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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.

GitHub: https://github.com/topics/sbml
Wikipedia: https://en.wikipedia.org/wiki/SBML
Repo: https://github.com/sbmlteam
Released: March 2001
Related Topics: xml, systems-biology, computational-biology,
Last updated: 2024-12-06 00:20:54 UTC
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https://github.com/sorgerlab/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, produce causal graphs and dynamical models.

bioinformatics biology computational-biology indra modeling nlp pysb sbml systems-biology

Last synced: 25 Jan 2025

https://github.com/AMICI-dev/AMICI

Advanced Multilanguage Interface to CVODES and IDAS

adjoint-sensitivities cvode cvodes differentialequations forward-sensitivities hacktoberfest idas kinetic-modeling mechanistic-models modeling ode parameter-estimation petab pysb python sbml sensitivities sensitivity-analysis simulation systemsbiology

Last synced: 13 Nov 2024

https://github.com/sciml/sbmltoolkit.jl

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

chemical-reaction-networks differential-equations gillespie-algorithm julia ode quantitative-systems-pharmacology sbml sciml systems-biology

Last synced: 10 Jan 2025

https://github.com/matthiaskoenig/sbmlutils

Python utilities for SBML

python sbml

Last synced: 20 Jan 2025

https://github.com/lcsb-biocore/sbml.jl

Julia interface to the Systems Biology Markup Language (SBML) library

cobra libsbml modeling sbml systems-biology

Last synced: 02 Dec 2024

https://github.com/lolab-msm/pyvipr

Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML

bionetgen cytoscapejs jupyter-widget jupyterlab-extension network-visualization networkx pysb sbgn sbml systems-biology tellurium visualization

Last synced: 13 Oct 2024

https://github.com/LoLab-MSM/pyvipr

Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML

bionetgen cytoscapejs jupyter-widget jupyterlab-extension network-visualization networkx pysb sbgn sbml systems-biology tellurium visualization

Last synced: 11 Oct 2024

https://github.com/matthiaskoenig/cy3sbml

cy3sbml: SBML for Cytoscape 3

cytoscape graphs sbml systems-biology visualization

Last synced: 09 Nov 2024

https://github.com/matthiaskoenig/dfba

Encoding Dynamic Flux Balance Analysis in SBML

dfba sbml simulation

Last synced: 04 Jan 2025

https://github.com/neuroml/org.neuroml.export

Export from NeuroML & LEMS

brian lems neuroml neuron pynn sbml

Last synced: 13 Dec 2024

https://github.com/carrascomj/rust_sbml

SBML parser + bindings to python

bioinformatics parser sbml

Last synced: 05 Nov 2024

https://github.com/matthiaskoenig/fbc_curation

FROG analysis in python for the reproducibility of FBC models

fbc fva sbml

Last synced: 09 Nov 2024

https://github.com/EBI-BioModels/SBO

The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling.

biosimulators computational-biology mathematical-modeling numerical-simulation obofoundry ontology sbml systems-biology

Last synced: 23 Oct 2024

https://github.com/lobolab/mergem

mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models

genome-scale-models sbml systems-biology

Last synced: 29 Nov 2024

https://github.com/spatialsimulator/XitoSBML

XitoSBML - the spatial SBML plugin for ImageJ

fiji imagej sbml spatial-sbml-plugin systems-biology

Last synced: 14 Nov 2024

https://github.com/paulflang/sbmlinterface.jl

Interface between the Systems Biology Markup Language and Julia

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

Last synced: 17 Oct 2024

https://github.com/paulflang/sbml2julia

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