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metabolism

Here are 89 public repositories matching this topic...

opencobra / cobrapy

Open

cobra.test.create_test_model("salmonella") results in incorrect exchange reaction names

5

jeremymchacon commented Aug 25, 2020

Hello maintainers of the amazing package,

I recently updated cobrapy and am experienced unexpected behavior with cobra.test.create_test_model("salmonella")

Two things are unusual:

Now, many warnings are given during loading of the model, whereas none were given in a previous version. Here are a few of the warnings:

`Model does not contain SBML fbc package information.
SBML package

SBML help-wanted good first issue

Open

fix: avoid scrambling of group members

9

Open

Inconsistency in finding blocked reactions

5

Find more good first issues

cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction

python modeling metabolism reconstruction genome-scale

Updated Oct 25, 2021
Python

franciscozorrilla / metaGEM

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

bioinformatics snakemake computational-biology metagenomics microbial-communities metabolism metabolic-models gut-microbiome mags community-simulations metagenome-assembled-genomes

Updated Feb 22, 2022
Python

SBRG / cobrame

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

python systems-biology computational-biology gene-expression metabolism cobra cobrapy metabolic-models

Updated Jan 11, 2019
Python

changwn / scFEA

Open

Input types

8

Hrovatin commented Mar 29, 2021

Could you add some documentation on what kind of inputs/file formats the tool accepts, e.g. expanding descriptions in

python src/scFEA.py --help

documentation good first issue

cdanielmachado / reframed

ReFramed: metabolic modeling package

python modeling metabolism

Updated Dec 20, 2021
Python

cdanielmachado / framed

framed: a metabolic modeling package for python

python modeling metabolism

Updated Nov 7, 2019
Python

cdanielmachado / embl_gems

EMBL GEMs: A collection of GEnome-scale Models for bacterial species

metabolism constraint-based-modeling genome-scale-models

Updated Mar 5, 2019

resendislab / corda

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

flux bioinformatics genome modeling systems-biology biochemistry metabolism reconstruction cobra cobrapy metabolic-models metabolic-network metabolic-reconstruction

Updated Oct 24, 2018
Python

Metaboverse / Metaboverse

Visualizing and Analyzing Metabolic Networks with Reaction Pattern Recognition

reaction pattern-recognition metabolism

Updated Mar 3, 2022
JavaScript

OSS-Lab / MetQy

Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)

data-mining metabolism r-package kegg

Updated Jan 21, 2022
R

adalbertobrant / metabolismobasal

Simple metabolic calculator to weight loss

javascript css calculator html5 metabolism hacktoberfest gimme-stars

Updated Sep 30, 2021
HTML

m-jahn / fluctuator

R package to Import and Modify SVG (XML) Graphic Files

svg network metabolism r-package svg-images metabolic-models omics-data

Updated Nov 18, 2021
R

MetabolicAtlas

MetabolicAtlas / MetabolicAtlas

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

metabolism atlas metabolic-models metabolic-network metabolic-atlas nbisweden

Updated Mar 8, 2022
Vue

MetExplore / miom

Constraint-based modeling of metabolism using Mixed Integer Optimization

python optimization modeling milp metabolism reconstruction cobrapy flux-balance-analysis constraint-based-modeling genome-scale

Updated Aug 28, 2021
Python

ChristianLieven / memote-m-capsulatus

Genome-scale metabolic model of Methylococcus capsulatus.

systems-biology metabolism metabolic-models metabolic-reconstruction constraint-based-modeling c1 genome-scale-models methylococcus methanotrophy

Updated Apr 12, 2019
HTML

draeger-lab / SBMLme

Encoding ME models in SBML

encoding modeling systems-biology gene-expression metabolism sbol sbml

Updated Dec 13, 2021
Java

Micromeda / pygenprop

A python library for programmatic usage of EBI InterPro Genome Properties.

genomics metabolism pathway-analysis metabolic-models genome-properties

Updated Jan 19, 2022
Python

mjenior / riptide

Reaction Inclusion by Parsimony and Transcript Distribution

metabolism transcriptomics cobrapy pfba flux-sampling flux-variability opencobra

Updated Oct 14, 2021
Python

SysBioChalmers / ecModels

A container for all enzyme constrained models created by GECKO.

systems-biology metabolism kinetics genome-scale-models

Updated Jul 30, 2021
MATLAB

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.

grass metabolism openalea morphogenesis fspm wheat

Updated Aug 17, 2021
Python

MetExplore / dexom

Diversity-based enumeration of optimal context-specific metabolic networks

optimization metabolism metabolic-network metabolic-reconstruction constraint-based-modeling metabolic-engineering cobra-toolbox omics-data-integration metabolic-pathways

Updated Jul 2, 2021
MATLAB

biosustain / multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.

python3 thermodynamics multivariate metabolism tfa cobrapy fba tmfa multitfa

Updated Jun 5, 2021
Python

SchlossLab / Jenior_Metatranscriptomics_mSphere_2018

Repository associated with Jenior ML, et al. (2018). mSphere.

machine-learning metagenomics metabolism metabolomics infection metatranscriptomics reproducible-paper clostridium-difficile colonization-resistance

Updated Jul 17, 2018
R

cdanielmachado / cooccurrence

Supplementary data for co-occurrence manuscript

microbial-communities metabolism genome-scale-models supplementary-data co-occurrence

Updated Dec 19, 2019
Jupyter Notebook

fawda123 / WtRegDO

A simple package to implement weighted regression on dissolved oxygen time series

metabolism weighted-regression detiding

Updated Sep 24, 2021
R

cdanielmachado / designmc

Designing microbial communities

design microbial-communities metabolism genome-scale-models

Updated Nov 15, 2021
Python

MetaSys-LISBP / PhysioFit

Estimation of extracellular fluxes and growth rate

metabolism metabolic-flux-analysis exometabolome extracellular-fluxes exchange-fluxes

Updated Mar 7, 2022
R

franciscozorrilla / SymbNET

Teaching materials for SymbNET course: from MAGs to GEMs

genome modeling models metabolism genomes metabolic metagenome assembled symbnet metagem

Updated Mar 2, 2022
Jupyter Notebook

ethrya / circadianGlucose

Physically Based Modelling of Cirdadian Glucose Dynamics

metabolism mathematical-biology glucose circadian

Updated Dec 11, 2018
MATLAB

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