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

View ORCID ProfileChristian Lieven, View ORCID ProfileMoritz E. Beber, Brett G. Olivier, View ORCID ProfileFrank T. Bergmann, View ORCID ProfileParizad Babaei, View ORCID ProfileJennifer A. Bartell, View ORCID ProfileLars M. Blank, View ORCID ProfileSiddharth Chauhan, View ORCID ProfileKevin Correia, View ORCID ProfileChristian Diener, View ORCID ProfileAndreas Dräger, View ORCID ProfileBirgitta E. Ebert, View ORCID ProfileJanaka N. Edirisinghe, View ORCID ProfileRonan M. T. Fleming, View ORCID ProfileBeatriz García-Jiménez, View ORCID ProfileWout van Helvoirt, View ORCID ProfileChristopher S. Henry, View ORCID ProfileHenning Hermjakob, View ORCID ProfileMarkus J. Herrgård, View ORCID ProfileHyun Uk Kim, View ORCID ProfileZachary King, View ORCID ProfileJasper J. Koehorst, View ORCID ProfileSteffen Klamt, View ORCID ProfileEdda Klipp, View ORCID ProfileMeiyappan Lakshmanan, View ORCID ProfileNicolas Le Novère, View ORCID ProfileDong-Yup Lee, View ORCID ProfileSang Yup Lee, View ORCID ProfileSunjae Lee, View ORCID ProfileNathan E. Lewis, View ORCID ProfileHongwu Ma, View ORCID ProfileDaniel Machado, View ORCID ProfileRadhakrishnan Mahadevan, View ORCID ProfilePaulo Maia, View ORCID ProfileAdil Mardinoglu, View ORCID ProfileGregory L. Medlock, View ORCID ProfileJonathan M. Monk, View ORCID ProfileJens Nielsen, View ORCID ProfileLars Keld Nielsen, View ORCID ProfileJuan Nogales, Intawat Nookaew, View ORCID ProfileOsbaldo Resendis-Antonio, View ORCID ProfileBernhard O. Palsson, View ORCID ProfileJason A. Papin, View ORCID ProfileKiran R. Patil, View ORCID ProfileNathan D. Price, View ORCID ProfileAnne Richelle, View ORCID ProfileIsabel Rocha, View ORCID ProfilePeter J. Schaap, View ORCID ProfileRahuman S. Malik Sheriff, View ORCID ProfileSaeed Shoaie, View ORCID ProfileNikolaus Sonnenschein, View ORCID ProfileBas Teusink, View ORCID ProfilePaulo Vilaça, View ORCID ProfileJon Olav Vik, Judith A. Wodke, View ORCID ProfileJoana C. Xavier, View ORCID ProfileQianqian Yuan, View ORCID ProfileMaksim Zakhartsev, View ORCID ProfileCheng Zhang
doi: https://doi.org/10.1101/350991
Christian Lieven
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Kgs. Lyngby, Denmark
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Moritz E. Beber
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Kgs. Lyngby, Denmark
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Brett G. Olivier
2Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Frank T. Bergmann
3BioQUANT/COS, Heidelberg University, Heidelberg, Germany
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Parizad Babaei
4Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Kemivägen 10, SE-412 96 Göteborg, Sweden
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Jennifer A. Bartell
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Kgs. Lyngby, Denmark
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Lars M. Blank
5iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
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Siddharth Chauhan
6Department of Bioengineering, University of California, San Diego, La Jolla, USA
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Kevin Correia
7Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
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Christian Diener
8Instituto Nacional de Medicina Genomica – INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610 Mexico City, CDMX and Human Systems Biology Laboratory. Coordinación de la Investigación Científica - Red de Apoyo a la Investigación, UNAM, Mexico
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Andreas Dräger
9University of Tübingen, Center for Bioinformatics (ZBIT), Applied Bioinformatics Group, Sand 14 #C320, 72076 Tübingen, Germany
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Birgitta E. Ebert
5iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
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Janaka N. Edirisinghe
10Argonne National Laboratory 9700 S. Cass Avenue Argonne, IL 60439, USA
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  • ORCID record for Janaka N. Edirisinghe
Ronan M. T. Fleming
11Luxembourg Center for Systems Biomedicine, Campus Belval, University of Luxembourg 7, Avenue des Hauts Fourneaux L-4362 Esch-sur-Alzette, Luxembourg
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Beatriz García-Jiménez
12Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
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Wout van Helvoirt
13Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Æs, Oslo, Norway
14Hanze University of Applied Sciences, Zernikeplein 1 9747AS Groningen, The Netherlands
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Christopher S. Henry
10Argonne National Laboratory 9700 S. Cass Avenue Argonne, IL 60439, USA
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Henning Hermjakob
15European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK
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Markus J. Herrgård
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Kgs. Lyngby, Denmark
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Hyun Uk Kim
16Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, BioInformatics Research Center, Institute for the BioCentury, KAIST, Daejeon, Korea
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Zachary King
6Department of Bioengineering, University of California, San Diego, La Jolla, USA
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Jasper J. Koehorst
17Department of Agrotechnology and Food Sciences, Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4 6708WE Wageningen, The Netherlands
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Steffen Klamt
18Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, Sandtorstrasse 1 39106 Magdeburg, Germany
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Edda Klipp
19Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
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Meiyappan Lakshmanan
20Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Singapore
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Nicolas Le Novère
21Babraham Institute, Babraham Campus Cambridge, CB22 3AT, UK
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Dong-Yup Lee
20Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668, Singapore
22School of Chemical Engineering Sungkyunkwan University 2066 Seobu-ro, Jangan-gu Suwon Gyeonggi-do 16419 Republic of Korea
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Sang Yup Lee
16Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, BioInformatics Research Center, Institute for the BioCentury, KAIST, Daejeon, Korea
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Sunjae Lee
23Science for Life Laboratory, Tomtebodavägen 23A, Solna, Sweden, SE-17165, Stockholm, Sweden
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Nathan E. Lewis
6Department of Bioengineering, University of California, San Diego, La Jolla, USA
24Department of Pediatrics, University of California, San Diego School of Medicine 4119 BRF2 9500 Gilman Drive, Mail Code 0760 La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at UC San Diego
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Hongwu Ma
25Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, P. R. China
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Daniel Machado
26Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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Radhakrishnan Mahadevan
7Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
27Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
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Paulo Maia
28SilicoLife, Lda. Rua do Canastreiro, 15, 4715-387, Braga, Portugal
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Adil Mardinoglu
4Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Kemivägen 10, SE-412 96 Göteborg, Sweden
23Science for Life Laboratory, Tomtebodavägen 23A, Solna, Sweden, SE-17165, Stockholm, Sweden
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Gregory L. Medlock
29Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
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Jonathan M. Monk
6Department of Bioengineering, University of California, San Diego, La Jolla, USA
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Jens Nielsen
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Kgs. Lyngby, Denmark
4Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Kemivägen 10, SE-412 96 Göteborg, Sweden
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Lars Keld Nielsen
30Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
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Juan Nogales
12Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
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Intawat Nookaew
31Department Biomedical Informatics, University of Arkansas for Medical Sciences (UAMS), 4301 W. Markham St. Little Rock, AR 72205, USA
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Osbaldo Resendis-Antonio
8Instituto Nacional de Medicina Genomica – INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610 Mexico City, CDMX and Human Systems Biology Laboratory. Coordinación de la Investigación Científica - Red de Apoyo a la Investigación, UNAM, Mexico
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Bernhard O. Palsson
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Kgs. Lyngby, Denmark
6Department of Bioengineering, University of California, San Diego, La Jolla, USA
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Jason A. Papin
29Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
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Kiran R. Patil
26Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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Nathan D. Price
32Institute for Systems Biology, 401 Terry Avenue North Seattle, WA 98109-5263, USA
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Anne Richelle
24Department of Pediatrics, University of California, San Diego School of Medicine 4119 BRF2 9500 Gilman Drive, Mail Code 0760 La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at UC San Diego
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Isabel Rocha
33Centre of Biological Engineering, University of Minho, Braga, Portugal
34Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
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Peter J. Schaap
14Hanze University of Applied Sciences, Zernikeplein 1 9747AS Groningen, The Netherlands
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Rahuman S. Malik Sheriff
15European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK
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Saeed Shoaie
35Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, SE1 9RT, UK
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Nikolaus Sonnenschein
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Kgs. Lyngby, Denmark
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  • For correspondence: niso@biosustain.dtu.dk
Bas Teusink
2Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Paulo Vilaça
28SilicoLife, Lda. Rua do Canastreiro, 15, 4715-387, Braga, Portugal
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Jon Olav Vik
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Kgs. Lyngby, Denmark
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Judith A. Wodke
19Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
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Joana C. Xavier
36Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
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Qianqian Yuan
25Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, P. R. China
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Maksim Zakhartsev
13Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Æs, Oslo, Norway
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Cheng Zhang
23Science for Life Laboratory, Tomtebodavägen 23A, Solna, Sweden, SE-17165, Stockholm, Sweden
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  • ORCID record for Cheng Zhang
  • Abstract
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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.

