Conversion tools

For this workflow we have developed some conversion tools to facilitate model developement.

The MATLAB® code takes the SBtab file in excel format and generates tab separeted file (.tsv) of this SBtab, an SBML file (.xml) of the model, and two MATLAB® versions of the model (.m and .sbproj). This conversion happens as a setup step of running any of the Matlab analysis, it might be added as a standalone option in the future.

SBtab (.xls,.xlsx) -> Matlab® model (.m .sbproj), SBtab (.tsv), Matlab® SBML (.xml)

We also have R code to perform other conversions in two external repositories:

• Code for fixing the SBML produced by MATLAB®

  https://github.com/a-kramer/simbiology-sbml-fix

  Matlab® SBML (.xml) -> SBML (.xml)

• A standalone SBtab to VFgen SBML and NEURON tool

  https://github.com/a-kramer/SBtabVFGEN

  SBtab (.tsv or .ods) -> VFGEN (.vf) + SBML (.xml) + Neuron (.mod)