Topic: metabolic-models Goto Github
Some thing interesting about metabolic-models
Some thing interesting about metabolic-models
metabolic-models,Python wrapper for the DIMEdb REST API.
Organization: aberystwythsystemsbiology
metabolic-models,From annotated genomes to metabolic screening in large scale microbiotas
Organization: aureme
Home Page: https://metage2metabo.readthedocs.io
metabolic-models, DeltaFBA is a set of MATLAB functions that employs constraint-based modeling, in combination with differential gene expression data, to evaluate changes in the intracellular flux distribution between two conditions.
Organization: cabsel
metabolic-models,Reconstruct and handle many genome-scale metabolic models in ScrumPy
User: caileancarter
metabolic-models,MMODES (Metabolic Models based Ordinary Differential Equations Simulation)
User: carrascomj
Home Page: https://mmodes.readthedocs.io/
metabolic-models,SMETANA: a tool to analyse interactions in microbial communities
User: cdanielmachado
metabolic-models,Genome-scale metabolic model of Methylococcus capsulatus.
User: christianlieven
metabolic-models,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!
Organization: cnapy-org
Home Page: https://cnapy-org.github.io/CNApy-guide/
metabolic-models,:world_map: A repository of CNApy projects
Organization: cnapy-org
metabolic-models,findCP CLI package - find ChokePoint reactions in genome-scale metabolic models
Organization: findcp
Home Page: https://findcpcli.readthedocs.io/en/latest/
metabolic-models,: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
User: franciscozorrilla
Home Page: https://franciscozorrilla.github.io/metaGEM/
metabolic-models,Materials and presentation for the 2022 ISB Microbiome course.
Organization: gibbons-lab
Home Page: https://isbscience.org/microbiome2022/
metabolic-models,Materials and presentation for the 2023 ISB Microbiome course.
Organization: gibbons-lab
Home Page: https://isbscience.org/microbiome2023
metabolic-models,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.
Organization: gibbslab
metabolic-models,MicrobeRX
Organization: groningen-microbiome-centre
Home Page: https://microberx.readthedocs.io
metabolic-models,Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data
User: jclachance
metabolic-models,Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
User: jotech
metabolic-models,Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method
Organization: klamt-lab
metabolic-models,Create stoichiometric metabolic network models of single-species or multi-species communities
Organization: klamt-lab
metabolic-models,Python implementation of mgpipe
Organization: korem-lab
Home Page: https://korem-lab.github.io/pymgpipe/
metabolic-models,R package to Import and Modify SVG (XML) Graphic Files
User: m-jahn
metabolic-models,Dynamically load balanced FVA through a hybrid MPI/OpenMP architecture.
User: marouenbg
metabolic-models,KEGG Module Evaluation Tool
User: matteopaluh
metabolic-models,Toolkit for Modelling and Simulation of Gene Expressions and Metabolism
User: mauriceling
Home Page: https://github.com/mauriceling/advancesyntoolkit/wiki
metabolic-models,Open source genome-scale metabolic models of human and model animals
Organization: metabolicatlas
Home Page: https://metabolicatlas.org
metabolic-models,Kinetic modeling of glucose and acetate metabolisms in E. coli
Organization: metasys-lisbp
Home Page: https://elifesciences.org/articles/63661
metabolic-models,Estimation of extracellular fluxes and growth rate
Organization: metasys-lisbp
Home Page: https://physiofit.readthedocs.io
metabolic-models,Environmental growth media for MICOM.
Organization: micom-dev
metabolic-models,Python package to study microbial communities using metabolic modeling.
Organization: micom-dev
Home Page: https://micom-dev.github.io/micom
metabolic-models,A Qiime plugin for MICOM.
Organization: micom-dev
Home Page: https://micom-dev.github.io/q2-micom
metabolic-models,A python library for programmatic usage of EBI InterPro Genome Properties.
Organization: micromeda
Home Page: http://pygenprop.rtfd.io/
metabolic-models,A Universal Modeling Language for Metabolic Flux Analysis
Organization: modsim
metabolic-models,Repository of tutorials for The COBRA Toolbox
Organization: opencobra
Home Page: https://git.io/COBRA.tutorials
metabolic-models,COBRApy is a package for constraint-based modeling of metabolic networks.
Organization: opencobra
Home Page: http://opencobra.github.io/cobrapy/
metabolic-models,The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
Organization: opencobra
Home Page: https://opencobra.github.io/cobratoolbox
metabolic-models,memote – the genome-scale metabolic model test suite
Organization: opencobra
Home Page: https://memote.readthedocs.io/
metabolic-models,Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models
User: rcolpo
Home Page: https://pgprec.bioinf.uni-leipzig.de/
metabolic-models,An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Organization: resendislab
Home Page: http://resendislab.github.io/corda
metabolic-models,A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Organization: sbrg
metabolic-models,Minimal Supplying Community Search with constraint-based optimization methods.
User: sirno
metabolic-models,epigenome scale metabolic modeling for cancer metabolism
Organization: sriram-lab
metabolic-models,A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism
Organization: sysbiochalmers
metabolic-models,The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
Organization: sysbiochalmers
Home Page: http://sysbiochalmers.github.io/RAVEN/
metabolic-models,Genome-scale model of Yarrowia lipolytica.
Organization: sysbiochalmers
Home Page: http://www.nature.com/articles/npjsba20165
metabolic-models,The consensus GEM for Saccharomyces cerevisiae
Organization: sysbiochalmers
Home Page: http://sysbiochalmers.github.io/yeast-GEM/
metabolic-models,Container of computational models of metabolism for different yeast species.
Organization: sysbiochalmers
metabolic-models,Infer metabolic directions from moment differences of mass-weighted intensity distributions
User: tubanlee
Home Page: https://doi.org/10.5281/zenodo.10616979
metabolic-models,The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.
Organization: virtualmetabolichuman
Home Page: http://virtualgut.org
metabolic-models,An R library for conducting analyses on COMPASS data.
Organization: yoseflab
metabolic-models,Curation and analysis of metabolic models
Organization: zhanglab
Home Page: https://zhanglab.github.io/psamm/
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