MEMOTE for standardized genome-scale metabolic model testing

Autor: Kiran Raosaheb Patil, Jens Nielsen, Vassily Hatzimanikatis, Hyun Uk Kim, Nathan D. Price, Edda Klipp, Parizad Babaei, Lars K. Nielsen, Moritz Emanuel Beber, Sang Yup Lee, Radhakrishnan Mahadevan, Meiyappan Lakshmanan, Lars M. Blank, Jon Olav Vik, Steffen Klamt, Nikolaus Sonnenschein, Saeed Shoaie, Bernhard O. Palsson, Georgios Fengos, Christian Diener, Christopher S. Henry, Andreas Dräger, Janaka N. Edirisinghe, Daniel Machado, Beatriz García-Jiménez, Osbaldo Resendis-Antonio, Hongwu Ma, Peter J. Schaap, Dong-Yup Lee, Wout van Helvoirt, José P. Faria, Judith A. H. Wodke, Adam M. Feist, Siddharth Chauhan, Isabel Rocha, Henning Hermjakob, Qianqian Yuan, Brett G. Olivier, Rahuman S. Malik Sheriff, Markus J. Herrgård, Frank Bergmann, Adil Mardinoglu, Anne Richelle, Filipe Liu, Joana C. Xavier, Maksim Zakhartsev, Paulo Vilaça, Cheng Zhang, Ronan M. T. Fleming, Birgitta E. Ebert, Gregory L. Medlock, Ali Kaafarani, Nathan E. Lewis, Mark G. Poolman, Intawat Nookaew, Jonathan M. Monk, Jason A. Papin, Benjamin Sanchez, Christian Lieven, Matthias König, Juan Nogales, Paulo Maia, Sunjae Lee, Jasper J. Koehorst, Meriç Ataman, Jennifer A. Bartell, Bas Teusink, Kevin Correia, Zachary A. King
Přispěvatelé: Systems Bioinformatics, AIMMS, Research Council of Norway, Innovation Fund Denmark, European Commission, National Institutes of Health (US), German Research Foundation, Novo Nordisk Foundation, W. M. Keck Foundation, Ministerio de Economía y Competitividad (España), Knut and Alice Wallenberg Foundation, Federal Ministry of Education and Research (Germany), Bill & Melinda Gates Foundation, National Research Foundation of Korea, Rural Development Administration (South Korea), Swiss National Science Foundation, University of Oxford, European Research Council, Washington Research Foundation, National Institute of General Medical Sciences (US), Universidade do Minho
Jazyk: angličtina
Rok vydání: 2020
Předmět:
endocrine system diseases
Applied Microbiology and Biotechnology
Biochemistry
Workflow
German
0302 clinical medicine
Bioinformatics: 475 [VDP]
Computational models
Systems and Synthetic Biology
Grand Challenges
media_common
0303 health sciences
Systeem en Synthetische Biologie
Genome
Health technology
Publisher Correction
language
ddc:660
Molecular Medicine
Bioinformatikk: 475 [VDP]
Systems biology
Administration (government)
Metabolic Networks and Pathways
Biotechnology
reconstruction
media_common.quotation_subject
Biomedical Engineering
Library science
Bioengineering
Models
Biological
Biokjemi
03 medical and health sciences
Excellence
Correspondence
media_common.cataloged_instance
Life Science
European union
030304 developmental biology
VLAG
Science & Technology
Biochemical networks
fungi
Systembiologi
Computational Biology
Molecular Sequence Annotation
language.human_language
Alliance
Information and Communications Technology
030217 neurology & neurosurgery
Software
Zdroj: Nature Biotechnology
Lieven, C, Beber, M E, Olivier, B G, Bergmann, F T, Ataman, M, Babaei, P, Bartell, J A, Blank, L M, Chauhan, S, Correia, K, Diener, C, Dräger, A, Ebert, B E, Edirisinghe, J N, Faria, J P, Feist, A M, Fengos, G, Fleming, R M T, García-Jiménez, B, Hatzimanikatis, V, van Helvoirt, W, Henry, C S, Hermjakob, H, Herrgard, M J, Kaafarani, A, Kim, H U, King, Z, Klamt, S, Klipp, E, Koehorst, J J, König, M, Lakshmanan, M, Lee, D-Y, Lee, S Y, Lee, S, Lewis, N E, Liu, F, Ma, H, Machado, D, Mahadevan, R, Maia, P, Mardinoglu, A, Medlock, G L, Monk, J M, Nielsen, J, Nielsen, L K, Nogales, J, Nookaew, I, Palsson, B O, Papin, J A, Patil, K R, Poolman, M, Price, N D, Resendis-Antonio, O, Richelle, A, Rocha, I, Sánchez, B J, Schaap, P J, Malik Sheriff, R S, Shoaie, S, Sonnenschein, N, Teusink, B, Vilaca, P, Vik, J O, Wodke, J A H, Xavier, J C, Yuan, Q, Zakhartsev, M & Zhang, C 2020, ' MEMOTE for standardized genome-scale metabolic model testing ', Nature Biotechnology, vol. 38, no. 3, pp. 272-276 . https://doi.org/10.1038/s41587-020-0446-y
Nature Biotechnology, 38(3), 272-276. Nature Publishing Group
Nature Biotechnology, 38(3), 272-276
Nature Biotechnology 38 (2020) 3
Nature biotechnology 38, 272-276 (2020). doi:10.1038/s41587-020-0446-y
Lieven, C, Beber, M E, Olivier, B G, Bergmann, F T, Ataman, M, Babaei, P, Bartell, J A, Blank, L M, Chauhan, S, Correia, K, Diener, C, Dräger, A, Ebert, B E, Edirisinghe, J N, Faria, J P, Feist, A M, Fengos, G, Fleming, R M T, García-Jiménez, B, Hatzimanikatis, V, van Helvoirt, W, Henry, C S, Hermjakob, H, Herrgård, M J, Kaafarani, A, Kim, H U, King, Z, Klamt, S, Klipp, E, Koehorst, J J, König, M, Lakshmanan, M, Lee, D Y, Lee, S Y, Lee, S, Lewis, N E, Liu, F, Ma, H, Machado, D, Mahadevan, R, Maia, P, Mardinoglu, A, Medlock, G L, Monk, J M, Nielsen, J, Nielsen, L K, Nogales, J, Nookaew, I, Palsson, B O, Papin, J A, Patil, K R, Poolman, M, Price, N D, Resendis-Antonio, O, Richelle, A, Rocha, I, Sánchez, B J, Schaap, P J, Malik Sheriff, R S, Shoaie, S, Sonnenschein, N, Teusink, B, Vilaça, P, Vik, J O, Wodke, J A H, Xavier, J C, Yuan, Q, Zakhartsev, M & Zhang, C 2020, ' MEMOTE for standardized genome-scale metabolic model testing ', Nature Biotechnology, vol. 38, no. 3, pp. 272-276 . https://doi.org/10.1038/s41587-020-0446-y
