AuReMe

The AuReMe general system

An original solution for a all-in-one workspace.
Customized workflow

Use either a pre-set pipeline or customize your own metabolic network reconstruction workflow with integrated or other tools.
Implemented methods

Five main modules: the PADMet core, the input manager, the user workspace based on Docker technology, the format for storing data and metadata and the included tools.
Transparency with metadata

A whole pool of metadata is associated to the model or its reconstruction and managed by the AuReMe workspace for storage and wiki-visualization.
Applied to non-model organisms

Interest of heterogeneous methods in pathway completion and filling, thanks to tracking of process metadata.
Reproducibility

A tracking system enables to reproduce the exact and complete analysis process automatically, by a simple command sequence.