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Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
Systems Biology Software Infrastructure overview
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

Overview presentation of the Systems Biology Software Infrastructure

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  • 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.,
  • Transcript

    • 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
    • 6. Parameter Estimation Problem
      • Building predictive models –challenging problem in Systems Biology
      • 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.
      • 11. Circadian clock modellers have existing high-quality time-series data to fit.
    • Global parameter optimisation is compute intensive !
      Weimann mammalian circadian core oscillator
      7 ODEs, 24 parameters
      Using synthetic data
      Parallelized genetic algorithm
    • 12. Performance scales well with increasing processor cores
    • 13. Testing, testing, testing….
      Rastrigin
      ‘abc_1’
      VderPol
      Goldbeter clock
      Biomodels clock
      models
    • 14.
    • 15. Multi-objective optimisation
    • 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
    • 17. Outline of SBSI design
      SBSI
      clients
      Integration of other CSBE
      projects
      BioPepa✔
      EPE
      SBSI Visual
      ✔ Desktop application
      ✔ Upload and edit SBML models
      ✔ Run simulations
      ✔ Interact with external repositories
      ✔ Visualisation of data and results
      SBSI Web
      Interface
      ✔Command
      line
      SBSI
      Dispatcher
      (Task Manager)
      • Compile C codes
      • 18. Submit jobs to HPC
      ✔Retrieve results
      ✔Provide job status
      SBSI Numerics
      Numerical algorithms and
      Frameworks for
      • Global optimisation ✔
      -Sensitivity analysis
      • Bifurcation analysis
      core
      Eddie (ECDF)
    • 19.
    • 20.
    • 21.
    • 22. Outline of SBSI design
      SBSI
      clients
      Integration of other CSBE
      projects
      BioPepa✔
      EPE
      SBSI Visual
      ✔ Desktop application
      ✔ Upload and edit SBML models
      ✔ Run local and remote simulations
      ✔ Interact with external repositories
      ✔ Visualisation of data and results
      SBSI Web
      Interface
      Command
      line
      SBSI
      Dispatcher
      (Task Manager)
      • Compile C codes
      • 23. Submit jobs to HPC
      ✔Retrieve results
      ✔Provide job status
      SBSI Numerics
      Numerical algorithms and
      Frameworks for
      • Global optimsation✔
      -Sensitivity analysis
      • Bifurcation analysis
      core
      Eddie (ECDF)
      SBSI repository
      Models (SBML)
      Data ( SBSI standard format):
      -experimental data
      -simulation results
      Plasmo, Robust
    • 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/
    • 26. Availability
      SBSI Numerics
      Numerical algorithms and
      Frameworks for
      • Global optimsation✔
      -Sensitivity analysis
      • Bifurcation analysis
      Command line on local machine,
      Bluegene, or ECDF
    • 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
    • 28. Availability
      Deployed on SBSI server.
      SBSI
      Dispatcher
      (Task Manager)
      • Compile C codes
      • 29. Submit jobs to HPC
      ✔Retrieve results
      ✔Provide job status
      Access to test server, Bluegene

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