PT  - JOURNAL ARTICLE
AU  - Christian Lieven
AU  - Moritz E. Beber
AU  - Brett G. Olivier
AU  - Frank T. Bergmann
AU  - Parizad Babaei
AU  - Jennifer A. Bartell
AU  - Lars M. Blank
AU  - Siddharth Chauhan
AU  - Kevin Correia
AU  - Christian Diener
AU  - Andreas Dräger
AU  - Birgitta E. Ebert
AU  - Janaka N. Edirisinghe
AU  - Ronan M. T. Fleming
AU  - Beatriz García-Jiménez
AU  - Wout van Helvoirt
AU  - Christopher S. Henry
AU  - Henning Hermjakob
AU  - Markus J. Herrgård
AU  - Hyun Uk Kim
AU  - Zachary King
AU  - Jasper J. Koehorst
AU  - Steffen Klamt
AU  - Edda Klipp
AU  - Meiyappan Lakshmanan
AU  - Nicolas Le Novère
AU  - Dong-Yup Lee
AU  - Sang Yup Lee
AU  - Sunjae Lee
AU  - Nathan E. Lewis
AU  - Hongwu Ma
AU  - Daniel Machado
AU  - Radhakrishnan Mahadevan
AU  - Paulo Maia
AU  - Adil Mardinoglu
AU  - Gregory L. Medlock
AU  - Jonathan M. Monk
AU  - Jens Nielsen
AU  - Lars Keld Nielsen
AU  - Juan Nogales
AU  - Intawat Nookaew
AU  - Osbaldo Resendis-Antonio
AU  - Bernhard O. Palsson
AU  - Jason A. Papin
AU  - Kiran R. Patil
AU  - Nathan D. Price
AU  - Anne Richelle
AU  - Isabel Rocha
AU  - Peter J. Schaap
AU  - Rahuman S. Malik Sheriff
AU  - Saeed Shoaie
AU  - Nikolaus Sonnenschein
AU  - Bas Teusink
AU  - Paulo Vilaça
AU  - Jon Olav Vik
AU  - Judith A. Wodke
AU  - Joana C. Xavier
AU  - Qianqian Yuan
AU  - Maksim Zakhartsev
AU  - Cheng Zhang
TI  - Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
AID  - 10.1101/350991
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 350991
4099  - http://biorxiv.org/content/early/2018/06/21/350991.short
4100  - http://biorxiv.org/content/early/2018/06/21/350991.full
AB  - 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.Here, 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 model’s performance parameters, which supports informed model development and facilitates error detection.Memote 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.