SBML Level 3: an extensible format for the exchange and reuse of biological models
2020; Springer Nature; Volume: 16; Issue: 8 Linguagem: Inglês
10.15252/msb.20199110
ISSN1744-4292
AutoresSarah Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank Bergmann, Andrew Finney, Colin S. Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S. Malik‐Sheriff, Stuart Moodie, Ion I. Moraru, Chris J. Myers, Aurélien Naldi, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Maciej J. Swat, Denis Thieffry, Leandro Watanabe, Darren J. Wilkinson, Michael L. Blinov, Kimberly Begley, James R. Faeder, Harold Gómez, Thomas M. Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson Lister, Daniel Lucio, Eric Mjolsness, Carole J. Proctor, Karthik Raman, Nicolás Rodríguez, Clifford A. Shaffer, Bruce E. Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M. Sauro, Bernhard Ø. Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C. Doyle, Michael Hucka, Richard R. Adams, Nicholas Allen, Bastian R. Angermann, Marco Antoniotti, Gary D. Bader, Jan Červený, Mélanie Courtot, Chris D. Cox, Piero Dalle Pezze, Emek Demir, William S. Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T. Evelo, Christoph Flamm, Ronan M. T. Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, D. Hachmeister, Leonard A. Harris, Ben Heavner, Ron Henkel, William S. Hlavacek, Bin Hu, Daniel R. Hyduke, Hidde de Jong, Nick Juty, Peter D. Karp, Jonathan R. Karr, Douglas B. Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M. Loew, Rainer Machné, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T. Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D. Phair, Tomas Radivoyevitch, Johann M. Rohwer, Oliver Ruebenacker, Julio Sáez-Rodríguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michaël Schubert, Roman Schulte, Stuart C. Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I. Stefan, Devin P. Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xénarios, Anna Zhukova, Jeremy Zucker,
Tópico(s)Bioinformatics and Genomic Networks
ResumoReview26 August 2020Open Access SBML Level 3: an extensible format for the exchange and reuse of biological models Sarah M Keating Sarah M Keating orcid.org/0000-0002-3356-3542 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK BioQuant/COS, Heidelberg University, Heidelberg, Germany Search for more papers by this author Dagmar Waltemath Dagmar Waltemath orcid.org/0000-0002-5886-5563 Medical Informatics, Institute for Community Health, University Medicine Greifswald, Greifswald, Germany Search for more papers by this author Matthias König Matthias König orcid.org/0000-0003-1725-179X Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany Search for more papers by this author Fengkai Zhang Fengkai Zhang orcid.org/0000-0001-7112-9328 Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA Search for more papers by this author Andreas Dräger Andreas Dräger orcid.org/0000-0002-1240-5553 Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany Department of Computer Science, University of Tübingen, Tübingen, Germany German Center for Infection Research (DZIF), Tübingen, Germany Search for more papers by this author Claudine Chaouiya Claudine Chaouiya orcid.org/0000-0003-2350-0756 Aix-Marseille Université, CNRS, Centrale Marseille, Marseille, France Instituto Gulbenkian de Ciência, Oeiras, Portugal Search for more papers by this author Frank T Bergmann Frank T Bergmann orcid.org/0000-0001-5553-4702 BioQuant/COS, Heidelberg University, Heidelberg, Germany Search for more papers by this author Andrew Finney Andrew Finney ANSYS UK Ltd, Milton Park, Oxfordshire, UK Search for more papers by this author Colin S Gillespie Colin S Gillespie orcid.org/0000-0003-1787-0275 School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK Search for more papers by this author Tomáš Helikar Tomáš Helikar orcid.org/0000-0003-3653-1906 Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE, USA Search for more papers by this author Stefan Hoops Stefan Hoops orcid.org/0000-0001-8503-8371 Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA, USA Search for more papers by this author Rahuman S Malik-Sheriff Rahuman S Malik-Sheriff orcid.org/0000-0003-0705-9809 European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK Search for more papers by this author Stuart L Moodie Stuart L Moodie orcid.org/0000-0001-6191-5595 Eight Pillars Ltd, Edinburgh, UK Search for more papers by this author Ion I Moraru Ion I Moraru orcid.org/0000-0002-3746-9676 Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA Search for more papers by this author Chris J Myers Chris J Myers orcid.org/0000-0002-8762-8444 Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA Search for more papers by this author Aurélien Naldi Aurélien Naldi orcid.org/0000-0002-6495-2655 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France Search for more papers by this author Brett G Olivier Brett G Olivier orcid.org/0000-0002-5293-5321 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA BioQuant/COS, Heidelberg University, Heidelberg, Germany