COBREXA/COBREXA.jl

COnstraint Based Reconstruction and EXascale Analysis (in Julia)

Language: Julia - Size: 8.77 MB - Last synced at: 3 days ago - Pushed at: about 1 month ago - Stars: 15 - Forks: 1

SysBioChalmers/RAVEN

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

Language: MATLAB - Size: 1010 MB - Last synced at: 7 days ago - Pushed at: 27 days ago - Stars: 112 - Forks: 56

opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Language: MATLAB - Size: 1.64 GB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 264 - Forks: 327

MetExplore/dexom-python

diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library

Language: Python - Size: 1.97 MB - Last synced at: about 10 hours ago - Pushed at: 18 days ago - Stars: 1 - Forks: 0

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: 6.78 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 54 - Forks: 8

xcsp3team/pycsp3

A Python Library for modeling combinatorial constrained problems

Language: Python - Size: 213 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 67 - Forks: 9

xcsp3team/PyCSP3-models

Models (and data) of constrained problems developped with the library PyCSP3

Language: Python - Size: 16.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 1

qwerty239qwe/pipeGEM

This is a package for visualizing and analyzing multiple metabolic models. It also allow users to integrate omic data, metabolic tasks, and medium data with genome-scale metabolic models (GEMs).

Language: Python - Size: 9.4 MB - Last synced at: 5 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

opencobra/COBRA.tutorials

Repository of tutorials for The COBRA Toolbox

Language: MATLAB - Size: 374 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 22 - Forks: 51

LCSB-BioCore/COBREXA.jl

Constraint-Based Reconstruction and EXascale Analysis

Language: Julia - Size: 25.8 MB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 44 - Forks: 9

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 at: 18 days ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 3

cnapy-org/efmtool_link

Language: Python - Size: 5.3 MB - Last synced at: 21 days ago - Pushed at: 3 months ago - Stars: 0 - 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 at: 1 day ago - Pushed at: 10 days ago - Stars: 22 - Forks: 18

MetExplore/dexom

Diversity-based enumeration of optimal context-specific metabolic networks

Language: MATLAB - Size: 2.32 MB - Last synced at: 2 months ago - Pushed at: almost 4 years ago - Stars: 6 - Forks: 1

stelmo/Escher.jl

Visualization of metabolic models in Makie.

Language: Julia - Size: 5.73 MB - Last synced at: 1 day ago - Pushed at: 4 months ago - Stars: 20 - Forks: 1

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: 138 MB - Last synced at: 2 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 2

SBRG/ssbio

A Python framework for structural systems biology

Language: Python - Size: 38.2 MB - Last synced at: 14 days ago - Pushed at: over 4 years ago - Stars: 107 - Forks: 28

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 at: 20 days ago - Pushed at: about 1 year ago - Stars: 13 - Forks: 6

SystemsBioinformatics/cbmpy

CBMPy is a Python based platform for constraint based modelling and analysis.

Language: Python - Size: 35.1 MB - Last synced at: 17 days ago - Pushed at: about 1 year ago - Stars: 19 - Forks: 5

sriram-lab/emt-cobra

Modeling the metabolic changes during the epithelial-to-mesenchymal transition.

Language: HTML - Size: 78.1 MB - Last synced at: 4 months ago - Pushed at: 6 months ago - Stars: 3 - Forks: 1

marouenbg/VFFVA

Dynamically load-balanced FVA through a hybrid MPI/OpenMP architecture.

Language: MATLAB - Size: 181 MB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 1

htpusa/moomin.jl

From differential gene expression to metabolic changes

Language: Julia - Size: 119 KB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 1

ChristianLieven/memote-m-capsulatus

Genome-scale metabolic model of Methylococcus capsulatus.

Language: HTML - Size: 14 MB - Last synced at: 3 months ago - Pushed at: about 6 years ago - Stars: 12 - Forks: 3

opencobra/COBRA.jl

High-level, high-performance, constraint-based reconstruction and analysis in Julia

Language: Julia - Size: 11.3 MB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 62 - Forks: 31

cnapy-org/optlang_enumerator

Language: Python - Size: 138 KB - Last synced at: 10 days ago - Pushed at: 8 months ago - Stars: 3 - Forks: 1

htpusa/moomin

MOOMIN is a tool for analysing differential expression data

Language: MATLAB - Size: 95.7 KB - Last synced at: 2 months ago - Pushed at: almost 5 years ago - Stars: 7 - Forks: 0

