SBML.jl

Julia interface to the Systems Biology Markup Language (SBML) library
Author LCSB-BioCore
Popularity
8 Stars
Updated Last
1 Year Ago
Started In
January 2021

SBML.jl

Build status Documentation
CI doc

This is a simple wrap of some of the libSBML functionality, mainly the model loading for purposes of COBRA analysis methods.

Other functionality will be added as needed. Feel free to submit a PR that increases the loading "coverage".

Acknowledgements

SBML.jl was developed at the Luxembourg Centre for Systems Biomedicine of the University of Luxembourg (uni.lu/lcsb). The development was supported by European Union's Horizon 2020 Programme under PerMedCoE project (permedcoe.eu) agreement no. 951773.

Uni.lu logo   LCSB logo   PerMedCoE logo

Installation

]add SBML # or
using Pkg; Pkg.add("SBML")

Usage

using SBML
m = readSBML("myModel.xml")

# m is now a Model structure with:
m.reactions
m.species
m.compartments
...

There are several helper functions, for example you can get a nice list of reactions, metabolites and the stoichiometric matrix as follows:

mets, rxns, S = getS(m)

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