constraint-based-modeling

There are 1 repository under constraint-based-modeling topic.

opencobra / cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
cobra cobra-toolbox constraint-based-modeling gap-filling human-metabolism metabolic-engineering metabolic-models metabolic-reconstruction metabolomics microbiome-analysis omics-data-integration reconstruction strain-engineering transcriptomics tutorial
Language:MATLAB 269
SysBioChalmers / RAVEN
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
constraint-based-modeling gap-filling genome-scale-models human-metabolism metabolic-engineering metabolic-models metabolic-reconstruction sysbio systems-biology
Language:MATLAB 117
SBRG / ssbio
A Python framework for structural systems biology
systems-biology protein-structure structural-biology constraint-based-modeling cobrapy structural-systems-biology
Language:Python 109
xcsp3team / pycsp3
A Python Library for modeling combinatorial constrained problems
modeling modeling-language modeling-tool constraint-based-modeling constraint-programming constraints python constrained-optimization constraint-satisfaction-problem library xcsp3 pycsp3
Language:Python 74
wanxinjin / Safe-PDP
Safe Pontryagin Differentiable Programming (Safe PDP) is a new theoretical and algorithmic safe differentiable framework to solve a broad class of safety-critical learning and control tasks.
safe-reinforcement-learning safe-control safety-critical safety-critical-systems constraint-programming constraint-based-modeling constrained-optimization constrained-reinforcement-learning constrained-learning differentiable-programming safe-planning robotics-control non-convex-optimization constraints safety-critical-learning optimization
Language:Python 71
opencobra / COBRA.jl
High-level, high-performance, constraint-based reconstruction and analysis in Julia
analysis cobra constraint-based-modeling high-level high-performance huge-scale julia large-scale
Language:Julia 62
CNApy
cnapy-org / CNApy
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!
metabolic-models constraint-programming bioinformatics flux-balance-analysis sbml systems-biology computational-biology cobra stoichiometric-modeling constraint-based-modeling constraint-based-analysis metabolic-reconstruction constraint-based-reconstruction metabolic-networks flux-variability metabolic-engineering fba fva
Language:Python 58
LCSB-BioCore / COBREXA.jl
Constraint-Based Reconstruction and EXascale Analysis
julia exascale high-performance hpc constraint-based-modeling cobra exascale-analysis
Language:Julia 44
cdanielmachado / embl_gems
EMBL GEMs: A collection of GEnome-scale Models for bacterial species
metabolism constraint-based-modeling genome-scale-models
29
draeger-lab / SBSCL
The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.
simulation sbml java flux-balance-analysis fba ordinary-differential-equations solver numerical-simulations ode-solver time-series-analysis sbml-model api library steady-state constraint-based-modeling linear-programming simulations systems-biology-simulation
Language:HTML 25
opencobra / COBRA.tutorials
Repository of tutorials for The COBRA Toolbox
tutorials cobra cobratoolbox systemsbiology reconstruction metabolic-models constraint-based-modeling
Language:MATLAB 23
stelmo / Escher.jl
Visualization of metabolic models in Makie.
cobra constraint-based-modeling julia visualization
Language:Julia 21
SystemsBioinformatics / cbmpy
CBMPy is a Python based platform for constraint based modelling and analysis.
constraint-based-modeling python sbml systems-biology console-application modelling-framework bioinformatics cbmpy
Language:Python 19
COBREXA / COBREXA.jl
COnstraint Based Reconstruction and EXascale Analysis (in Julia)
cobra constraint-based-modeling high-performance-computing hpc julia metabolic-engineering metabolic-models sbml sbml-simulation
Language:Julia 15
draeger-lab / pymCADRE
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
constraint-based-modeling flux-balance-analysis tissue-specific-models host-virus-model metabolic-network-reconstruction genome-scale-modeling python systems-biology-simulation sbml-model
Language:Jupyter Notebook 14
ThierryMondeel / Systems_Biology_FBA_tutorial
Python, modeling and Flux balance analysis tutorials for the undergraduate Systems Biology course in Amsterdam
flux-balance-analysis systems-biology constraint-based-modeling teaching-materials
Language:Jupyter Notebook 14
ChristianLieven / memote-m-capsulatus
Genome-scale metabolic model of Methylococcus capsulatus.
