MEMOTE for standardized genome-scale metabolic model testing

Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organism’s metabolism under different conditions1. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites and reactions that are assigned to subcellular locations. Gene–protein–reaction (GPR) rules and annotations using database information can add meta-information to GEMs. GEMs with metadata can be built using standard reconstruction protocols2, and guidelines have been put in place for tracking provenance and enabling interoperability, but a standardized means of quality control for GEMs is lacking3. Here we report a community effort to develop a test suite named MEMOTE (for metabolic model tests) to assess GEM quality.

Bibliographic Details

Main Authors:	Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, Van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda, Koehorst, Jasper J., König, Matthias, Lakshmanan, Meiyappan, Lee, Dong-Yup, Lee, Sang Yup, Lee, Sunjae, Lewis, Nathan E., Liu, Filipe, Ma, Hongwu, Machado, Daniel, Mahadevan, Radhakrishnan, Maia, Paulo, Mardinoglu, Adil, Medlock, Gregory L., Monk, Jonathan M., Nielsen, Jens, Nielsen, Lars K., Nogales, Juan, Nookaew, Intawat, Palsson, Bernhard Ø, Papin, Jason A., Patil, Kiran R., Poolman, Mark, Price, Nathan D., Resendis-Antonio, Osbaldo, Richelle, Anne, Rocha, Isabel, Sánchez, Benjamín J., Schaap, Peter J., Malik Sheriff, Rahuman S., Shoaie, Saeed, Sonnenschein, Nikolaus, Teusink, Bas, Vilaça, Paulo, Vik, Jon Olav, Wodke, Judith A. H., Xavier, Joana C., Yuan, Qianqian, Zakhartsev, Maksim, Zhang, Cheng
Other Authors:	Research Council of Norway
Format:	carta al director biblioteca
Published:	Springer Nature 2020-03
Subjects:	Biochemical networks, Computational models, Software,
Online Access:	http://hdl.handle.net/10261/230245 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100002347 http://dx.doi.org/10.13039/501100001659 http://dx.doi.org/10.13039/501100004063 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/100000057 http://dx.doi.org/10.13039/100000865 http://dx.doi.org/10.13039/501100003725 http://dx.doi.org/10.13039/501100003627 http://dx.doi.org/10.13039/501100000769 http://dx.doi.org/10.13039/100000888 http://dx.doi.org/10.13039/100001906 http://dx.doi.org/10.13039/100000002 http://dx.doi.org/10.13039/501100000780
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