MetExplore/miom

Constraint-based modeling of metabolism using Mixed Integer Optimization

Language: Python - Size: 1020 KB - Last synced at: 2 days ago - Pushed at: 9 months ago - Stars: 11 - Forks: 2

james-pack/ludicrous_llama

Ludicrous Llama parametric CAD

Language: C++ - Size: 564 KB - Last synced at: 10 months ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

rjrequina/Cebuano-POS-Tagger

Rule-Based Cebuano POS Tagger using Constraint-Based Grammar

Language: Jupyter Notebook - Size: 2.96 MB - Last synced at: 10 months ago - Pushed at: about 7 years ago - Stars: 4 - Forks: 6

draeger-lab/C_striatum_GEMs

This repository contains all changes made to the strain specific models of Corynebacterium striatum.

Language: HTML - Size: 68.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

babessell1/MADRID Fork of HelikarLab/COMO

Metabolic Drug Repurposing Pipeline

Language: Python - Size: 733 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0

SysBioChalmers/Yarrowia_lipolytica_W29-GEM

Genome-scale model of Yarrowia lipolytica.

Language: MATLAB - Size: 3.61 MB - Last synced at: 2 months ago - Pushed at: almost 4 years ago - Stars: 8 - Forks: 8

surajsept/cyanoRBA

A coarse-grained biochemical resource allocation model of phototrophic growth.

Language: Python - Size: 3.46 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

pwendering/model-prm

Constraint-based modeling of photorespiratory mutants using metabolomics in TMFA

Language: MATLAB - Size: 204 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

r2rahul/sybilMosek

A RMosek optimization interface for the Sybil package

Language: R - Size: 277 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

sriram-lab/metabolicmodeling

Constraint-based metabolic modeling software from the Chandrasekaran Lab

Language: HTML - Size: 22.8 MB - Last synced at: over 1 year ago - Pushed at: over 4 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 at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 10 - Forks: 4

taketam/GridProd

Language: Matlab - Size: 1.6 MB - Last synced at: over 1 year ago - Pushed at: almost 7 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 at: over 1 year ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0

nirjarigandhi/Tetris-Constraint-Solving

Language: Python - Size: 191 KB - Last synced at: over 1 year ago - Pushed at: about 4 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 at: over 1 year ago - Pushed at: over 1 year 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 at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

cdanielmachado/embl_gems

EMBL GEMs: A collection of GEnome-scale Models for bacterial species

Size: 1.56 GB - Last synced at: almost 2 years ago - Pushed at: over 6 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 at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

VonAlphaBisZulu/geneVa Fork of LMSE/move 📦

geneVa

Language: MATLAB - Size: 661 KB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

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 at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 52 - Forks: 6

sysbiolux/DCcov

Drug repositioning of single and drug combinations using Flux Balance Analysis.

Language: Jupyter Notebook - Size: 841 MB - Last synced at: almost 2 years ago - Pushed at: over 3 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 at: about 2 years ago - Pushed at: over 2 years 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 at: over 2 years ago - Pushed at: over 9 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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

maranasgroup/scRBA

S. cerevisiae Resource Balance Analysis model

Language: GAMS - Size: 70.8 MB - Last synced at: about 2 years ago - Pushed at: about 2 years 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 at: 2 months ago - Pushed at: almost 3 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 at: about 1 month ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 0

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 at: about 2 years ago - Pushed at: almost 3 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 at: 14 days ago - Pushed at: over 3 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 at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

maranasgroup/uncFBA

Language: Jupyter Notebook - Size: 5.18 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

NYXFLOWER/MeMo

Constraint-based metabolic modelling with sparse IPOPT

Language: Python - Size: 34.2 KB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

sriram-lab/gemini

Integrating the transcriptional regulatory network with genome-scale metabolic models.

Language: MATLAB - Size: 23.3 MB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1

SysBioChalmers/rhto-GEM

Genome-scale metabolic model of Rhodotorula toruloides

Language: MATLAB - Size: 22.7 MB - Last synced at: 2 months ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 3

KB9/JindoshRiddleSolver

A constraint solver for Dishonored 2's Jindosh Riddle.

Language: JavaScript - Size: 3.32 MB - Last synced at: 6 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

shyamsrinivasan/emilio

EMILiO

Language: Matlab - Size: 1.63 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 1