BioRxiv
bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"
standard-GEM: standardization of open-source genome-scale metabolic models
The field of metabolic modelling at the genome-scale continues to grow with more models being created and curated. This comes with an increasing demand for adopting common principles regarding transparency and versioning, in addition to standardisation efforts regarding file formats, annotation and testing. Here, we present a standardised template for git-based and GitHub-hosted genome-scale metabolic models (GEMs) supporting both new models and curated ones, following FAIR principles (findability, accessibility, interoperability, and reusability), and incorporating best-practices. Standard-GEM facilitates the reuse of GEMs across web services and platforms in the metabolic modelling field and enables automatic validation of GEMs. The use of this template for new models, and its adoption for existing ones, paves the way for increasing model quality, openness, and accessibility with minimal effort.
Anton, M., Almaas, E., Benfeitas, R., Benito-Vaquerizo, S., Blank, L. M., Dräger, A., Hancock, J. M., Kittikunapong, C., König, M., Li, F., Liebal, U. W., Lu, H., Ma, H., Mahadevan, R., Mardinoglu, A., Nielsen, J., Nogales, J., Pagni, M., Papin, J. A., Patil, K. R., Price, N. D., Robinson, J. L., Sanchez, B. J., Suarez Diez, M., Sulheim, S., Svensson, L. T., Teusink, B., Vongsangnak, W., Wang, H., Zeidan, A. A., Kerkhoven, E. J.
March 24, 2023
http://biorxiv.org/cgi/content/short/2023.03.21.512712v1?rss=1