Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: constraint-based-modeling
SysBioChalmers/RAVEN
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
Language: MATLAB - Size: 1010 MB - Last synced: about 4 hours ago - Pushed: about 11 hours ago - Stars: 97 - Forks: 52
opencobra/cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
Language: MATLAB - Size: 1.02 GB - Last synced: about 6 hours ago - Pushed: about 6 hours ago - Stars: 237 - Forks: 302
LCSB-BioCore/COBREXA.jl
Constraint-Based Reconstruction and EXascale Analysis
Language: Julia - Size: 25.8 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 41 - Forks: 8
babessell1/MADRID Fork of HelikarLab/COMO
Metabolic Drug Repurposing Pipeline
Language: Python - Size: 733 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 4 - Forks: 0
xcsp3team/PyCSP3
A Python Library for modeling combinatorial constrained problems
Language: Python - Size: 204 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 56 - Forks: 7
xcsp3team/PyCSP3-models
Models (and data) of constrained problems developped with the library PyCSP3
Language: Python - Size: 15.7 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 6 - Forks: 0
SBRG/ssbio
A Python framework for structural systems biology
Language: Python - Size: 38.2 MB - Last synced: 9 days ago - Pushed: over 3 years ago - Stars: 101 - Forks: 28
opencobra/COBRA.jl
High-level, high-performance, constraint-based reconstruction and analysis in Julia
Language: Julia - Size: 11.3 MB - Last synced: 12 days ago - Pushed: about 1 year ago - Stars: 58 - Forks: 31
draeger-lab/pymCADRE
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
Language: Jupyter Notebook - Size: 37.5 MB - Last synced: 9 days ago - Pushed: about 1 month ago - Stars: 12 - Forks: 5
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!
Language: Python - Size: 6.92 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 39 - Forks: 7
SystemsBioinformatics/cbmpy
CBMPy is a Python based platform for constraint based modelling and analysis.
Language: Python - Size: 34.9 MB - Last synced: 28 days ago - Pushed: 6 months ago - Stars: 14 - Forks: 6
stelmo/Escher.jl
Visualization of metabolic models in Makie.
Language: Julia - Size: 5.73 MB - Last synced: 20 days ago - Pushed: 4 months ago - Stars: 16 - Forks: 1
surajsept/cyanoRBA
A coarse-grained biochemical resource allocation model of phototrophic growth.
Language: Python - Size: 3.46 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
draeger-lab/C_striatum_GEMs
This repository contains all changes made to the strain specific models of Corynebacterium striatum.
Language: HTML - Size: 67.5 MB - Last synced: 5 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0
pwendering/model-prm
Constraint-based modeling of photorespiratory mutants using metabolomics in TMFA
Language: MATLAB - Size: 204 MB - Last synced: 3 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0
r2rahul/sybilMosek
A RMosek optimization interface for the Sybil package
Language: R - Size: 277 KB - Last synced: 6 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0
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.
Language: HTML - Size: 237 MB - Last synced: 3 months ago - Pushed: 10 months ago - Stars: 20 - Forks: 12
sriram-lab/metabolicmodeling
Constraint-based metabolic modeling software from the Chandrasekaran Lab
Language: HTML - Size: 22.8 MB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 2 - Forks: 2
ThierryMondeel/Systems_Biology_FBA_tutorial
Python, modeling and Flux balance analysis tutorials for the undergraduate Systems Biology course in Amsterdam
Language: Jupyter Notebook - Size: 33.6 MB - Last synced: 6 months ago - Pushed: almost 5 years ago - Stars: 10 - Forks: 4
taketam/GridProd
Language: Matlab - Size: 1.6 MB - Last synced: 6 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0
Spherotob/gcOpt
Determination of product-growth-coupled strain designs employing stoichiometric metabolic models.
Language: MATLAB - Size: 45.9 KB - Last synced: 6 months ago - Pushed: over 4 years ago - Stars: 2 - Forks: 0
nirjarigandhi/Tetris-Constraint-Solving
Language: Python - Size: 191 KB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1
pwendering/RENZO_paper
Impose constraints on enzyme abundances ratios in enzyme-constraint metabolic models
Language: MATLAB - Size: 1.71 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 1 - Forks: 0
Lygeri-Sakellaridi/Evaluation-of-gap-filling-algorithms-for-genome-scale-metabolic-models
Msc thesis project. Evaluation of gap-filling tools for constraint-based, genome-scale models.
Language: Python - Size: 5.7 MB - Last synced: 8 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0
SysBioChalmers/Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.
Language: MATLAB - Size: 3.61 MB - Last synced: 6 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 7
cdanielmachado/embl_gems
EMBL GEMs: A collection of GEnome-scale Models for bacterial species
Size: 1.56 GB - Last synced: 9 months ago - Pushed: about 5 years ago - Stars: 23 - Forks: 9
LMSE/emilio Fork of shyamsrinivasan/emilio
Source code for EMILiO: A fast algorithm for genome-scale strain design.
