SBML
SBML (the Systems Biology Markup Language) is an XML-based format for communicating and storing representations of biological processes. Its aim is to be a lingua franca for representing models in biology. SBML is suitable for models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others.
Here are 44 public repositories matching this topic...
MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.
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Dec 7, 2019 - Python
Trim, extract, and convert GEMs
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Jun 8, 2021 - Python
Python package for building SBML models without needing to use libSBML.
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Aug 18, 2021 - Python
findCP CLI package - find ChokePoint reactions in genome-scale metabolic models
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Oct 7, 2021 - Python
Summary of the technical documentation for BioSimulators
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Dec 14, 2021 - Python
CBMPy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
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Dec 14, 2021 - Python
BoolNet biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
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Dec 14, 2021 - Python
CBMPy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
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Feb 23, 2022 - Python
COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
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Feb 23, 2022 - Python
MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container
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Feb 23, 2022 - Python
GillesPy2 biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
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Feb 25, 2022 - Python
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.
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Mar 7, 2022 - Python
Python package and workflow for EFM calculation via (mp)lrs and efmtool
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Nov 9, 2022 - Python
A desktop app, web app and CLI to operate and find vulnerabilities in SBML metabolic networks.
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Dec 27, 2022 - Python