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Name: Arnaud Belcour

Type: User

Company: Inria

Bio: I am ... euh ... human?

Blog: https://arnaudbelcour.github.io/blog/

Hello!

I am a post-doc in the MICROCOSME team of Inria Grenoble.

Research interests

My work focuses on modelling the metabolism at different levels (specific metabolic pathways, single organism or environmental communities). My reseach combines knowledge representation and reasoning, DNA sequence analyses and systems biology. The methods I have particiapted in can be found in this GitHub account or in the AuReMe repository (owned by the Dyliss team of Inria).

Modelling metabolism

I participate in the development of several methods and tools to reconstruct and study metabolic networks:

mpwt: a little multiprocessing wrapper for Pathway Tools to help reconstructing draft metabolic networks at a large-scale.
metage2metabo: a method to compute the producible metabolites by a microbial community and predict the synthetic minimal communities able to produce these metabolites. It relies on menetools, miscoto, mpwt and padmet.
esmecata: a method to estimate functions of taxonomic affiliations using comparative genomics of proteomes from UniProt database.
pathmodel: a prototype implementing the Metabolic Pathway Drift to predict alternative metabolic pathways.
aucome: a method to homogenise the reconstruction of metabolic networks from genomes of public databases.

Conversion of file format

emapper2gbk: a conversion tool to create GenBank file from eggnog-mapper results.

Singularity recipes

Singularity recipe for: mpwt with Pathway Tools, CarveMe recipe (fork of cfrioux/carveme_singularity), UBCG recipe and Circos singularity.

I try to answer the issues but my available time for this is variable and I can be slow to answer.

Arnaud Belcour's Projects

arnaudbelcour

asp-syntax-highlight

Visual Studio Code syntax highlighting for Answer Set Programming

bacdive-api

bioservices

Access to Biological Web Services from Python.

blog

Personal website (WIP).

bubble-tools

python routines related to bubble format

carveme_singularity

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

circos-singularity

Singularity recipe for Circos.

clyngor

Handy python wrapper around Potassco's Clingo ASP solver.

deepec-singularity

Singularity recipe for DeepEC.

docker-clingo

Dockerfile for Clingo with Python3.5 and Lua5.3.

ecmapper

Test to map EC number to BIGG and ModelSEED reactions.

gapseq

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

gff_to_gbk

Convert GFF, fastas, annotation table and species name into Genbank.

gostag-for-more-species

Python and R scripts to use goSTAG on exotic species.

kegg2bipartitegraph

Reconstruct metabolic graphs using KEGG database.

menetools

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

metage2metabo-metacom_singularity

Singularity recipe for Metage2Metabo metacom.

noun-verb_relations

Noun/Verb couple extraction (project for Text Mining and Analytics course).

pbsea

Deprecated, use Pingouin instead.

phylogeny-singularity

Singularity recipe for some phylogeny tools.

python_modules_installation

A module to install automatically a python module.

radarboxplot-python

rhea_mapper

[Not maintained and not updated] Draft metabolic network reconstruction using Rhea database, Uniprot and SPARQL queries.

singularity_ubcg

Singularity recipe for UBCG Bacterial Core Genes

test_method

Repository containing test for some methods.

workflow_genelist_analysis

Analysis of genes list. Not working!

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