Converter from COBRA format to SBML Level 3 "FBC" Version 2

[mhucka]

Background

A popular technique in systems biology is Constraint-Based Reconstruction and Analysis (COBRA). Toolboxes exist for this approach, of which COBRA toolbox for MATLAB and COBRApy for Python are probably the most widely used. Recently, the modeling community put out an updated definition of how to represent such models in SBML, in the form of Version 2 of the SBML Level 3 "Flux Balance Constraints" (FBC) package. The format standardizes how these models can be represented more precisely, but meanwhile, models in COBRA format exist and will never be updated until a converter is created.

Goal

Develop a converter from COBRA format to SBML Level 3 FBC Version 2 format. Time permitting, incorporate this converter as a module in JSBML, the pure Java library for SBML. Optionally also add it as a converter in the Systems Biology Format Converter (SBFC) system.

Potential Mentors

Andreas Dräger Nicolas Rodriguez

Contact

SBML Team

Useful pointers to documentation related to GSOC for student on the main NRNB web site :

• Resources
• How to apply

[niko-rodrigue]

@tmHamm is implementing those converters at the moment.