, testing, testing….<br />Rastrigin<br />‘abc_1’<br />VderPol<br />Goldbeter clock<br />Biomodels clock<br /> models <br />
    14. 14.
    15. 15. Multi-objective optimisation<br />
    16. 16. Optimizing Circadian Clock models with experimental data<br />Locke 2 loop model from Biomodels (57 params, 13 species)<br />Using BG/L 128 nodes,<br /> it finished at 63140th <br />generation by <br />non-improvement criteria.<br />Run-time 46 hours. <br />0-6740 :FFT +Chi-squared<br />674o – end : Chi-squared<br />
    17. 17. Outline of SBSI design<br />SBSI <br />clients<br />Integration of other CSBE<br />projects<br />BioPepa✔<br /> EPE<br />SBSI Visual <br />✔ Desktop application<br />✔ Upload and edit SBML models<br />✔ Run simulations<br />✔ Interact with external repositories<br />✔ Visualisation of data and results<br />SBSI Web <br />Interface<br />✔Command <br /> line<br />SBSI <br />Dispatcher<br />(Task Manager)<br /><ul><li>Compile C codes
    18. 18. Submit jobs to HPC</li></ul>✔Retrieve results<br />✔Provide job status<br />SBSI Numerics<br />Numerical algorithms and <br />Frameworks for <br /><ul><li>Global optimisation ✔</li></ul>-Sensitivity analysis<br /><ul><li>Bifurcation analysis</li></ul>core<br />Eddie (ECDF)<br />
    19. 19.
    20. 20.
    21. 21.
    22. 22. Outline of SBSI design<br />SBSI <br />clients<br />Integration of other CSBE<br />projects<br />BioPepa✔<br /> EPE<br />SBSI Visual <br />✔ Desktop application<br />✔ Upload and edit SBML models<br />✔ Run local and remote simulations<br />✔ Interact with external repositories<br />✔ Visualisation of data and results<br />SBSI Web <br />Interface<br />Command <br />line<br />SBSI <br />Dispatcher<br />(Task Manager)<br /><ul><li>Compile C codes
    23. 23. Submit jobs to HPC</li></ul>✔Retrieve results<br />✔Provide job status<br />SBSI Numerics<br />Numerical algorithms and <br />Frameworks for <br /><ul><li>Global optimsation✔</li></ul>-Sensitivity analysis<br /><ul><li>Bifurcation analysis</li></ul>core<br />Eddie (ECDF)<br />SBSI repository<br />Models (SBML)<br />Data ( SBSI standard format):<br />-experimental data<br />-simulation results<br />Plasmo, Robust<br />
    24. 24. Aims early 2010<br />Move all code to SourceForge, encourage open-source access<br />Publish SBSI paper <br />Integrate Edinburgh Pathway Editor<br />Develop plugin mechanism for SBSI Dispatcher to connect to other HPCs, Grid?<br />
    25. 25. SBSI resources<br />www.sbsi.ed.ac.uk<br />http://sourceforge.net/projects/sbsi/ <br />
    26. 26. Availability<br />SBSI Numerics<br />Numerical algorithms and <br />Frameworks for <br /><ul><li>Global optimsation✔</li></ul>-Sensitivity analysis<br /><ul><li>Bifurcation analysis</li></ul>Command line on local machine,<br />Bluegene, or ECDF<br />
    27. 27. Availability<br />SBSI Visual <br />✔ Desktop application<br />✔ Upload and edit SBML models<br />✔ Run simulations<br />✔ Interact with external repositories<br />✔ Visualisation of data and results<br />Available for Windows XP/Vista,<br /> MacOSX10.5, 64bit Linux .<br />Access to local or remote SBSINumerics<br />
    28. 28. Availability<br />Deployed on SBSI server.<br />SBSI <br />Dispatcher<br />(Task Manager)<br /><ul><li>Compile C codes
    29. 29. Submit jobs to HPC</li></ul>✔Retrieve results<br />✔Provide job status<br />Access to test server, Bluegene<br />

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