Ecosyste.ms: Awesome

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: 07 Nov 2024

https://github.com/biosustain/shu

Multi-dimensional, trans-omics metabolic maps.

metabolism systems-biology visualization

Last synced: 17 Dec 2024

https://github.com/adalbertobrant/metabolismobasal

Simple metabolic calculator to weight loss

calculator css gimme-stars hacktoberfest html5 javascript metabolism

Last synced: 19 Dec 2024

https://github.com/robaina/brendapyrser

A Python parser for the BRENDA database

biochemistry bioinformatics brenda computational-biology enzyme enzyme-kinetics metabolism python

Last synced: 01 Nov 2024

https://github.com/sysbiochalmers/ecmodels

A container for all enzyme constrained models created by GECKO.

genome-scale-models kinetics metabolism systems-biology

Last synced: 03 Dec 2024

https://github.com/biosustain/multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.

cobrapy fba metabolism multitfa multivariate python3 tfa thermodynamics tmfa

Last synced: 15 Nov 2024

https://github.com/robaina/netflowpy

A python tool to optimize chemical concentration trajectories in network-based chemical systems

alternative-optima bioinformatics chemical-networks chemistry computational-biology dynamical-systems linear-programming metabolic-networks metabolism optimization python

Last synced: 22 Dec 2024

https://github.com/biosustain/incawrapper

A python wrapper for Metabolic Flux Analysis (MFA) using INCA with additional functionalities

flux metabolism modeling

Last synced: 15 Nov 2024

https://github.com/carrascomj/kair

COnstraint-Based Reconstruction and Analysis in Rust

cobra metabolism modeling simulation systems-biology

Last synced: 05 Nov 2024

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: 03 Dec 2024

https://github.com/earmingol/sccellfie

scCellFie, inspired by the MATLAB-based CellFie tool, offers advanced analysis of metabolic functions on Python using single-cell and spatial transcriptomics. Efficient and user-friendly, it integrates with Scanpy to extend CellFie's capabilities, enabling in-depth single-cell and spatial metabolic task analysis.

metabolic-modeling metabolic-pathways metabolism single-cell single-cell-transcriptomics spatial-transcriptomics systems-biology

Last synced: 14 Oct 2024

https://github.com/lcsb-biocore/cufluxsampler.jl

GPU-accelerated algorithms for flux sampling in CUDA.jl

cobra cuda gpu julia metabolic-network metabolism sampling

Last synced: 02 Dec 2024

https://github.com/sysbiochalmers/overflow

Supplementary code and results from doi:10.1101/2020.02.20.957662

genome-scale-models metabolism proteomics yeast

Last synced: 03 Dec 2024

https://github.com/sysbiochalmers/gecko2_simulations

Collection of scripts for reproduction of simulation results in "Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0".

constraint-based-modeling enzyme-constraints metabolism

Last synced: 03 Dec 2024

https://github.com/ivandomenzain/diverseyeasts_metabolism

enzyme-constraints gem metabolism systems-biology

Last synced: 02 Nov 2024

https://github.com/vwernay/vorp_metabolism-lua

Conversion of VORP-Metabolism C# to Lua

metabolism rdr2 redm vorp vorpcore

Last synced: 19 Nov 2024

https://github.com/sysbiochalmers/pclactis

Proteome-constrained model of Lactococcus lactis

genome-scale-models metabolism proteome-constraint

Last synced: 03 Dec 2024