Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Lieven, C.; Beber, M. E.; Olivier, B. G.; Bergmann, F. T.; Babaei, P.; Bartell, J. A.; Blank, L. M.; Chauhan, S.; Correia, K.; Diener, C.; Dräger, A.; Ebert, B. E.; Edirisinghe, J. N.; Fleming, R. M. T.; Garcia-Jimenez, B.; van Helvoirt, W.; Henry, C.; Hermjakob, H.; Herrgard, M. J.; Kim, H. U.; King, Z.; Koehorst, J. J.; Klamt, S.; Klipp, E.; Lakshmanan, M.; Le Novere, N.; Lee, D.-Y.; Lee, S. Y.; Lee, S.; Lewis, N. E.; Ma, H.; Machado, D.; Mahadevan, R.; Maia, P.; Mardinoglu, A.; Medlock, G. L.; Monk, J.; Nielsen, J.; Nielsen, L. K.; Nogales, J.; Nookaew, I.; Resendis, O.; Palsson, B.

doi:10.1101/350991

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bioRxiv · 10.1101/350991

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

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Abstract

Several studies have shown that neither the formal representation nor the functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability of models across groups and software tools cannot be guaranteed.\n\nHere, we present memote (https://github.com/opencobra/memote) an open-source software containing a community-maintained, standardized set of metabolic model tests. The tests cover a range of aspects from annotations to conceptual integrity and can be extended to include experimental datasets for automatic model validation. In addition to testing a model once, memote can be configured to do so automatically, i.e., while building a GEM. A comprehensive report displays the models performance parameters, which supports informed model development and facilitates error detection.\n\nMemote provides a measure for model quality that is consistent across reconstruction platforms and analysis software and simplifies collaboration within the community by establishing workflows for publicly hosted and version controlled models.

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Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B. E., Edirisinghe, J. N., Fleming, R. M. T., Garcia-Jimenez, B., van Helvoirt, W., Henry, C., Hermjakob, H., Herrgard, M. J., Kim, H. U., King, Z., Koehorst, J. J., Klamt, S., Klipp, E., Lakshmanan, M., Le Novere, N., Lee, D.-Y., Lee, S. Y., Lee, S., Lewis, N. E., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G. L., Monk, J., Nielsen, J., Nielsen, L. K., Nogales, J., Nookaew, I., Resendis, O., Palsson, B.. 2018-06-21. Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite. https://doi.org/10.1101/350991

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