Título: | MEMOTE for standardized genome-scale metabolic model testing |
Autor: | 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 CSIC ORCID ; 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 |
Palabras clave: | Biochemical networks Computational models Software |
Fecha de publicación: | mar-2020 |
Editor: | Springer Nature |
Citación: | Nature Biotechnology 38: 272-276 (2020) |
Resumen: | 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. |
Versión del editor: | http://dx.doi.org/10.1038/s41587-020-0446-y |
URI: | http://hdl.handle.net/10261/230245 |
DOI: | 10.1038/s41587-020-0446-y |
ISSN: | 1087-0156 |
E-ISSN: | 1546-1696 |
Aparece en las colecciones: | (CNB) Artículos (INIA) Artículos
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