metabolic-network

There are 62 repositories under metabolic-network topic.

  • opencobra/cobrapy

    COBRApy is a package for constraint-based modeling of metabolic networks.

    Language:Python47637675218

  • 20n/act

    Computational synthetic biology: Predicting DNA edits for bioengineering

    Language:Java8314126

  • johon-lituobang/MM

    Infer metabolic directions from moment differences of mass-weighted intensity distributions

    Language:R619015

  • GeomScale/dingo

    A python library for metabolic networks sampling and analysis

    Language:Python4563528

  • namin/biohacker

    debugging biological networks to reach coherence, completeness and consistency

    Language:Common Lisp44608

  • zhanglab/psamm

    Curation and analysis of metabolic models

    Language:Python34143915

  • resendislab/corda

    An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

    Language:Python246148

  • bebop/ark

    Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL

    Language:Go235556
  • MetabolicAtlas

    MetabolicAtlas/MetabolicAtlas

    Open source genome-scale metabolic models of human and model animals

    Language:Vue20104772

  • AuReMe/mpwt

    Pathway Tools multiprocessing wrapper (for PathoLogic).

    Language:Python155660

  • modsim/FluxML

    A Universal Modeling Language for Metabolic Flux Analysis

    Language:C++1011246

  • barupal/metamapp

    R codes for creating metamapp graphs and files

    Language:JavaScript8624

  • SysBioChalmers/Yarrowia_lipolytica_W29-GEM

    Genome-scale model of Yarrowia lipolytica.

    Language:MATLAB85148

  • htpusa/moomin

    MOOMIN is a tool for analysing differential expression data

    Language:MATLAB7000

  • MetaSys-LISBP/acetate_regulation

    Kinetic modeling of glucose and acetate metabolisms in E. coli

    Language:Component Pascal7202

  • cnapy-org/CNApy-projects

    :world_map: A repository of CNApy projects

    Language:Tcl6331

  • AuReMe/padmet

    Python library for hAndling metaData of METabolism.

    Language:Python5452
  • MetEvolSim

    charlesrocabert/MetEvolSim

    MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.

    Language:Python5200

  • gibbslab/g2f

    An R package to find the gaps in metabolic networks, and fill it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also include the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database.

    Language:R5513

  • HassounLab/ELP

    Enzymatic Link Prediction

    Language:Python5400

  • MetExplore/dexom

    Diversity-based enumeration of optimal context-specific metabolic networks

    Language:MATLAB5631

  • 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

  • BeeAnka/EFMlrs

    Python package and workflow for EFM calculation via (mp)lrs and efmtool

    Language:Python4411

  • Angione-Lab/Synechococcus7002-metabolic-modelling

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

    Language:MATLAB3312

  • findCP/findCPcli

    findCP CLI package - find ChokePoint reactions in genome-scale metabolic models

    Language:Python3100

  • 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

  • klamt-lab/CommModelPy

    Create stoichiometric metabolic network models of single-species or multi-species communities

    Language:Python3200

  • Waschina/Eutropia

    Agent-based metabolic modelling of microbial communities in time and continuous µ-meter-scale space

    Language:R3320

  • binfalse/GEMtractor

    Trim, extract, and convert GEMs

    Language:Python2303

  • bioasp/precursor

    Compute minimal metabolic precursors sets that enable the production of target metabolites

    Language:Python2300

  • CompBtBs/FalseDiscoveriesAnalysis

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

    Language:Jupyter Notebook2000

  • dbkgroup/reaction-balancer

    Chemical reaction balancing web service

    Language:Python2210

  • sysbiomics/aspergillus_model

    Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

    Language:MATLAB2100

  • eMetaboHUB/SBML2RDF

    SBML to RDF conversion

    Language:Java1100

  • LCSB-BioCore/CuFluxSampler.jl

    GPU-accelerated algorithms for flux sampling in CUDA.jl

    Language:Julia122

  • r2rahul/sybilMosek

    A RMosek optimization interface for the Sybil package

    Language:R1100