Waschina

cobrar

COnstraint-based Reconstruction and Analysis (COBRA) of metabolic networks in R

gapseqEval

Data and scripts for evaluations tests

Eutropia

Agent-based metabolic modelling of microbial communities in time and continuous µ-meter-scale space

MicrobiomeGS2

AGORA2_auxotrophies

gapseq.biochem

Exploring gapseq's biochemistry database

21_diet_microbiome

Metabolic modelling of microbial community metabolism (Diet-Microbiome-Study 2021)

atlas

ATLAS - Three commands to start analyzing your metagenome data

atp8_metabopwy

chem_shift_imaging_NMR

gapseq

Informed prediction and analysis of bacteria metabolic pathways and genome-scale networks

gapseq.tutorial.data

Files and scripts for gapseq tutorials

bioconda-recipes

Conda recipes for the bioconda channel.

cobrarCPLEX

CPLEX support for the R-package cobrar

gapsnake

A snakemake workflow for gapseq reconstructions

Graz_Cortison

HCC_microbiota2022

homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

homebrew-core

🍻 Default formulae for the missing package manager for macOS (or Linux)

libsbml

LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.

mxe

MXE (M cross environment)

particles

A particle simulation engine based on a port of d3-force

recipes

System for building static dependent libraries for CRAN packages

sybil

Efficient Constrained Based Modelling in R

sybil.diagnostics

A set of simple diagnostics tests for sybil metabolic models.