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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 ProfileMeric Ataman, 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 ProfileJose P. Faria, View ORCID ProfileAdam Feist, View ORCID ProfileGeorgios Fengos, View ORCID ProfileRonan M. T. Fleming, View ORCID ProfileBeatriz García-Jiménez, View ORCID ProfileVassily Hatzimanikatis, 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 ProfileMark Poolman, View ORCID ProfileNathan D. Price, View ORCID ProfileAnne Richelle, View ORCID ProfileIsabel Rocha, View ORCID ProfileBenjamin J. Sanchez, 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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  • ORCID record for Christian Lieven
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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Meric Ataman
4Ecole Polytechnique Fédérale de Lausanne, Laboratory of Computational Systems Biotechnology, Lausanne, Switzerland
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Parizad Babaei
5Chalmers 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
6iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
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Siddharth Chauhan
7Department of Bioengineering, University of California, San Diego, La Jolla, USA
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Kevin Correia
8Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
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Christian Diener
9Instituto 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
10University of Tübingen, Center for Bioinformatics (ZBIT), Applied Bioinformatics Group, Sand 14 #C320, 72076 Tübingen, Germany
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Birgitta E. Ebert
5Chalmers 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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Janaka N. Edirisinghe
11Argonne National Laboratory 9700 S. Cass Avenue Argonne, IL 60439, USA
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Jose P. Faria
11Argonne National Laboratory 9700 S. Cass Avenue Argonne, IL 60439, USA
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Adam Feist
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, 2800 Kgs. Lyngby, Denmark
6iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
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Georgios Fengos
4Ecole Polytechnique Fédérale de Lausanne, Laboratory of Computational Systems Biotechnology, Lausanne, Switzerland
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Ronan M. T. Fleming
12Luxembourg 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
13Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
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Vassily Hatzimanikatis
4Ecole Polytechnique Fédérale de Lausanne, Laboratory of Computational Systems Biotechnology, Lausanne, Switzerland
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Wout van Helvoirt
14Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Oslo, Norway
15Hanze University of Applied Sciences, Zernikeplein 1 9747AS Groningen, The Netherlands
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Christopher S. Henry
10University of Tübingen, Center for Bioinformatics (ZBIT), Applied Bioinformatics Group, Sand 14 #C320, 72076 Tübingen, Germany
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Henning Hermjakob
16European 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
17Department 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
6iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
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Jasper J. Koehorst
18Department 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
19Analysis 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
20Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
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Meiyappan Lakshmanan
21Bioprocessing 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
22Babraham Institute, Babraham Campus Cambridge, CB22 3AT, UK
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Dong-Yup Lee
20Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
23School of Chemical Engineering Sungkyunkwan University 2066 Seobu-ro, Jangan-gu Suwon Gyeonggi-do 16419 Republic of Korea
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Sang Yup Lee
17Department 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
24Science for Life Laboratory, Tomtebodavägen 23A, Solna, Sweden, SE-17165, Stockholm, Sweden
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Nathan E. Lewis
6iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
25Department 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
26Key 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
27Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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  • ORCID record for Daniel Machado
Radhakrishnan Mahadevan
8Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
28Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
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Paulo Maia
29SilicoLife, Lda. Rua do Canastreiro, 15, 4715-387, Braga, Portugal.
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Adil Mardinoglu
5Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Kemivägen 10, SE-412 96 Göteborg, Sweden
24Science for Life Laboratory, Tomtebodavägen 23A, Solna, Sweden, SE-17165, Stockholm, Sweden
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Gregory L. Medlock
30Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
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Jonathan M. Monk
7Department 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
5Chalmers 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
31Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
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Juan Nogales
13Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
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Intawat Nookaew
32Department 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
9Instituto 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
7Department of Bioengineering, University of California, San Diego, La Jolla, USA
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Jason A. Papin
5Chalmers 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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Kiran R. Patil
27Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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Mark Poolman
33Oxford Brookes University
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Nathan D. Price
34Institute for Systems Biology, 401 Terry Avenue North Seattle, WA 98109-5263, USA
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Anne Richelle
25Department 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
35Centre of Biological Engineering, University of Minho, Braga, Portugal
36Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
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Benjamin J. Sanchez
5Chalmers 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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Peter J. Schaap
15Hanze University of Applied Sciences, Zernikeplein 1 9747AS Groningen, The Netherlands
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Rahuman S. Malik Sheriff
16European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK
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Saeed Shoaie
37Centre 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
29SilicoLife, Lda. Rua do Canastreiro, 15, 4715-387, Braga, Portugal.
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Jon Olav Vik
14Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Oslo, Norway
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Judith A. Wodke
20Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
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Joana C. Xavier
38Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
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Qianqian Yuan
26Key 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
14Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Oslo, Norway
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Cheng Zhang
24Science for Life Laboratory, Tomtebodavägen 23A, Solna, Sweden, SE-17165, Stockholm, Sweden
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  • 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 July 11, 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, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E. Ebert, Janaka N. Edirisinghe, Jose P. Faria, Adam Feist, Georgios Fengos, Ronan M. T. Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, 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, Mark Poolman, Nathan D. Price, Anne Richelle, Isabel Rocha, Benjamin J. Sanchez, 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, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E. Ebert, Janaka N. Edirisinghe, Jose P. Faria, Adam Feist, Georgios Fengos, Ronan M. T. Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, 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, Mark Poolman, Nathan D. Price, Anne Richelle, Isabel Rocha, Benjamin J. Sanchez, 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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