metabolic-network

There are 5 repositories under metabolic-network topic.

opencobra / cobrapy
COBRApy is a package for constraint-based modeling of metabolic networks.
modeling metabolic-models metabolic-network metabolism flux bioinformatics biochemistry computational-biology systems-biology cell-design strain-engineering python cobra sbml sbml-model sbml-simulation
Language:Python 456
20n / act
Computational synthetic biology: Predicting DNA edits for bioengineering
synthetic-biology deep-learning bioengineering data-mining computational-synthetic-biology fermentation acetaminophen biochemistry reaction-operators enzyme-function metabolic-network metabolic-engineering
Language:Java 81
tubanlee / MM
Infer metabolic directions from moment differences of mass-weighted intensity distributions
annotations mass-spectra mass-spectrometry mass-spectrometry-data mass-spectrum metabolic-flux-analysis metabolic-models metabolic-network metabolic-networks metabolic-pathways metabolic-engineering metabolomics moment moments
Language:R 60
GeomScale / dingo
A python library for metabolic networks sampling and analysis
sampling metabolic-network polytope random-walk systems-biology hacktoberfest
Language:Python 42
namin / biohacker
debugging biological networks to reach coherence, completeness and consistency
metabolic-network common-lisp ai reasoning expert-system ncats-translator truth-maintenance
Language:Common Lisp 42
zhanglab / psamm
Curation and analysis of metabolic models
python metabolic-models bioinformatics metabolic-network
Language:Python 34
bebop / ark
Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL
api blast chembl genbank metabolic-engineering metabolic-network metabolic-pathways metabolomics rest-api rhea uniprot
Language:Go 22
resendislab / corda
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
metabolism reconstruction cobra cobrapy modeling metabolic-models flux biochemistry systems-biology genome bioinformatics metabolic-network metabolic-reconstruction
Language:Python 22
MetabolicAtlas
MetabolicAtlas / MetabolicAtlas
Open source genome-scale metabolic models of human and model animals
metabolism metabolic-models metabolic-network atlas metabolic-atlas nbisweden
Language:Vue 19
AuReMe / mpwt
Pathway Tools multiprocessing wrapper (for PathoLogic).
metabolic-network multiprocessing pathway-tools
Language:Python 12
modsim / FluxML
A Universal Modeling Language for Metabolic Flux Analysis
metabolic-engineering metabolic-models metabolic-network modeling-language specification-language metabolic-flux-analysis 13c-mfa
Language:C++ 9
barupal / metamapp
R codes for creating metamapp graphs and files
metabolomics bioinformatics metabolic-network
Language:JavaScript 8
SysBioChalmers / Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.
yarrowia-lipolytica metabolic-engineering metabolic-reconstruction systems-biology stoichiometric-reactions omics-data-integration constraint-based-modeling metabolic-models metabolic-network genome-scale-models
Language:MATLAB 8
htpusa / moomin
MOOMIN is a tool for analysing differential expression data
metabolic-network gene-expression differential-expression constraint-based-modeling matlab moomin
Language:MATLAB 7
cnapy-org / CNApy-projects
:world_map: A repository of CNApy projects
computational-biology-datasets stoichiometric-modeling metabolic-models metabolic-network
Language:Tcl 6
MetEvolSim
charlesrocabert / MetEvolSim
MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.
metabolic-abundances systems-biology metabolic-network evolution sbml copasi simulation metabolome biochemical-networks
Language:Python 5
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.
bioinformatics fill-gaps gap metabolic-network metabolism reactions stoichiometric-reactions
Language:R 5
MetaSys-LISBP / acetate_regulation
Kinetic modeling of glucose and acetate metabolisms in E. coli
systems-biology metabolic-models metabolic-flux-analysis isotope-labeling-experiments 13c-fluxomics metabolomics escherichia-coli fluxomics dynamical-systems dynamical-modeling kinetic-modeling regulation metabolic-control copasi acetate-overflow metabolism metabolic-network
Language:Component Pascal 5
MetExplore / dexom
Diversity-based enumeration of optimal context-specific metabolic networks
metabolic-network metabolic-reconstruction metabolic-engineering metabolic-pathways metabolism constraint-based-modeling optimization cobra-toolbox omics-data-integration
Language:MATLAB 5
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.
