metabolism

There are 6 repositories under metabolism 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 442
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
metagenomics computational-biology metabolic-models gut-microbiome snakemake metagenome-assembled-genomes mags metabolism bioinformatics flux-balance-analysis genome-scale-metabolic-model metabolic-modeling microbial-ecology microbiome systems-biology
Language:Python 165
cdanielmachado / carveme
CarveMe: genome-scale metabolic model reconstruction
genome-scale metabolism modeling python reconstruction
Language:Python 137
changwn / scFEA
single cell Flux Estimation Analysis (scFEA) Try the below web server!
metabolic-modules metabolism scrna-seq single-cell
Language:Jupyter Notebook 80
cdanielmachado / reframed
ReFramed: metabolic modeling package
metabolism modeling python
Language:Python 51
Metaboverse / Metaboverse
Visualization and analysis platform for metabolic data and network pattern recognition
chemical d3 metabolism metabolomics network networkx pattern-recognition proteomics reaction sequencing
Language:JavaScript 38
biosustain / shu
Multi-dimensional, trans-omics metabolic maps.
metabolism systems-biology visualization
Language:Rust 35
SBRG / cobrame
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
cobra python metabolic-models systems-biology cobrapy gene-expression metabolism computational-biology
Language:Python 32
cdanielmachado / framed
framed: a metabolic modeling package for python
metabolism modeling python
Language:Python 26
cdanielmachado / embl_gems
EMBL GEMs: A collection of GEnome-scale Models for bacterial species
constraint-based-modeling genome-scale-models metabolism
24
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 21
adalbertobrant / metabolismobasal
Simple metabolic calculator to weight loss
calculator metabolism javascript css html5 hacktoberfest gimme-stars
Language:HTML 20
m-jahn / fluctuator
R package to Import and Modify SVG (XML) Graphic Files
r-package svg svg-images network metabolism metabolic-models omics-data
Language:R 20
MetabolicAtlas
MetabolicAtlas / MetabolicAtlas
Open source genome-scale metabolic models of human and model animals
atlas metabolic-atlas metabolic-models metabolic-network metabolism nbisweden
Language:Vue 18
OSS-Lab / MetQy
Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)
r-package kegg metabolism data-mining
Language:R 18
BRENDApyrser
Robaina / BRENDApyrser
A Python parser for the BRENDA database
biochemistry brenda computational-biology metabolism bioinformatics enzyme enzyme-kinetics python
Language:Python 17
Knowledge-Graph-Hub / kg-microbe
knowledge-graph anatomical-knowledge chebi chemicals environments envo go media metabolism microbiology phenotypes traits cell-shapes ncbitaxonomy data-modeling named-entity-recognition nlp oaklib robot
Language:Jupyter Notebook 14
SCMeTA / SCMeTA
A python library for single-cell metabolism data analysis.
data-science metabolism single-cell
Language:Python 12
franciscozorrilla / SymbNET
Teaching materials for SymbNET course: from MAGs to GEMs
metabolic modeling genome models metagenome assembled genomes symbnet metagem metabolism
Language:Jupyter Notebook 11
MetExplore / miom
Constraint-based modeling of metabolism using Mixed Integer Optimization
cobrapy constraint-based-modeling flux-balance-analysis genome-scale metabolism milp modeling optimization python reconstruction
Language:Python 11
rcolpo / pgp_reconstruction
Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models
bioinformatics community-simulations computational-biology fba flux-balance-analysis genome-scale-metabolic-model genome-scale-model metabolic-modeling metabolic-models metabolism microbial-communities
Language:Python 11
cdanielmachado / cooccurrence
Supplementary data for co-occurrence manuscript
co-occurrence genome-scale-models metabolism microbial-communities supplementary-data
Language:Jupyter Notebook 10
ChristianLieven / memote-m-capsulatus
Genome-scale metabolic model of Methylococcus capsulatus.
genome-scale-models systems-biology methylococcus methanotrophy c1 metabolism constraint-based-modeling metabolic-models metabolic-reconstruction
Language:HTML 10
openalea-incubator / WheatFspm
WheatFspm is a Functional Structural Plant Model (FSPM) of wheat based on an innovative modelling framework for a better understanding of grass morphogenesis and C-N economy in interaction with environmental conditions.
fspm grass wheat morphogenesis metabolism openalea
Language:Python 10
Micromeda / pygenprop
A python library for programmatic usage of EBI InterPro Genome Properties.
genomics genome-properties metabolism metabolic-models pathway-analysis
Language:Python 9
mjenior / riptide
Reaction Inclusion by Parsimony and Transcript Distribution
cobrapy transcriptomics metabolism pfba flux-sampling flux-variability opencobra
Language:Python 9
SysBioChalmers / ecModels
A container for all enzyme constrained models created by GECKO.
systems-biology genome-scale-models metabolism kinetics
Language:MATLAB 9
biosustain / multitfa
Multivariate thermodynamics-based metabolic flux analysis in Python.
python3 cobrapy tmfa tfa fba multivariate thermodynamics multitfa metabolism
Language:Python 8
jbpauly / fasting
A Python package to interact with fasting logs from apps like Zero.
fasting metabolism metabolic-health python jupyter pytest biomarkers
Language:Python 8
draeger-lab / SBMLme
Encoding ME models in SBML
metabolism gene-expression modeling systems-biology sbml sbol encoding
Language:Java 7
jrcramos / Hybrid-modeling-of-bioreactor-with-LSTM
Deep hybrid modeling of bioreactor cell culture data using Long Short-Term Memory (LSTM) networks combined with first principles equations
bioreactors cell cultures deep-learning digital-twin hybrid-modeling mathematical-modelling neural-networks bioprocess metabolism
Language:MATLAB 7
yaoguangluo / ChromosomeDNA
《DNA元基催化与肽计算》在进化计算中, 软件函数文件进行 DNA 语义元基索引编码的 PDE 新陈代谢优化方式, 是一种有效的进化方式.
dnn big-data-analytics shell-script plsql dataswap prediction vision database etl-pipeline sorting-algorithms data-science dna word-segmentation nerotechnology vpcs-rest search-engine metabolism catalyst
Language:Java 7
DenisTitovLab / Glycolysis.jl
Package for modeling glycolysis activity
metabolism modeling ode-model systems-biology
Language:Julia 6
MetaSys-LISBP / PhysioFit
Estimation of extracellular fluxes and growth rate
metabolism metabolic-flux-analysis exometabolome extracellular-fluxes exchange-fluxes metabolic-models systems-biology fluxomics mass-spectrometry nuclear-magnetic-resonance isotope-labeling-experiments
Language:Python 6
pub-calculator-io / bmr-calculator
Free WordPress Plugin: Free BMR calculator uses well-known algorithms to calculate the basal metabolic rate. Also, find out more about the factors that influence BMR. www.calculator.io/bmr-calculator/
basal-metabolic-rate bmr bmr-calculator calculator calculator-plugin online-calculator plugin wordpress wordpress-plugin basal-metabolic-rate-calculator basalmetabolicrate basal-rate-calculation metabolic-rate metabolism
Language:JavaScript 6
opentecr / opentecr
contains general information about the openTECR database
opentecr thermodynamics database enzymes metabolism
5