Skip to content

COBREXA/MATFBCModels.jl

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

44 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

MATFBCModels.jl -- Import and export of MatLab-formatted flux-balanced constrained models

Build status
CI codecov

This package defines an instance of the AbstractFBCModel interface (from the package AbstractFBCModels.jl) for models saved as MAT files (typically produced by cobratoolbox and RAVEN). This allows you to easily use the MAT formatted models in constraint-based modeling packages in Julia, and convert them to other constraint-based metabolic modeling data formats. MAT.jl is used for the lower-level work with MatLab data.

The primary purpose of this is to provide MAT model loading functionality for COBREXA.jl and FBCModelTests.jl, but is otherwise completely generic and can be used independently of these packages.

You should be able to load the .mat models (called MATFBCModel) via the AbstractFBCModels interface:

import AbstractFBCModels as M
import MATFBCModels

model = M.load("my_model.mat")

Documentation of AbstractFBCModels.jl provides details on the use of the loaded model.

Acknowledgements

MATFBCModels.jl was developed at the Luxembourg Centre for Systems Biomedicine of the University of Luxembourg (uni.lu/lcsb) and at Institute for Quantitative and Theoretical Biology at Heinrich Heine University Düsseldorf (qtb.hhu.de). The development was supported by European Union's Horizon 2020 Programme under PerMedCoE project (permedcoe.eu), agreement no. 951773.

Uni.lu logo   LCSB logo   HHU logo   QTB logo   PerMedCoE logo