Language: MATLAB - Size: 1.63 MB - Last synced: 9 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0
VonAlphaBisZulu/geneVa Fork of LMSE/move 📦
geneVa
Language: MATLAB - Size: 661 KB - Last synced: 9 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0
MetExplore/dexom-python
diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library
Language: Python - Size: 1.61 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 0
htpusa/moomin.jl
From differential gene expression to metabolic changes
Language: Julia - Size: 119 KB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1
htpusa/moomin
MOOMIN is a tool for analysing differential expression data
Language: MATLAB - Size: 95.7 KB - Last synced: 10 months ago - Pushed: almost 4 years ago - Stars: 7 - Forks: 0
rjrequina/Cebuano-POS-Tagger
Rule-Based Cebuano POS Tagger using Constraint-Based Grammar
Language: Jupyter Notebook - Size: 2.96 MB - Last synced: 24 days ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 5
marouenbg/VFFVA
Dynamically load balanced FVA through a hybrid MPI/OpenMP architecture.
Language: MATLAB - Size: 181 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 4 - Forks: 1
SysBioInra/rbatools
Programming interface to resource allocation modelling with the Resource Balance Analysis (RBA) method. This is version 1.0.3
Language: Python - Size: 5.03 MB - Last synced: 28 days ago - Pushed: 11 months ago - Stars: 2 - Forks: 2
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.
Language: Python - Size: 25.2 MB - Last synced: 12 months ago - Pushed: almost 2 years ago - Stars: 52 - Forks: 6
opencobra/COBRA.tutorials
Repository of tutorials for The COBRA Toolbox
Language: MATLAB - Size: 298 MB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 18 - Forks: 45
MetExplore/miom
Constraint-based modeling of metabolism using Mixed Integer Optimization
Language: Python - Size: 2.24 MB - Last synced: 26 days ago - Pushed: about 2 years ago - Stars: 11 - Forks: 2
sysbiolux/DCcov
Drug repositioning of single and drug combinations using Flux Balance Analysis.
Language: Jupyter Notebook - Size: 841 MB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 5 - Forks: 4
maranasgroup/iRhto_memote
Memote-created repository for Rhodosporidium toruloides model iRhto
Language: HTML - Size: 12.9 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 4
sandervandorsten/sudoku-csp-solver
Pretty awesome generic sudoku solver that is faster that you will ever be.
Language: Python - Size: 712 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 3
maranasgroup/iSace_GSM
Repository of a genome-scale metabolic model for Saccharomyces cerevisiae
Language: Jupyter Notebook - Size: 3.79 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 1
maranasgroup/scRBA
S. cerevisiae Resource Balance Analysis model
Language: GAMS - Size: 70.8 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
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.
Language: MATLAB - Size: 184 MB - Last synced: 5 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
SysBioChalmers/GECKO2_simulations
Collection of scripts for reproduction of simulation results in "Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0".
Language: MATLAB - Size: 17 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0
stelmo/eQuilibrator.jl
A lightweight interface to eQuilibrator and equilibrator_api through Julia.
Language: Julia - Size: 317 KB - Last synced: 3 days ago - Pushed: 4 months ago - Stars: 5 - Forks: 0
sriram-lab/emt-cobra
Modeling the metabolic changes during the epithelial-to-mesenchymal transition.
Language: HTML - Size: 78.1 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1
Biomathsys/DPM-SAU-in-HSA-nose
This repository introduces the codes applied to the nasal microbial community of the latest available curated GEMs of D. pigrum and S. aureus.
Language: Jupyter Notebook - Size: 3.35 MB - Last synced: 11 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
biosimulators/Biosimulators_COBRApy
COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
Language: Python - Size: 2.26 MB - Last synced: 27 days ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0
Biomathsys/ncmw Fork of manuelgloeckler/ncmw
A metabolic modeling workflow for communities of organisms in an nasal medium.
Language: Python - Size: 27.5 MB - Last synced: 11 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
maranasgroup/uncFBA
Language: Jupyter Notebook - Size: 5.18 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0
cnapy-org/optlang_enumerator
Language: Python - Size: 101 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 1
cnapy-org/efmtool_link
Language: Python - Size: 5.3 MB - Last synced: 6 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
NYXFLOWER/MeMo
Constraint-based metabolic modelling with sparse IPOPT
Language: Python - Size: 34.2 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
ChristianLieven/memote-m-capsulatus
Genome-scale metabolic model of Methylococcus capsulatus.
Language: HTML - Size: 14 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 7 - Forks: 2
MetExplore/dexom
Diversity-based enumeration of optimal context-specific metabolic networks
Language: MATLAB - Size: 2.32 MB - Last synced: 6 months ago - Pushed: almost 3 years ago - Stars: 5 - Forks: 1
sriram-lab/gemini
Integrating the transcriptional regulatory network with genome-scale metabolic models.
Language: MATLAB - Size: 23.3 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 1
SysBioChalmers/rhto-GEM
Genome-scale metabolic model of Rhodotorula toruloides
Language: MATLAB - Size: 22.7 MB - Last synced: 2 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 2
KB9/JindoshRiddleSolver
A constraint solver for Dishonored 2's Jindosh Riddle.
Language: JavaScript - Size: 3.32 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0
shyamsrinivasan/emilio
EMILiO
Language: Matlab - Size: 1.63 MB - Last synced: 11 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1