Projects

Updated 9 months ago

cobra • Rank 21.0 • Science 59%

COBRApy is a package for constraint-based modeling of metabolic networks.

biochemistry bioinformatics cell-design cobra computational-biology flux metabolic-models metabolic-network metabolism modeling python sbml sbml-model sbml-simulation strain-engineering systems-biology

Updated 9 months ago

sbml2julia • Rank 5.4 • Science 51%

A tool to for optimizing parameters of ordinary differential equation (ODE) models. SBML2Julia translates a model from SBML/PEtab format into Julia for Mathematical Programming (JuMP), performs the optimization task and returns the results.

julia modelling ode optimization ordinary-differential-equations sbml sbml-model systems-biology

Updated 9 months ago

jeweler • Science 67%

Test and grade genome-scale metabolic models (GEMs).

cobra gem gsmm memote nextflow nf-core sbml sbml-model

Updated 9 months ago

petab • Science 44%

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology

combine-archive data-format hacktoberfest modelling parameter-estimation sbml sbml-model systems-biology

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Open Source Science

cobra • Rank 21.0 • Science 59%

sbml2julia • Rank 5.4 • Science 51%

jeweler • Science 67%

petab • Science 44%