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a-microbiologist-wants-to-compute

This repo collects the list of learning online resources related to microbiome computational science and tools.

adinteractions

Repository provided as supplementary for the paper "Revealing metabolic mechanism of interactions in the anaerobic digestion microbiome by flux balance"

arianccbasile

Config files for my GitHub profile.

carveme

CarveMe: genome-scale metabolic model reconstruction

cmg_alpha

cobra.papers

Repository for scripts related to reproducing the results of an individual publication

cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

codebase

Code depository for papers

codename

complexheatmap

Make Complex Heatmaps

copasi

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

cytoscape-automation

Collection of scripts that include programmatic io and control of Cytoscape

designmc

Designing microbial communities

dnafeaturesviewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

ecmtool

Uncover organisms' metabolic blueprints

fba_olissipo_winter_school

fgdfg

genome-scale-models

Genome scale metabolic models in SBML format

genome_uploader

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)

gprtransform

Stoichiometric representation of GPR associations (transformation method and gene-based simulation methods)

gpruler

GPRuler, an open-source computational framework to automate the reconstruction process of Gene-Protein-Reaction (GPR) rules within metabolic networks of a given organism based on the corresponding list of genes involved in catalysis of each metabolic reaction, and genes-to-reaction associations.

isosim

IsoSim: stoichiometric, kinetic and isotopic modeling of metabolic systems

melanie_screen_gems

This repo contains inputs, outputs, and step-by-step details regarding how genome scale metabolic models were reconstructed for strains used in Melanie's screen.

ml_gapfiller

nemetex

NEMETEX (NEtwork for METabolic EXchanges) is designed for giving graphical visualizations of metabolite exchanges within complex communities. Flux Balance Analysis (FBA) results are not easy to interpret, and certainly not intuitive. NEMETEX aims to provide a simple and useful visualization for managing high-throughput data from metagenomic and FBA analyses. NEMETEX directly work on SMETANA output files.

paragem

spacem

systems-biology-practical2022

Practical exercises of flux balance analysis for beginners

tanya-data-viz

Personal data visualization side projects.

wolfpsort

WoLFPSort v0.2 source code as original server no longer available