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agora

The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.

alphafold

Open source code for AlphaFold.

bigg_models

The BiGG Models website server

bioconda-recipes

Conda recipes for the bioconda channel.

biopython-notebook

Notebooks to introduce biopython

cmgfunc

CMGfunc, functional protein annotation of bacterial proteins (Comparative Microbial Genomics functions)

cobra.jl

High-level, high-performance, constraint-based reconstruction and analysis in Julia

cobra.tutorials

Repository of tutorials for The COBRA Toolbox

cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

compass

A tool to predict sub-networks from metabolic networks

cp2k_qmmm_tutorials_for_biological_simulations

Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.

crisprcasfinder

A Perl script allowing to identify CRISPR arrays and associated Cas proteins from DNA sequences

curated-bifidobacterial-gsm

Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

deep-purpose-tutorial

Repository for the HackBio'2021 Internship for Team Drug-Development-A

escherconverter

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

export_fig

A MATLAB toolbox for exporting publication quality figures

fastsl-py

Python implementation of FastSL

g_mmpbsa

MM-PBSA method for GROMACS. For full description, please visit homepage:

gapseq

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

gapseqeval

Data and scripts for evaluations tests

github-cheat-sheet

A list of cool features of Git and GitHub.

gromacs

Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.

happy-birthday

Wish your friend/loved-ones happy birthday in a nerdy way.

icomic

icomic_doc

iCOMIC is an open source genomic data analysis tool characterized by a user friendly GUI. It integrates many independent core workflows for Whole Genome/Exome Sequencing and RNA-Seq data analysis.

intro_to_wc_modeling

Whole-cell modeling tutorials

ipau21

matlab-networks-toolbox

A set of graph/networks analysis functions in Octave. This fork focuses on MATLAB compatibility.

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

medusa

Analysis of ensembles of metabolic network reconstructions