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 tutorial

October 10, 8.30-12.30 a.m - tutorial "BioUML - integrated platform for building virtual cell and virtual physiological human" on ICSB 2010 conference.

SBML tests passed 100%

BioUML version 0.9.0 have passed all tests from SBML test suite version 2.0 (SBML L1v2, L2v1-4, L3v1) Test details.

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