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Soaking up the sun.
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ArnaudBelcour/README.md

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 time available for this varies and I can be slow to respond.

Pinned Loading

  1. AuReMe/mpwt AuReMe/mpwt Public

    Pathway Tools multiprocessing wrapper (for PathoLogic).

    Python 15

  2. pathmodel/pathmodel pathmodel/pathmodel Public

    Prototype to infer new biochemical reactions and new metabolite structures to investigate metabolic pathway drift.

    Python 2

  3. AuReMe/metage2metabo AuReMe/metage2metabo Public

    From annotated genomes to metabolic screening in large scale microbiotas

    Jupyter Notebook 53 7

  4. AuReMe/esmecata AuReMe/esmecata Public

    From taxonomic affiliations to annotated proteins using UniProt database.

    Python 3 1

  5. asp-syntax-highlight asp-syntax-highlight Public

    Visual Studio Code syntax highlighting for Answer Set Programming

    14 3

  6. AuReMe/aucome AuReMe/aucome Public

    Automatic Comparison of Metabolism

    Python 5