genome-scale-models systems-biology methylococcus methanotrophy c1 metabolism constraint-based-modeling metabolic-models metabolic-reconstruction
Language:HTML 12
MetExplore / miom
Constraint-based modeling of metabolism using Mixed Integer Optimization
python metabolism modeling reconstruction genome-scale optimization cobrapy flux-balance-analysis constraint-based-modeling milp
Language:Python 12
xcsp3team / PyCSP3-models
Models (and data) of constrained problems developped with the library PyCSP3
constrained-optimization constraint-based-modeling constraint-programming constraint-satisfaction-problem constraints data library modeling modeling-language models python xcsp3 pycsp3
Language:Python 11
SysBioChalmers / Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.
yarrowia-lipolytica metabolic-engineering metabolic-reconstruction systems-biology stoichiometric-reactions omics-data-integration constraint-based-modeling metabolic-models metabolic-network genome-scale-models
Language:MATLAB 10
htpusa / moomin
MOOMIN is a tool for analysing differential expression data
constraint-based-modeling differential-expression gene-expression matlab metabolic-network moomin
Language:MATLAB 7
MetExplore / dexom
Diversity-based enumeration of optimal context-specific metabolic networks
metabolic-network metabolic-reconstruction metabolic-engineering metabolic-pathways metabolism constraint-based-modeling optimization cobra-toolbox omics-data-integration
Language:MATLAB 7
rjrequina / Cebuano-POS-Tagger
Rule-Based Cebuano POS Tagger using Constraint-Based Grammar
cebuano-pos-tagger constraint-based-modeling natural-language-processing pos-tagger rule-based
Language:Jupyter Notebook 5
stelmo / eQuilibrator.jl
A lightweight interface to eQuilibrator and equilibrator_api through Julia.
equilibrator julia constraint-based-modeling thermodynamics
Language:Julia 5
babessell1 / MADRID
Metabolic Drug Repurposing Pipeline
metabolism omics-data omics-data-integration constraint-based-modeling transcriptomics proteomics pipeline drug-repurposing drug-discovery
Language:Python 4
htpusa / moomin.jl
From differential gene expression to metabolic changes
metabolic-models constraint-based-modeling gene-expression differential-expression transcriptomics
Language:Julia 4
marouenbg / VFFVA
Dynamically load-balanced FVA through a hybrid MPI/OpenMP architecture.
metabolic-models constraint-based-modeling flux-balance-analysis
Language:MATLAB 4
sriram-lab / emt-cobra
Modeling the metabolic changes during the epithelial-to-mesenchymal transition.
constraint-based-modeling omics-data-integration bioinformatics
Language:HTML 4
cnapy-org / optlang_enumerator
python constraint-based-modeling bioinformatics-algorithms computational-biology stoichiometric-modeling metabolic-engineering
Language:Python 3
Spherotob / gcOpt
Determination of product-growth-coupled strain designs employing stoichiometric metabolic models.
metabolic-engineering systems-biology constraint-based-modeling
Language:MATLAB 3
SysBioChalmers / CellFactory-ecYeastGEM
Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeastGEM model avaiable at ecModels.
cell-factory constraint-based-modeling enzyme-constraints yeast
Language:MATLAB 3
SysBioInra / rbatools
Programming interface to resource allocation modelling with the Resource Balance Analysis (RBA) method. This is version 1.0.3
bioinformatics biotechnology modeling python resource-allocation simulation systems-biology whole-cell-modeling genome-scale-models constraint-based-modeling
Language:Python 3
Biosimulators_COBRApy
biosimulators / Biosimulators_COBRApy
COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
cobrapy sbml sed-ml combine-archive flux-balance-analysis fba systems-biology computational-biology constraint-based-modeling biochemical-networks simulation omex-metadata docker biosimulators python
Language:Python 2
gbacpp
charlesrocabert / gbacpp
Growth Balance Analysis for C++
constraint-based-modeling metabolic-models non-linear-optimization systems-biology growth-balance-analysis
Language:Jupyter Notebook 2
pwendering / model-prm
Constraint-based modeling of photorespiratory mutants using metabolomics in TMFA
arabidopsis-thaliana constraint-based-modeling metabolic-models metabolomics thermodynamics tmfa photorespiration matlab
Language:MATLAB 2
pwendering / RENZO_paper
Impose constraints on enzyme abundances ratios in enzyme-constraint metabolic models
metabolic-models enzyme-constraints constraint-based-modeling metabolic-engineering proteomics
Language:MATLAB 2