Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. GEMs often encompass thousands of reactions, metabolites and genes, whose manipulation require complex data structures.
Metabolic Atlas, through the web platform available at https://metabolicatlas.org, aims to make the entire GEM content available for easy navigation. This is achieved through both tabular and map views (2D and 3D), each suited for different usage scenarios. In addition, Metabolic Atlas aims to meet the needs of the community through the development of specific tools and features though iterative releases.
Currently, Metabolic Atlas facilitates exploration and visualization of two open-source GEMs: Human1, an integration and extensive curation of the most recent human metabolic models (Robinson et al., 2020), and Yeast8, a consensus metabolic model for S. cerevisiae (Lu et al., 2019).
The history of Metabolic Atlas starts before 2015 (Pornputtapong et al., 2015). The present website has been re-developed from the ground up, following open-source standards. It was made publicly available mid 2019, and is now at version 1.7 (Robinson et al., 2020). We plan to continue the development in a tic-toc method: a major release altering the foundation of the website, followed by several smaller releases. We are actively engaging the community to address the challenges in accessing GEMs for curation, analysis and biological understanding, under the guidance of FAIR principles.
Mihail Anton (1), Pierre-Etienne Cholley (1), Jonathan L. Robinson (1), Shan Huang (2), L. Thomas Svensson (1), Jens Nielsen (3)
(1) Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Sweden
(2) Department of Biology and Biological Engineering, Chalmers University of Technology, Sweden
(3) Department of Biology and Biological Engineering, Wallenberg Center for Protein Research, Chalmers University of Technology; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; BioInnovation Institute (Denmark), Sweden