SBML | Ecosyste.ms: Awesome

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: 15 May 2025

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

High-performance sensitivity analysis for large ordinary differential equation models

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: 21 Oct 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: 04 May 2025

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: 06 May 2025

https://github.com/matthiaskoenig/sbmlutils

Python utilities for SBML

python sbml

Last synced: 06 Apr 2025

https://github.com/darrenjw/smfsb

Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology

gillespie-algorithm inference mcmc sbml systems-biology

Last synced: 21 Jun 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 Apr 2025

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: 28 Oct 2025

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: 10 Apr 2025

https://github.com/sbmlteam/sbml-test-suite

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.

ode sbml sbml-models simulation stochastic systems-biology test-automation testing testing-framework testing-tools

Last synced: 25 Dec 2025

https://github.com/matthiaskoenig/cy3sbml

cy3sbml: SBML for Cytoscape 3

cytoscape graphs sbml systems-biology visualization

Last synced: 13 May 2025

https://github.com/biosimulators/Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface

combine computational-biology docker kinetic-model kisao mathematical-model omex reproducibility reuse sbml sbo sed-ml simulation systems-biology

Last synced: 14 Oct 2025

https://github.com/sbmlteam/moccasin

MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.

conversion differential-equations matlab ode ode-model python sbml systems-biology

Last synced: 17 Dec 2025

https://github.com/matthiaskoenig/dfba

Encoding Dynamic Flux Balance Analysis in SBML

dfba sbml simulation

Last synced: 23 Feb 2025

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

Export from NeuroML & LEMS

brian lems neuroml neuron pynn sbml

Last synced: 28 Apr 2025

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: 11 Mar 2025

https://github.com/carrascomj/rust_sbml

SBML parser + bindings to python

bioinformatics parser sbml

Last synced: 06 Aug 2025

https://github.com/matthiaskoenig/fbc_curation

FROG analysis in python for the reproducibility of FBC models

fbc fva sbml

Last synced: 19 Oct 2025

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: 22 Jul 2025

https://github.com/spatialsimulator/XitoSBML

XitoSBML - the spatial SBML plugin for ImageJ

fiji imagej sbml spatial-sbml-plugin systems-biology

Last synced: 07 May 2025

https://github.com/sbmlteam/sbml-spatial-models

Repository of models to test exchange of sbml-spatial models.

sbml

Last synced: 25 Dec 2025

https://github.com/matthiaskoenig/sbmlsim

sbmlsim: SBML simulation made easy

sbml sbml-simulation

Last synced: 23 Feb 2025

https://github.com/sbmlteam/deviser

Design Explorer and Viewer for Iterative SBML Enhancement of Representations

automation code-generation code-generator libsbml python sbml systems-biology xml

Last synced: 25 Dec 2025

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

Last synced: 15 Apr 2025

https://github.com/brsynth/neo4jsbml

Bridge the gap between SBML data and Neo4j

bioinformatics neo4j sbml

Last synced: 16 Jan 2026

https://github.com/rivm-syso/euromix-to-sbml

Antimony/SBML re-implementation of the EuroMix Generic PBK model.

model pbk pbpk sbml

Last synced: 17 Jan 2026

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: 15 Apr 2025

https://github.com/darrenjw/dsmts

Discrete stochastic models test suite

sbml testing

Last synced: 21 Jun 2025

https://github.com/sbmlteam/sbmlpkgspec

A LaTeX document class providing a standard format for SBML Level 3 package specification documents.

documentation documents latex sbml

Last synced: 25 Dec 2025

https://github.com/gibbslab/minval

An R package to identify orphan metabolites and evaluate the mass and charge balance of stoichiometric reactions. The package also includes functions to characterize and write models in TSV and SBML formats, extract all reactants, products, metabolite names and compartments from a metabolic reconstruction.

bioinformatics charge-balance cran mass-balance metabolic-models metabolism minval sbml stoichiometric-reactions