9 results found Sort:

opencobra
cobrapy opencobra
216
481
gpl-2.0
37
COBRApy is a package for constraint-based modeling of metabolic networks.
flux sbml cobra python modeling metabolism sbml-model cell-design biochemistry bioinformatics sbml-simulation systems-biology metabolic-models metabolic-network strain-engineering computational-biology
Created 2012-11-02
2,742 commits to devel branch, last one 24 days ago
sorgerlab
indra sorgerlab
68
182
bsd-2-clause
23
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...
nlp pysb sbml indra biology modeling bioinformatics systems-biology computational-biology
Created 2014-08-11
13,981 commits to master branch, last one 2 days ago
opencobra
memote opencobra
30
129
apache-2.0
20
memote – the genome-scale metabolic model test suite
sbml cobra unit-testing standardization metabolic-models metabolic-reconstruction
Created 2016-05-13
893 commits to develop branch, last one about a year ago
AMICI-dev
AMICI AMICI-dev
31
112
other
11
Advanced Multilanguage Interface to CVODES and IDAS
ode idas pysb sbml cvode petab cvodes python modeling simulation hacktoberfest sensitivities systemsbiology kinetic-modeling mechanistic-models parameter-estimation sensitivity-analysis adjoint-sensitivities differentialequations forward-sensitivities
Created 2015-10-05
4,036 commits to master branch, last one about a month ago
PEtab-dev
PEtab PEtab-dev
12
62
mit
18
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
sbml modelling sbml-model data-format hacktoberfest combine-archive systems-biology parameter-estimation
Created 2018-11-27
501 commits to main branch, last one about a month ago
iVis-at-Bilkent
newt iVis-at-Bilkent
26
54
lgpl-3.0
11
A web application to visualize and edit pathway models
sif newt sbgn sbml editor layout biology pathways celldesigner visualization bioinformatics pathway-models systems-biology pathway-analysis network-visualization web-based-visualization
Created 2017-01-24
1,758 commits to master branch, last one 5 months ago
cnapy-org
CNApy cnapy-org
7
50
apache-2.0
3
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, ...
fba fva sbml cobra bioinformatics systems-biology flux-variability metabolic-models metabolic-networks computational-biology flux-balance-analysis metabolic-engineering constraint-programming stoichiometric-modeling metabolic-reconstruction constraint-based-analysis constraint-based-modeling constraint-based-reconstruction
Created 2019-11-15
777 commits to master branch, last one 2 months ago
sbmlteam
libsbml sbmlteam
29
45
other
8
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, JavaSc...
api sbml library libsbml systems-biology
Created 2020-05-27
14,873 commits to development branch, last one 22 days ago
SciML
SBMLToolkit.jl SciML
10
40
mit
9
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
ode sbml julia sciml systems-biology gillespie-algorithm differential-equations chemical-reaction-networks quantitative-systems-pharmacology
Created 2021-06-16
520 commits to main branch, last one about a month ago