JLibSEDML update April 2011
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JLibSEDML update April 2011

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Progress on the jlibsedml library, a Java library for manipulating SED-ML files

Progress on the jlibsedml library, a Java library for manipulating SED-ML files

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  • Edinburgh castle
  • Cricket in Scotland – reference to Harmony2011 attendees attending a basedball match.
  • Version 1.1.0 is new since Combine 2010 and implements the final specification of SEDML. Stable API from now on for l1v1 Welcome any requests for features, bug reports etc.,
  • Jlibsedml just provides core API for manipulating SED-ML files – application support needs to build on top of this. Next few slides show some tools we’re developing in Edinburgh
  • A simple web-app to validate SEDML files. Upload a SED_ML file and see if it’s valid SED-ML Validates against XML schema, but also semantic validations E.g., Are uniform time coures attributes consistent (e.g., is start time < end time?) Are there cycles in model references ( there should be no cycles, i.e., modelA should not refer to model B as source and model B use model A as source) Are variables in MathML statements correctly defined as SEDML variables? Click on slide , screenshot of validated file with errors appears showing UTC values invalid.
  • Nascent web service – WSDL link at bottom Plan to extend to run simulations, at least for SBML models
  • 3. SEDML support is built into SBSI, systems biology software we’re developing in Edinburgh. Next release ( due early May) will implement the level1 version 1 final spec. Example screenshot shows that one can export a simulation configuration to SED-ML using the SBSI software (www.sbsi.ed.ac.uk) Configure simulation Configure output including SEDML export Export to SEDML archive or file.
  • View validation errors, SEDML document, etc.,
  • 1. Click on a SEDML file 2. Choose your output If the software can handle the modelling language and simulation type, it will produce the output. Screenshot shows the Elowitz repressilator example from the specification, reproducing the plots of normalized levels of protein.
  • This is under development – a graphical editor for SEDML. SEDML files can get quite complicated to look at once there are several models and tasks defined Aims are to allow easy viewing, editing and annotation, validating input, help with generating Xpath etc., and viewing models and their changes. Will be available as standalone app, Eclipse plugin, or SBSI plugin. Screenshot shows simple example and simulation configuration dialog.
  • 2 parts of schema not clearly resolved are: add/remove element, and range operations on maths.

Transcript

  • 1. Libraries and tools for SED-ML Harmony workshop April 2011
    • April 22nd, 2011
    [email_address]
  • 2.  
  • 3. JlibSEDML – a Java library for SED-ML “ Pioneering research and infrastructure development to model the dynamic aspects of biology”
    • JlibSEDML update
    • Application support
  • 4. Aims and scope of JlibSEDML
    • API to read/write and interpret SED-ML files.
    • Native Java, light-weight, few dependencies.
    • Two independent implementations from VCell and SBSI teams merged in Spring 2010.
  • 5. http://sourceforge.net/projects/jlibsedml/ Java library for SED-ML Open-source MIT license Version 1.1.0 implements SED-ML level 1 version 1 JlibSEDML on Sourceforge… “ Pioneering research and infrastructure development to model the dynamic aspects of biology”
  • 6. Scope of jlibSEDML SED Simulator 1 Simulator 2 Simulator 3 Export simulation configuration Execute configuration Simulator 1 Simulator 2 Simulator 3 SED-ML file CORE Application Support “ Pioneering research and infrastructure development to model the dynamic aspects of biology”
  • 7. Applications 1 - online SED-ML validator http://www.sbsi.ed.ac.uk/html/sedml/
  • 8. Applications 2 - SED-ML web service http://mook.inf.ed.ac.uk:8848/SedMLWebService/sedmlws?wsdl Provides the following methods: // Applies changes to a model and returns the new model String applyChanges( String modelID, String originalModel, String sedML) //Validates the SEDML document and returns errors SedmlError validate ( String sedMLDoc)
  • 9. SED-ML support in SBSI- www.sbsi.ed.ac.uk “ Pioneering research and infrastructure development to model the dynamic aspects of biology”
  • 10. SED-ML support in SBSI – viewing SEDML “ Pioneering research and infrastructure development to model the dynamic aspects of biology”
  • 11. SED-ML support in SBSI – executing SED-ML “ Pioneering research and infrastructure development to model the dynamic aspects of biology”
  • 12. A SED-ML editor “ Pioneering research and infrastructure development to model the dynamic aspects of biology”
  • 13. Future implementation work
    • Jlibsedml
      • Bugfix /maintenance releases
    • Providing executable SED-ML through web service
    • SBSI ( www.sbsi.ed.ac.uk )
      • Rich editor for editing and annotating SED-ML
    “ Pioneering research and infrastructure development to model the dynamic aspects of biology”
  • 14. Acknowledgements
    • VCell
      • Ion Moraru
      • Dan Vasilescu
      • Anuradha Lakshminarayana
    • CSBE
      • Stephen Gilmore
    • SED-ML editors
      • Frank Bergmann
      • Dagmar Waltemath
      • Nicholas le Novere
    “ Pioneering research and infrastructure development to model the dynamic aspects of biology”