Section: New Software and Platforms

Pathmodel

Keywords: ASP - Answer Set Programming - Metabolic networks - Metabolic Pathway Drift - Bioinformatics - Systems Biology - Metabolomics

Scientific Description: This tool is a prototype of the Metabolic Pathway Drift concept. This concept states that metabolic pathways undergo substantial turnover. The reactions involved in a pathway can change between species (change in reaction order or replacement of an enzyme by another one). Another goal of this tool is to linked genomics and metabolomics data. To implement this concept, Pathmodel uses the Answer Set Programming language. The input are the reactants and products involved in the pathway, known reactions occurring between these molecules, known m/z ratio, known domains shard by these molecules, an initial molecule and a goal molecule. Using these data, Pathmodel will infer reactions between molecules to reach the goal molecule using the known reactions. The result consist of potential alternative pathways for the studied organism.

Functional Description: A metabolic pathway is a series of biochemical reactions. These reactions modify metabolites in order to synthesize a new metabolite or to produce energy. One difficulties when dealing with pathways in non-model organism is their incomplete conservation during evolution. To deal with this problem, we developed a prototype inferring new biochemical reactions using reactions and metabolites from known metabolic pathways and metabolomics data. This method produce alternative pathway that could occurred in the species of interest.

Release Functional Description: Fix an issue with test data.

News Of The Year: (1) Add a container in Singularity Hub (https://singularity-hub.org/collections/3758). (2) Rewrite data files (sterol and MAA). (3) Add creation of pictures of new molecules from MZ. (4) Add new output files to ease understanding of PathModel output. (5) Rewrite the Readme.

• Participants: Arnaud Belcour, Jacques Nicolas, Gabriel Markov and Anne Siegel

• Partner: Station Biologique de Roscoff

• Contact: Anne Siegel

• Publication: Inferring biochemical reactions and metabolite structures to cope with metabolic pathway drift

• URL: https://github.com/pathmodel