COBRApy is a package for constraint-based modeling of metabolic networks.
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Updated
Apr 8, 2024 - Python
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.
COBRApy is a package for constraint-based modeling of metabolic networks.
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
Advanced Multilanguage Interface to CVODES and IDAS
LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.
memote – the genome-scale metabolic model test suite
A web application to visualize and edit pathway models
JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.
The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Python package for building SBML models without needing to use libSBML.
Julia interface to the Systems Biology Markup Language (SBML) library
A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.
A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
The official PySCeS project source code repository.