metabolic-regulatory-model knock-out-phenotype-prediction knock-out-flux-prediction bayesian-network metabolic-network genome-scale-models flux-balance-analysis transcriptional-regulations
Language:MATLAB 5
AuReMe / padmet
Python library for hAndling metaData of METabolism.
metabolic-network
Language:Python 4
BeeAnka / EFMlrs
Python package and workflow for EFM calculation via (mp)lrs and efmtool
cobrapy mplrs efmtool lexicographic-reverse-search systems-biology computational-biology biochemistry bioinformatics metabolism metabolic-network metabolic-models python sbml sbml-model flux elementary-flux-modes
Language:Python 4
HassounLab / ELP
Enzymatic Link Prediction
machine-learning bioinformatics enzyme-function metabolic-network metabolic-reconstruction metabolic-engineering
Language:Python 4
Angione-Lab / Synechococcus7002-metabolic-modelling
Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002
machine-learning cyanobacteria flux-balance-analysis metabolic-network multiobjective-optimization multiomics
Language:MATLAB 3
findCP / findCPcli
findCP CLI package - find ChokePoint reactions in genome-scale metabolic models
metabolic-models metabolic-network chokepoint sbml cobrapy modelling metabolism genome-scale dead-end fva
Language:Python 3
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.
bioinformatics fba-fluxes flux-balance-analysis gene-expression metabolic-models metabolic-network metabolism
Language:R 3
klamt-lab / CommModelPy
Create stoichiometric metabolic network models of single-species or multi-species communities
bioinformatics systems-biology metabolic-models metabolic-network computational-biology
Language:Python 3
Waschina / Eutropia
Agent-based metabolic modelling of microbial communities in time and continuous µ-meter-scale space
metabolic-models metabolic-network agent-based-simulation microbiome ecology-modelling
Language:R 3
binfalse / GEMtractor
Trim, extract, and convert GEMs
trim extract genome-scale-models metabolic-network filtering sbml subnetwork graphml gml dot csv enzyme phenotype
Language:Python 2
bioasp / precursor
Compute minimal metabolic precursors sets that enable the production of target metabolites
metabolic-network
Language:Python 2
CompBtBs / FalseDiscoveriesAnalysis
Adjusting for false discoveries in constraint- and sampling-based differential metabolic flux analysis
biomedical-informatics biotechnology cobrapy flux-analysis flux-balance-analysis metabolic-models metabolic-network
Language:Jupyter Notebook 2
dbkgroup / reaction-balancer
Chemical reaction balancing web service
systems-biology chemistry cheminformatics metabolic-models metabolic-network metabolic-reconstruction metabolic-engineering bioinformatics python web-service microservice
Language:Python 2
findCP / findCPcore
findCP core package - find ChokePoint reactions in genome-scale metabolic models
metabolic-models metabolic-network cobrapy smbl chokepoint dead-end fva
Language:HTML 1
LCSB-BioCore / CuFluxSampler.jl
GPU-accelerated algorithms for flux sampling in CUDA.jl
cobra cuda gpu julia metabolic-network metabolism sampling
Language:Julia 1
r2rahul / sybilMosek
A RMosek optimization interface for the Sybil package
fba r mosek rmosek cobra flux-balance-analysis mosek-solver sybil constraint-based-modeling metabolic-engineering metabolic-reconstruction metabolic-network
Language:R 1
WalhoutLab / MERGE
A new computational pipeline that can be used to convert expression (RNA-seq) data into predicted flux potentials that indicate metabolic function
fba metabolic-network expression
Language:MATLAB 1