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Isab 11 for_slideshare


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This presentation describes the current status of SBSI in May 2011, and was presented at CSBE's annual scientific advisory board visit.

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Isab 11 for_slideshare

  1. 1. Systems Biology Software Infrastructure (SBSI) ISAB visit May 19 th 2011 Allan Clark, Nikos Tsorman, Neil Hanlon Richard Adams, Stephen Gilmore
  2. 2. Talk outline <ul><li>SBSI scope and purpose </li></ul><ul><li>Progress since last ISAB </li></ul><ul><li>Current priorities and future work </li></ul>
  3. 3. SBSI objective ‘ 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’
  4. 4. Goals of SBSI <ul><li>Facilitate the incorporation of experimental data into modelling approaches </li></ul><ul><li>Develop computational capacity for analyzing larger models </li></ul><ul><li>Allow integration of novel scientific methods </li></ul><ul><li>Allow customization by external developers </li></ul><ul><li>Initially, focus on parameter estimation problem </li></ul>
  5. 5. Data and model results How to get models to reproduce experimental data?
  6. 6. Parameter Estimation Problem <ul><li>Building predictive models – a challenging problem in Systems Biology </li></ul><ul><li>Parameter estimation – critical stage in model development </li></ul><ul><li>Multiple data sets for model calibration </li></ul><ul><li>Global optimization needed due to complex cost landscapes </li></ul><ul><ul><li>Genetic /evolutionary techniques perform well. </li></ul></ul><ul><li>Circadian clock modellers have existing high-quality time-series data to fit. </li></ul>
  7. 7. 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 Systems Biology Research, CSBE view Circadian clock C holesterol metabolism
  8. 8. The SBSI Software Suite
  9. 9. The SBSI Software Suite Using SBSI we can fit to oscillating data ( green line).
  10. 10. The SBSI Software Suite SBSIVisual client organizes & displays resources, access SBSINumerics.
  11. 11. Outreach & documentation <ul><li>Practical SBSI tutorial workshops at: </li></ul><ul><ul><li>ICSB2010, Edinburgh </li></ul></ul><ul><ul><li>EraSysBio Summer School, 2010 </li></ul></ul><ul><ul><li>Several internal training sessions </li></ul></ul><ul><ul><li>Plant Systems Biology Summer School , 2011 </li></ul></ul><ul><li>Course material available for download from Sourceforge </li></ul><ul><ul><li>( </li></ul></ul><ul><li>Comprehensive HTML and pdf user manuals for SBSINumerics and SBSIVisual </li></ul><ul><li>Tutorial videos on YouTube ( channel sbsi23) </li></ul>
  12. 12. Integration - databases Data sources Integration with Plasmo & Robust databases
  13. 13. Integration - databases Data sources Data Standards High performance computing Modelling languages Software Plasmo search..
  14. 14. HPC access Data sources Data Standards High performance computing Modelling languages ROBuST ECDF Software SBSI installed on Hector, the UK national supercomputer BioPepa
  15. 15. Community standards involvement Data Standards
  16. 16. SED-ML purpose Dagmar Waltemath -
  17. 17. MIASE / SED-ML contributors > 21 collaborating institutions worldwide.
  18. 18. SED-ML developments 2009 - present MIASE paper published 2011
  19. 19. SED-ML developments 2009 - present   SED-ML specification published
  20. 20. SED-ML developments 2009 - present   XML schema and Java library released..
  21. 21. SED-ML support in SBSI
  22. 22. Executing SED-ML
  23. 23. Editing SED-ML
  24. 24. Integration across projects Garuda collaborating institutions Software CellDesigner
  25. 25. Integration across projects Garuda collaborating institutions
  26. 26. Garuda functionality Knowledge Led by Kitano group, SBI, Tokyo Pathway visualization Model creation Model analysis Text mining Pathway databases Molecular databases
  27. 27. CellDesigner / Garuda plugin Download from
  28. 28. Integration across projects Modelling languages Garuda collaborating institutions BioPepa  appa – RuleBase Eclipse plugin works in SBSI
  29. 29. Integration across projects The Kappa rule-based modelling environment
  30. 30. Vertical integration Web interface to SBSI REST-ful web service at Reuse of software components
  31. 31. Coding challenge How can a fixed number of developers continue to maintain and develop new code?
  32. 32. Solution 1 – manage dependencies Avoid cycles at all costs!
  33. 33. Solution 2 – continuous testing
  34. 34. Solution 3 – involve more developers Plugin contributions can be independently developed, licensed and deployed.
  35. 35. Current work <ul><li>Supporting core users for parameter estimation </li></ul><ul><ul><li>(Circadian clock and cholesterol pathway modelling) </li></ul></ul><ul><li>Exploring collaboration with other computational groups in CSBE (Swain, Grima, Danos, Plotkin) for modelling language support in SBSI. </li></ul><ul><li>Developing external collaborations </li></ul>
  36. 36. Acknowledgements <ul><li>Allan Clark </li></ul><ul><li>Nikos Tsorman </li></ul><ul><li>Neil Hanlon </li></ul><ul><li>Richard Adams </li></ul><ul><li>Stephen Gilmore </li></ul>Current Development Team Past developers Azusa Yamaguchi Millar Group Carl Troein Steve Watterson Maria-Louisa Guerriero Robert Smith Simon Bordage Martin Beaton Tomasz Zielinski Thanks for watching… If you’re interested follow us on Twitter @CSBE_SBSI