SysBioLab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands Search for more papers by this author Sven Sahle Sven Sahle BioQuant/COS, Heidelberg University, Heidelberg, Germany Search for more papers by this author James C Schaff James C Schaff orcid.org/0000-0003-3286-7736 Applied BioMath, LLC, Concord, MA, USA Search for more papers by this author Lucian P Smith Lucian P Smith orcid.org/0000-0001-7002-6386 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA Department of Bioengineering, University of Washington, Seattle, WA, USA Search for more papers by this author Maciej J Swat Maciej J Swat Simcyp (a Certara company), Sheffield, South Yorkshire, UK Search for more papers by this author Denis Thieffry Denis Thieffry orcid.org/0000-0003-0271-1757 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France Search for more papers by this author Leandro Watanabe Leandro Watanabe orcid.org/0000-0001-7030-8690 Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA Search for more papers by this author Darren J Wilkinson Darren J Wilkinson orcid.org/0000-0003-0736-802X School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK The Alan Turing Institute, British Library, London, UK Search for more papers by this author Michael L Blinov Michael L Blinov orcid.org/0000-0002-9363-9705 Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA Search for more papers by this author Kimberly Begley Kimberly Begley orcid.org/0000-0002-1642-7493 California Institute of Technology, Pasadena, CA, USA Search for more papers by this author James R Faeder James R Faeder orcid.org/0000-0001-8127-609X Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA Search for more papers by this author Harold F Gómez Harold F Gómez Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland Search for more papers by this author Thomas M Hamm Thomas M Hamm orcid.org/0000-0001-9579-7267 Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany Department of Computer Science, University of Tübingen, Tübingen, Germany Search for more papers by this author Yuichiro Inagaki Yuichiro Inagaki orcid.org/0000-0003-4011-8487 Management & IT Consulting Division, Mizuho Information & Research Institute, Inc., Tokyo, Japan Search for more papers by this author Wolfram Liebermeister Wolfram Liebermeister orcid.org/0000-0002-2568-2381 Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France Search for more papers by this author Allyson L Lister Allyson L Lister orcid.org/0000-0002-7702-4495 Oxford e-Research Centre (OeRC), Department of Engineering Science, University of Oxford, Oxford, UK Search for more papers by this author Daniel Lucio Daniel Lucio orcid.org/0000-0002-8912-7213 College of Sciences, NC State University, Raleigh, NC, USA Search for more papers by this author Eric Mjolsness Eric Mjolsness orcid.org/0000-0002-9085-9171 Department of Computer Science, University of California, Irvine, CA, USA Search for more papers by this author Carole J Proctor Carole J Proctor orcid.org/0000-0002-1366-1399 Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK Search for more papers by this author Karthik Raman Karthik Raman orcid.org/0000-0002-9311-7093 Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India Initiative for Biological Systems Engineering (IBSE), IIT Madras, Chennai, India Robert Bosch Centre for Data Science and Artificial Intelligence (RBC-DSAI), IIT Madras, Chennai, India Search for more papers by this author Nicolas Rodriguez Nicolas Rodriguez orcid.org/0000-0002-9290-7894 The Babraham Institute, Cambridge, UK Search for more papers by this author Clifford A Shaffer Clifford A Shaffer orcid.org/0000-0003-0001-0295 Department of Computer Science, Virginia Tech, Blacksburg, VA, USA Search for more papers by this author Bruce E Shapiro Bruce E Shapiro Department of Mathematics, California State University, Northridge, CA, USA Search for more papers by this author Joerg Stelling Joerg Stelling orcid.org/0000-0002-1145-891X Department of Biosystems Science and Engineering, SIB Swiss Institute of Bioinformatics, ETH Zürich, Basel, Switzerland Search for more papers by this author Neil Swainston Neil Swainston orcid.org/0000-0001-7020-1236 Institute of Integrative Biology, University of Liverpool, Liverpool, UK Search for more papers by this author Naoki Tanimura Naoki Tanimura Science Solutions Division, Mizuho Information & Research Institute, Inc., Tokyo, Japan Search for more papers by this author John Wagner John Wagner IBM Research Australia, Melbourne, Vic., Australia Search for more papers by this author Martin Meier-Schellersheim Martin Meier-Schellersheim orcid.org/0000-0002-8754-6377 Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA Search for more papers by this author Herbert M Sauro Herbert M Sauro orcid.org/0000-0002-3659-6817 Department of Bioengineering, University of Washington, Seattle, WA, USA Search for more papers by this author Bernhard Palsson Bernhard Palsson orcid.org/0000-0003-2357-6785 Department of Bioengineering, University of California San Diego, La Jolla, CA, USA Search for more papers by this