constraint-based-modeling
There are 64 repositories under constraint-based-modeling topic.
opencobra/cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
SysBioChalmers/RAVEN
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
SBRG/ssbio
A Python framework for structural systems biology
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.
xcsp3team/pycsp3
A Python Library for modeling combinatorial constrained problems
opencobra/COBRA.jl
High-level, high-performance, constraint-based reconstruction and analysis in Julia
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!
LCSB-BioCore/COBREXA.jl
Constraint-Based Reconstruction and EXascale Analysis
cdanielmachado/embl_gems
EMBL GEMs: A collection of GEnome-scale Models for bacterial species
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.
opencobra/COBRA.tutorials
Repository of tutorials for The COBRA Toolbox
stelmo/Escher.jl
Visualization of metabolic models in Makie.
SystemsBioinformatics/cbmpy
CBMPy is a Python based platform for constraint based modelling and analysis.
COBREXA/COBREXA.jl
COnstraint Based Reconstruction and EXascale Analysis (in Julia)
draeger-lab/pymCADRE
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
ThierryMondeel/Systems_Biology_FBA_tutorial
Python, modeling and Flux balance analysis tutorials for the undergraduate Systems Biology course in Amsterdam
ChristianLieven/memote-m-capsulatus
Genome-scale metabolic model of Methylococcus capsulatus.
MetExplore/miom
Constraint-based modeling of metabolism using Mixed Integer Optimization
SysBioChalmers/Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.
xcsp3team/PyCSP3-models
Models (and data) of constrained problems developped with the library PyCSP3
htpusa/moomin
MOOMIN is a tool for analysing differential expression data
MetExplore/dexom
Diversity-based enumeration of optimal context-specific metabolic networks
rjrequina/Cebuano-POS-Tagger
Rule-Based Cebuano POS Tagger using Constraint-Based Grammar
stelmo/eQuilibrator.jl
A lightweight interface to eQuilibrator and equilibrator_api through Julia.
babessell1/MADRID
Metabolic Drug Repurposing Pipeline
htpusa/moomin.jl
From differential gene expression to metabolic changes
marouenbg/VFFVA
Dynamically load-balanced FVA through a hybrid MPI/OpenMP architecture.
sriram-lab/emt-cobra
Modeling the metabolic changes during the epithelial-to-mesenchymal transition.
Spherotob/gcOpt
Determination of product-growth-coupled strain designs employing stoichiometric metabolic models.
SysBioInra/rbatools
Programming interface to resource allocation modelling with the Resource Balance Analysis (RBA) method. This is version 1.0.3
biosimulators/Biosimulators_COBRApy
COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
pwendering/model-prm
Constraint-based modeling of photorespiratory mutants using metabolomics in TMFA
pwendering/RENZO_paper
Impose constraints on enzyme abundances ratios in enzyme-constraint metabolic models
sriram-lab/metabolicmodeling
Constraint-based metabolic modeling software from the Chandrasekaran Lab
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.