SBML topic
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
COBRApy is a package for constraint-based modeling of metabolic networks.
indra
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, p...
AMICI
Advanced Multilanguage Interface to CVODES and IDAS
memote
memote – the genome-scale metabolic model test suite
smfsb
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
parPE
Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.
newt
A web application to visualize and edit pathway models
python-libsbml
Standalone Python package containing libSBML with support for SBML Level 3 Core and accepted SBML Level 3 packages.
jsbml
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...
SBMLToolkit.jl
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit