Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
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Section: New Software and Platforms


Automatic Reconstruction of Metabolic networks

Keywords: Workflow - Bioinformatics - Metabolic networks - Omic data - Toolbox - Data management

Functional Description: AuReMe enables the reconstruction of metabolic networks from different sources based on sequence annotation, orthology, gap-filling and manual curation. The metabolic network is exported as a local wiki allowing to trace back all the steps and sources of the reconstruction. It is highly relevant for the study of non-model organisms, or the comparison of metabolic networks for different strains or a single organism.

Five modules are composing AuReMe: 1) The Model-management PADmet module allows manipulating and traceing all metabolic data via a local database. 2) The meneco python package allows the gaps of a metabolic network to be filled by using a topological approach that implements a logical programming approach to solve a combinatorial problem 3) The shogen python package allows genome and metabolic network to be aligned in order to identify genome units which contain a large density of genes coding for enzymes, it also implements a logical programming approach. 4) The manual curation assistance PADmet module allows the reported metabolic networks and their metadata to be curated. 5) The Wiki-export PADmet module enables the export of the metabolic network and its functional genomic unit as a local wiki platform allowing a user-friendly investigation.

Release Functional Description: - Reworking padmet and padmet-utils to allow full-python workflow in the future - Adding new script padmet-utils/exploration/prot2genome with exonerate - Fixing minor errors

News Of The Year: (1) Pantograph replaced by OrthoFinder (2) Create a readthedocs for AuReMe, padmet and padmet-utils (3) Reworking padmet and padmet-utils to allow full python workflow (4) Adding new script padmet-utils/exploration/prot2genome with exonerate (5) Modify template data structure (6) Fixing errors