metabolic-reconstruction

There are 29 repositories under metabolic-reconstruction topic.

  • opencobra/cobratoolbox

    The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

    Language:MATLAB23934290304

  • jotech/gapseq

    Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

    Language:R145918729

  • opencobra/memote

    memote – the genome-scale metabolic model test suite

    Language:HTML1222046726

  • SysBioChalmers/RAVEN

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

    Language:MATLAB971413052
  • 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:Python4232227

  • raeslab/omixer-rpm

    A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.

    Language:Java244108

  • Matteopaluh/KEMET

    KEGG Module Evaluation Tool

    Language:Python233155

  • resendislab/corda

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

    Language:Python216148

  • raeslab/GMMs

    A manually curated database of human gut metabolic modules.

    15335

  • ChristianLieven/memote-m-capsulatus

    Genome-scale metabolic model of Methylococcus capsulatus.

    Language:HTML11333

  • bioasp/meneco

    :m: Metabolic network completion

    Language:Jupyter Notebook910129

  • omixer/omixer-rpmR

    An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles

    Language:R9265

  • SysBioChalmers/Yarrowia_lipolytica_W29-GEM

    Genome-scale model of Yarrowia lipolytica.

    Language:MATLAB85148

  • korem-lab/pymgpipe

    Python implementation of mgpipe

    Language:JetBrains MPS6230

  • MetExplore/dexom

    Diversity-based enumeration of optimal context-specific metabolic networks

    Language:MATLAB5631

  • GioStamoulos/PLFG-Toolkit

    A pathologic file generator (PLFG) is implemented to assist and facilitate the curation progress of every computationally predicted pathway genome database (PGDB).

    Language:Python4100

  • HassounLab/ELP

    Enzymatic Link Prediction

    Language:Python4400

  • sriram-lab/egem

    epigenome scale metabolic modeling for cancer metabolism

    Language:MATLAB41212

  • franciscozorrilla/systems-biology-fba-practical

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

    Language:HTML31

  • dbkgroup/reaction-balancer

    Chemical reaction balancing web service

    Language:Python2210

  • cfrioux/fluto

    Language:Python1421

  • earmingol/cobra_utils

    Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.

    Language:Jupyter Notebook1201
  • MNXref

    MetaNetX/MNXref

    MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks

    1300

  • r2rahul/sybilMosek

    A RMosek optimization interface for the Sybil package

    Language:R1100

  • SysBioChalmers/rhto-GEM

    Genome-scale metabolic model of Rhodotorula toruloides

    Language:MATLAB1352

  • JorgeACGomes/TSM-Rec

    Tool for the reconstruction of context-specific metabolic models based on omics data from several sources

    Language:Python0001

  • MariaPessoa/thesis_annexes

    Software developed and main results obtained in the Master dissertation: A model validation pipeline for healthy tissue genome-scale metabolic models. Dissertation link to be added.

    Language:Jupyter Notebook0100

  • hallamlab/chap

    CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)

    Language:Python501

  • hallamlab/triUMPF

    Metabolic pathway inference using non-negative matrix factorization with community detection

    Language:Python421