COBRApy is a package for constraint-based modeling of metabolic networks.
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Updated
Sep 4, 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.
An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
The official PySCeS project source code repository.
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
CBMPy is a Python based platform for constraint based modelling and analysis.
Python package for working with PEtab files
Registry of containerized biosimulation tools that support a standard command-line interface
Python package for building SBML models without needing to use libSBML.
MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.
mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models
Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
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.
MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.
Python package and workflow for EFM calculation via (mp)lrs and efmtool