flux-balance-analysis

There are 58 repositories under flux-balance-analysis topic.

  • franciscozorrilla/metaGEM

    :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

    Language:Python189512041
  • 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!

    Language:Python4432257

  • 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:HTML2095413

  • 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 Notebook12345

  • MetExplore/miom

    Constraint-based modeling of metabolism using Mixed Integer Optimization

    Language:Python114172

  • rcolpo/pgp_reconstruction

    Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

    Language:Python11110

  • ThierryMondeel/Systems_Biology_FBA_tutorial

    Python, modeling and Flux balance analysis tutorials for the undergraduate Systems Biology course in Amsterdam

    Language:Jupyter Notebook11205

  • franciscozorrilla/EMBOMicroCom

    Metabolic modeling tutorial for EMBO practical course: Metabolite and species dynamics in microbial communities 2022

    Language:R10111

  • korem-lab/pymgpipe

    Python implementation of mgpipe

    Language:JetBrains MPS7230

  • brsynth/straindesign

    Library to perform metabolic engineering tasks

    Language:Python5130

  • niupuhua1234/TRIMER

    TRIMER is a package for building integrated metabolic–regulatory models base on Bayesian network. TRIMER can be used for knockout phenotype prediction and knock flux prediction.

    Language:MATLAB5101

  • marouenbg/VFFVA

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

    Language:MATLAB4211

  • Angione-Lab/Synechococcus7002-metabolic-modelling

    Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002

    Language:MATLAB3312

  • franciscozorrilla/systems-biology-fba-practical

    University of Cambridge Part III Systems Biology course, practical exercises for learning flux balance analysis

    Language:HTML3001

  • gibbslab/exp2flux

    An R package to incorporate in a continuous way the gene-expression data as FBA flux boundaries in a metabolic model. Also, functions to calculate and plot the differences between model fluxes in different metabolic scenarios was included. This is an implementation of the algorithm described by Lee et al. (2012) in DOI: 10.1186/1752-0509-6-73.

    Language:R3300

  • openCONTRABASS/CONTRABASS

    Constraint-based model vulnerabilities analysis - Python analysis tool http://contrabass.unizar.es

    Language:HTML3120
  • Biosimulators_COBRApy

    biosimulators/Biosimulators_COBRApy

    COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

    Language:Python2630

  • CompBtBs/FalseDiscoveriesAnalysis

    Adjusting for false discoveries in constraint- and sampling-based differential metabolic flux analysis

    Language:Jupyter Notebook2000

  • SysBioChalmers/KMG060-Systems-Biology-course

    KMG060 Systems Biology course - repo for students

    Language:MATLAB2337

  • ThierryMondeel/HCC_flux_balance_analysis

    Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines | Ewelina Węglarz-Tomczak, Thierry D.G.A. Mondeel, Diewertje G.E. Piebes, Hans V. Westerhoff | Biomolecules 2021

    Language:Jupyter Notebook2101
  • biosimulations-bigg

    biosimulations/biosimulations-bigg

    Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

    Language:Python11100

  • cfrioux/fluto

    Language:Python1421

  • draeger-lab/C_striatum_GEMs

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

    Language:HTML118

  • he-hai/PubSuppl

    A collection of supplementary script files of publications

    Language:Jupyter Notebook1101

  • juanvillada/iJV803

    iJV803: a genome-scale metabolic model for Methylomicrobium album BG8

    1100

  • LucoDevro/sequentialScanner

    A sequential gene scanner for both gene deletions and upregulations, based on flux balance analysis

    Language:MATLAB1111

  • maranasgroup/scRBA

    S. cerevisiae Resource Balance Analysis model

    Language:GAMS1402

  • maranasgroup/uncFBA

    Language:Jupyter Notebook1401

  • r2rahul/sybilMosek

    A RMosek optimization interface for the Sybil package

    Language:R1100

  • ScottCampit/dfa

    Fitting time-course metabolomics onto genome-scale metabolic models for inferring metabolic activity.

    Language:MATLAB1000

  • shyamsrinivasan/emilio

    EMILiO

    Language:Matlab1201

  • stolarczyk/metaboLITE

    Shiny app for visualization of the toy GENREs

    Language:R11311

  • sysbiomics/aspergillus_model

    Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

    Language:MATLAB1100

  • duartebred/fba-Flux-Balance-Analysis

    Repositório para apresentação de código e posterior análise, desenvolvido pelo grupo 1 para a UC Biologia de Sistemas, do Mestraddo em Bioinformática, ano lectivo 23-24.

    Language:Jupyter Notebook0100

  • ShwetaNagre/Masters_Thesis

    Investigating metabolic re-wiring in the children cohort using the Genome-Scale Metabolic (GEM) models by incorporating transcriptomics data.

    Language:R00

  • franciscozorrilla/EMBOMicroCom2

    Metabolic modeling tutorial for EMBO practical course: Metabolite and species dynamics in microbial communities 2024

    Language:HTML10