Digital.CSIC. Repositorio Institucional del CSIC
instname
ISSN: 1546-1696
1087-0156
Popis: Supplementary information is available for this paper at https://doi.org/10.1038/s41587-020-0446-y
Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organisms 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. Geneproteinreaction (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.
We acknowledge D. Dannaher and A. Lopez for their supporting work on the Angular parts of MEMOTE; resources and support from the DTU Computing Center; J. Cardoso, S. Gudmundsson, K. Jensen and D. Lappa for their feedback on conceptual details; and P. D. Karp and I. Thiele for critically reviewing the manuscript. We thank J. Daniel, T. Kristjánsdóttir, J. Saez-Saez, S. Sulheim, and P. Tubergen for being early adopters of MEMOTE and for providing written testimonials. J.O.V. received the Research Council of Norway grants 244164 (GenoSysFat), 248792 (DigiSal) and 248810 (Digital Life Norway); M.Z. received the Research Council of Norway grant 244164 (GenoSysFat); C.L. received funding from the Innovation Fund Denmark (project “Environmentally Friendly Protein Production (EFPro2)”); C.L., A.K., N. S., M.B., M.A., D.M., P.M, B.J.S., P.V., K.R.P. and M.H. received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement 686070 (DD-DeCaF); B.G.O., F.T.B. and A.D. acknowledge funding from the US National Institutes of Health (NIH, grant number 2R01GM070923-13); A.D. was supported by infrastructural funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections; N.E.L. received funding from NIGMS R35 GM119850, Novo Nordisk Foundation NNF10CC1016517 and the Keck Foundation; A.R. received a Lilly Innovation Fellowship Award; B.G.-J. and J. Nogales received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no 686585 for the project LIAR, and the Spanish Ministry of Economy and Competitivity through the RobDcode grant (BIO2014-59528-JIN); L.M.B. has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement 633962 for project P4SB; R.F. received funding from the US Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program, grant DE-SC0010429; A.M., C.Z., S.L. and J. Nielsen received funding from The Knut and Alice Wallenberg Foundation, Advanced Computing program, grant #DE-SC0010429; S.K.’s work was in part supported by the German Federal Ministry of Education and Research (de.NBI partner project “ModSim” (FKZ: 031L104B)); E.K. and J.A.H.W. were supported by the German Federal Ministry of Education and Research (project “SysToxChip”, FKZ 031A303A); M.K. is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054); J.A.P. and G.L.M. acknowledge funding from US National Institutes of Health (T32-LM012416, R01-AT010253, R01-GM108501) and the Wagner Foundation; G.L.M. acknowledges funding from a Grand Challenges Exploration Phase I grant (OPP1211869) from the Bill & Melinda Gates Foundation; H.H. and R.S.M.S. received funding from the Biotechnology and Biological Sciences Research Council MultiMod (BB/N019482/1); H.U.K. and S.Y.L. received funding from the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries (grants NRF-2012M1A2A2026556 and NRF-2012M1A2A2026557) from the Ministry of Science and ICT through the National Research Foundation (NRF) of Korea; H.U.K. received funding from the Bio & Medical Technology Development Program of the NRF, the Ministry of Science and ICT (NRF-2018M3A9H3020459); P.B., B.J.S., Z.K., B.O.P., C.L., M.B., N.S., M.H. and A.F. received funding through Novo Nordisk Foundation through the Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517); D.-Y.L. received funding from the Next-Generation BioGreen 21 Program (SSAC, PJ01334605), Rural Development Administration, Republic of Korea; G.F. was supported by the RobustYeast within ERA net project via SystemsX.ch; V.H. received funding from the ETH Domain and Swiss National Science Foundation; M.P. acknowledges Oxford Brookes University; J.C.X. received support via European Research Council (666053) to W.F. Martin; B.E.E. acknowledges funding through the CSIRO-UQ Synthetic Biology Alliance; C.D. is supported by a Washington Research Foundation Distinguished Investigator Award. I.N. received funding from National Institutes of Health (NIH)/National Institute of General Medical Sciences (NIGMS) (grant P20GM125503).
info:eu-repo/semantics/publishedVersion
Databáze: OpenAIRE
Externí odkaz: