Projects in Awesome Lists tagged with metabolic-models

https://github.com/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

bioinformatics computational-biology flux-balance-analysis genome-scale-metabolic-model gut-microbiome mags metabolic-modeling metabolic-models metabolism metagenome-assembled-genomes metagenomics microbial-ecology microbiome snakemake systems-biology

Last synced: 11 Apr 2025

https://github.com/sysbiochalmers/raven

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

constraint-based-modeling gap-filling genome-scale-models human-metabolism metabolic-engineering metabolic-models metabolic-reconstruction sysbio systems-biology

Last synced: 04 Apr 2025

https://github.com/sysbiochalmers/yeast-gem

The consensus GEM for Saccharomyces cerevisiae

biology consensus genome-scale-models hacktoberfest matlab metabolic-models python reconstruction saccharomyces-cerevisiae standard-gem systems-biology yeast

Last synced: 05 Apr 2025

https://github.com/christianlieven/memote-m-capsulatus

Genome-scale metabolic model of Methylococcus capsulatus.

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

Last synced: 04 Mar 2025

https://github.com/sysbiochalmers/ecfactory

A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism

cell-factory enzyme-constraints metabolic-models microbes

Last synced: 03 Dec 2024

https://github.com/sysbiochalmers/yarrowia_lipolytica_w29-gem

Genome-scale model of Yarrowia lipolytica.

constraint-based-modeling genome-scale-models metabolic-engineering metabolic-models metabolic-network metabolic-reconstruction omics-data-integration stoichiometric-reactions systems-biology yarrowia-lipolytica

Last synced: 03 Dec 2024

https://github.com/carrascomj/mmodes

MMODES (Metabolic Models based Ordinary Differential Equations Simulation)

bioinformatics metabolic-models modelling python3 systems-biology

Last synced: 08 Apr 2025

https://github.com/htpusa/moomin.jl

From differential gene expression to metabolic changes

constraint-based-modeling differential-expression gene-expression metabolic-models transcriptomics

Last synced: 11 Apr 2025

https://github.com/alexoarga/findcritical

A desktop app, web app and CLI to operate and find vulnerabilities in SBML metabolic networks.

cobra metabolic-models sbml

Last synced: 17 Mar 2025

https://github.com/sysbiochalmers/yeastsmodels

Container of computational models of metabolism for different yeast species.

gems metabolic-models metabolism systems-biology yeast-species

Last synced: 26 Mar 2025

https://github.com/cfrioux/fluto

answer-set-programming bioinformatics flux-balance-analysis gap-filling linear-programming metabolic-models metabolic-network metabolic-reconstruction

Last synced: 24 Feb 2025

https://github.com/sysbiochalmers/kmg060-systems-biology-course

KMG060 Systems Biology course - repo for students

enzyme-constraints flux-balance-analysis metabolic-models rna-seq-analysis systems-biology

Last synced: 03 Dec 2024

https://github.com/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.

biochemistry bioinformatics cobra cobrapy computational-biology metabolic-models metabolic-network metabolic-reconstruction modeling modeling-tool python systems-biology

Last synced: 24 Mar 2025

https://github.com/nyxflower/memo

Constraint-based metabolic modelling with sparse IPOPT

constraint-based-modeling interior-point-optimizer metabolic-models non-linear-optimization

Last synced: 22 Feb 2025

https://github.com/cobrexa/abstractfbcmodels.jl

General interface for flux-based constrained metabolic models

file-formats metabolic-models

Last synced: 02 Mar 2025

https://github.com/ibchgenomic/metabolic-json

a metabolic json parser and streamlit for BIGG database

bioinformatics genome-analysis genome-bioinformatics genome-informatics json json-api json-data metabolic-models metabolic-pathways metabolic-reconstruction

Last synced: 18 Mar 2025

https://github.com/ibchgenomic/bigg-metabolic-analyzer-api

a API to BIGG metabolic databases

bioinformatics bioinformatics-data bioinformatics-scripts genome-analysis genome-annotation metabolic metabolic-database metabolic-models

Last synced: 18 Mar 2025

https://github.com/gauravcodepro/streamlit-bigg-metabolic-analyzer-api

streamlit application to analyze the BIGG Metabolic models.

metabolic-models metabolic-network streamlit-application streamlit-webapp

Last synced: 22 Feb 2025

https://github.com/compcode1/risk-reduction-potentials

This small project demonstrated the value of leveraging metabolic profiles and related calculations in a synthetic dataset. This type of analysis greatly expands upon the binary Metabolic Syndrome classification.

algorithms dataset metabolic-models

Last synced: 18 Mar 2025