author Hamid Bolouri Hamid Bolouri Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA Search for more papers by this author Hiroaki Kitano Hiroaki Kitano orcid.org/0000-0002-3589-1953 The Systems Biology Institute, Tokyo, Japan Okinawa Institute of Science and Technology, Okinawa, Japan Search for more papers by this author Akira Funahashi Akira Funahashi orcid.org/0000-0003-0605-239X Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan Search for more papers by this author Henning Hermjakob Henning Hermjakob orcid.org/0000-0001-8479-0262 European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK Search for more papers by this author John C Doyle John C Doyle orcid.org/0000-0002-1828-2486 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA Search for more papers by this author Michael Hucka Corresponding Author Michael Hucka [email protected] orcid.org/0000-0001-9105-5960 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA Search for more papers by this author SBML Level 3 Community members SBML Level 3 Community membersA complete list of members and affiliations appears in the Appendix 1Search for more papers by this author Sarah M Keating Sarah M Keating orcid.org/0000-0002-3356-3542 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK BioQuant/COS, Heidelberg University, Heidelberg, Germany Search for more papers by this author Dagmar Waltemath Dagmar Waltemath orcid.org/0000-0002-5886-5563 Medical Informatics, Institute for Community Health, University Medicine Greifswald, Greifswald, Germany Search for more papers by this author Matthias König Matthias König orcid.org/0000-0003-1725-179X Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany Search for more papers by this author Fengkai Zhang Fengkai Zhang orcid.org/0000-0001-7112-9328 Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA Search for more papers by this author Andreas Dräger Andreas Dräger orcid.org/0000-0002-1240-5553 Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany Department of Computer Science, University of Tübingen, Tübingen, Germany German Center for Infection Research (DZIF), Tübingen, Germany Search for more papers by this author Claudine Chaouiya Claudine Chaouiya orcid.org/0000-0003-2350-0756 Aix-Marseille Université, CNRS, Centrale Marseille, Marseille, France Instituto Gulbenkian de Ciência, Oeiras, Portugal Search for more papers by this author Frank T Bergmann Frank T Bergmann orcid.org/0000-0001-5553-4702 BioQuant/COS, Heidelberg University, Heidelberg, Germany Search for more papers by this author Andrew Finney Andrew Finney ANSYS UK Ltd, Milton Park, Oxfordshire, UK Search for more papers by this author Colin S Gillespie Colin S Gillespie orcid.org/0000-0003-1787-0275 School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK Search for more papers by this author Tomáš Helikar Tomáš Helikar orcid.org/0000-0003-3653-1906 Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE, USA Search for more papers by this author Stefan Hoops Stefan Hoops orcid.org/0000-0001-8503-8371 Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA, USA Search for more papers by this author Rahuman S Malik-Sheriff Rahuman S Malik-Sheriff orcid.org/0000-0003-0705-9809 European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK Search for more papers by this author Stuart L Moodie Stuart L Moodie orcid.org/0000-0001-6191-5595 Eight Pillars Ltd, Edinburgh, UK Search for more papers by this author Ion I Moraru Ion I Moraru orcid.org/0000-0002-3746-9676 Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA Search for more papers by this author Chris J Myers Chris J Myers orcid.org/0000-0002-8762-8444 Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA Search for more papers by this author Aurélien Naldi Aurélien Naldi orcid.org/0000-0002-6495-2655 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France Search for more papers by this author Brett G Olivier Brett G Olivier orcid.org/0000-0002-5293-5321 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA BioQuant/COS, Heidelberg University, Heidelberg, Germany SysBioLab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands Search for more papers by this author Sven Sahle Sven Sahle BioQuant/COS, Heidelberg University, Heidelberg, Germany Search for more papers by this author James C Schaff James C Schaff orcid.org/0000-0003-3286-7736 Applied BioMath, LLC, Concord, MA, USA Search for more papers by this author Lucian P Smith Lucian P Smith orcid.org/0000-0001-7002-6386 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA Department of Bioengineering, University of Washington, Seattle, WA, USA Search for more papers by this author Maciej J Swat Maciej J Swat Simcyp (a Certara company), Sheffield, South Yorkshire, UK Search for more papers by this author Denis Thieffry Denis Thieffry orcid.org/0000-0003-0271-1757 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France Search for more papers by this author Leandro Watanabe Leandro Watanabe orcid.org/0000-0001-7030-8690 Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA Search for