SBGN super-hackathon materials


BioUML - open source Java framework for systems biology

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SBGN super-hackathon materials

These are materials for virtual participation of BioUML team in SBGN super-hackathon in Okinawa.

BioUML - new feartures - MS Power point presentation (2 Mb).
SBGN formal definition as an XML document
- MS Word document (2.8 Mb) - describes how SBGN specification for each node type is mapped to corresponding part of XML document and treated by BioUML workbench
- DTD - DTD for XML document that defines graphic notation
- sbgn(ER).xml - defintion of SBGN ER diagram type
- sbgn(ST).xml - defintion of SBGN ST diagram type
- sbgn(ST, compact).xml - defintion of SBGN ST diagram type in compact form.
BioUML workbench version 0.7.8 alpha (16 Mb)
Main feartures are:
- Graphic Notation Editor
- SBGN implementation (prototype)
- Library of predefined kinetic law functions on the base of SBO
- SBML extension point and extensions:
  - graphic notation
  - BioPAX
BioModels - comparison with other simulators (Copasi, CVODE, RoadRunner, Jarnac, JSim, Oscill8 Core, SBWOdeSolver, MathSBML and SBToolbox2)
Results

BioUML and BioModels

BioUML workbench version 0.7.8 (beta) was able to simulate all 150 SBML models from BioModlels database (release 9). According to our metrics now BioUML is the best simulator for SBML models.
Details...

SBGN super-hackathon

Materials for virtual participation of BioUML team in SBGN super-hackathon in Okinawa.

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SBML tests passed 100%

Both simulation engines (Java and MATLAB) provided by BioUML workbench version 0.7.5 passed 100% SBML semantic test suite.
Test details

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