Section: New Software and Platforms


PortAble Database for Metabolism

Keywords: Bioinformatics - Toolbox - Metabolic networks - Standardization

Functional Description

The PADMet package allows conciliating genomics and metabolic network information used to produce a genome-scale constraint-based metabolic model within a database that traces all the reconstruction process steps. It allows representing the metabolic model in the form of a Wiki containing all the used/traced information. Other standard outputs are made available with the package. The main concept underlying PADMet-Package is to provide solutions that ensure the consistency, the internal standardization and the reconciliation of the information used within any workflow that combines several tools involving metabolic networks reconstruction or analysis. The PADMet package is at the core of the AuReMe workflow, dedicated to the primary reconstruction of genome-scale metabolic networks from raw data. It allows the study of organisms for which few experimental data are available. Its main feature is to undergo the reconstruction of the metabolic network by combining several heterogeneous knowledge and data sources, including the information reported by several scaffold metabolic networks for cousin species.