cfrioux

miscoto

Python package for large-scale community selection in microbiota

MeneTools

MeneTools are Python3 tools to explore the topology of metabolic networks. It includes Menecheck, Menescope, Menepath and Menecof.

outreach

A repository dedicated to scientific outreach with resources for teaching metagenomics and metabolic modelling to young people and non profesional scientists.

carveme_singularity

SIngularity image definition to install Cplex and Carveme in a container (e.g. for using the software on a cluster)

fluto

meneco

metabolic network completion

BNMTF_ARD

Python code for "Comparative Study of Inference Methods for Bayesian Nonnegative Matrix Factorisation", published at European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2017).

cfrioux.github.io

my web pages

conda-training

Conda repository for training

deadend_detector

Detection of deadends in metabolic networks

docker-libsbml-cobra

docker-matlab-runtime-v83

docker_cbc_solver

dockerfile for building images with CBC solver

docker_conda_ssh

Dockerfile for an image containing Conda, open-ssh and java-ready for installing IBM products

dotfiles

Helper to manage my dotfiles and some basic configurations on terminal based Operating Systems

metaGEM

An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

padmet-tricks

Some tiny scripts involving padmet to hack metabolic networks

pyasp

A convenience wrapper for the ASP tools gringo, gringo4 and clasp

readthedocs.org

The source code that powers readthedocs.org

scikit-learn

scikit-learn: machine learning in Python

supervenn

supervenn: precise and easy-to-read multiple sets visualization in Python

taxodist_for_reactions

Basis to get taxonomic information for reactions, starting from their affiliation to pathways