The AuReMe-PADMet Solution

Genome-scale metabolic model reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by an explosion of databases and bioinformatics methods that, although very useful, hardly interact with each other, causing loss of traceability and reproducibility of the reconstruction process.

This represents a real obstacle, especially when considering less studied species whose metabolic reconstruction can greatly benefit from the existence of good quality models of related organisms whose construction is transparent and documented with relevant metadata.

This work proposes a modular and adaptable workspace for reproducible reconstruction of genomic-scale metabolic models. Additionally, the workspace establishes a new way to explore, visualize and distribute genome-scale models and their metadata through the generation of ad-hoc local wikis.

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Reconstructions can be generated using different data formats and tools through customizable pipelines. In each step, relevant information is stored ensuring the process is reproducible and documented.

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Among relevant applications, this workspace opens the opportunity to handle, in an integrated way, the metabolic reconstruction of unexplored organisms or microbial communities found in environmental samples.

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