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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 21, 2018.
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Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
Christian Lieven, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E. Ebert, Janaka N. Edirisinghe, Ronan M. T. Fleming, Beatriz García-Jiménez, Wout van Helvoirt, Christopher S. Henry, Henning Hermjakob, Markus J. Herrgård, Hyun Uk Kim, Zachary King, Jasper J. Koehorst, Steffen Klamt, Edda Klipp, Meiyappan Lakshmanan, Nicolas Le Novère, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L. Medlock, Jonathan M. Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Osbaldo Resendis-Antonio, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Nathan D. Price, Anne Richelle, Isabel Rocha, Peter J. Schaap, Rahuman S. Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
bioRxiv 350991; doi: https://doi.org/10.1101/350991
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Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
Christian Lieven, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E. Ebert, Janaka N. Edirisinghe, Ronan M. T. Fleming, Beatriz García-Jiménez, Wout van Helvoirt, Christopher S. Henry, Henning Hermjakob, Markus J. Herrgård, Hyun Uk Kim, Zachary King, Jasper J. Koehorst, Steffen Klamt, Edda Klipp, Meiyappan Lakshmanan, Nicolas Le Novère, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L. Medlock, Jonathan M. Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Osbaldo Resendis-Antonio, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Nathan D. Price, Anne Richelle, Isabel Rocha, Peter J. Schaap, Rahuman S. Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
bioRxiv 350991; doi: https://doi.org/10.1101/350991

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