more papers by this author Darren J Wilkinson Darren J Wilkinson orcid.org/0000-0003-0736-802X School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK The Alan Turing Institute, British Library, London, UK Search for more papers by this author Michael L Blinov Michael L Blinov orcid.org/0000-0002-9363-9705 Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA Search for more papers by this author Kimberly Begley Kimberly Begley orcid.org/0000-0002-1642-7493 California Institute of Technology, Pasadena, CA, USA Search for more papers by this author James R Faeder James R Faeder orcid.org/0000-0001-8127-609X Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA Search for more papers by this author Harold F Gómez Harold F Gómez Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland Search for more papers by this author Thomas M Hamm Thomas M Hamm orcid.org/0000-0001-9579-7267 Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany Department of Computer Science, University of Tübingen, Tübingen, Germany Search for more papers by this author Yuichiro Inagaki Yuichiro Inagaki orcid.org/0000-0003-4011-8487 Management & IT Consulting Division, Mizuho Information & Research Institute, Inc., Tokyo, Japan Search for more papers by this author Wolfram Liebermeister Wolfram Liebermeister orcid.org/0000-0002-2568-2381 Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France Search for more papers by this author Allyson L Lister Allyson L Lister orcid.org/0000-0002-7702-4495 Oxford e-Research Centre (OeRC), Department of Engineering Science, University of Oxford, Oxford, UK Search for more papers by this author Daniel Lucio Daniel Lucio orcid.org/0000-0002-8912-7213 College of Sciences, NC State University, Raleigh, NC, USA Search for more papers by this author Eric Mjolsness Eric Mjolsness orcid.org/0000-0002-9085-9171 Department of Computer Science, University of California, Irvine, CA, USA Search for more papers by this author Carole J Proctor Carole J Proctor orcid.org/0000-0002-1366-1399 Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK Search for more papers by this author Karthik Raman Karthik Raman orcid.org/0000-0002-9311-7093 Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India Initiative for Biological Systems Engineering (IBSE), IIT Madras, Chennai, India Robert Bosch Centre for Data Science and Artificial Intelligence (RBC-DSAI), IIT Madras, Chennai, India Search for more papers by this author Nicolas Rodriguez Nicolas Rodriguez orcid.org/0000-0002-9290-7894 The Babraham Institute, Cambridge, UK Search for more papers by this author Clifford A Shaffer Clifford A Shaffer orcid.org/0000-0003-0001-0295 Department of Computer Science, Virginia Tech, Blacksburg, VA, USA Search for more papers by this author Bruce E Shapiro Bruce E Shapiro Department of Mathematics, California State University, Northridge, CA, USA Search for more papers by this author Joerg Stelling Joerg Stelling orcid.org/0000-0002-1145-891X Department of Biosystems Science and Engineering, SIB Swiss Institute of Bioinformatics, ETH Zürich, Basel, Switzerland Search for more papers by this author Neil Swainston Neil Swainston orcid.org/0000-0001-7020-1236 Institute of Integrative Biology, University of Liverpool, Liverpool, UK Search for more papers by this author Naoki Tanimura Naoki Tanimura Science Solutions Division, Mizuho Information & Research Institute, Inc., Tokyo, Japan Search for more papers by this author John Wagner John Wagner IBM Research Australia, Melbourne, Vic., Australia Search for more papers by this author Martin Meier-Schellersheim Martin Meier-Schellersheim orcid.org/0000-0002-8754-6377 Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA Search for more papers by this author Herbert M Sauro Herbert M Sauro orcid.org/0000-0002-3659-6817 Department of Bioengineering, University of Washington, Seattle, WA, USA Search for more papers by this author Bernhard Palsson Bernhard Palsson orcid.org/0000-0003-2357-6785 Department of Bioengineering, University of California San Diego, La Jolla, CA, USA Search for more papers by this author Hamid Bolouri Hamid Bolouri Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA Search for more papers by this author Hiroaki Kitano Hiroaki Kitano orcid.org/0000-0002-3589-1953 The Systems Biology Institute, Tokyo, Japan Okinawa Institute of Science and Technology, Okinawa, Japan Search for more papers by this author Akira Funahashi Akira Funahashi orcid.org/0000-0003-0605-239X Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan Search for more papers by this author Henning Hermjakob Henning Hermjakob orcid.org/0000-0001-8479-0262 European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK Search for more papers by this author John C Doyle John C Doyle orcid.org/0000-0002-1828-2486 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA Search for more papers by this author Michael Hucka Corresponding Author Michael Hucka [email protected] orcid.org/0000-0001-9105-5960 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA Search for more papers by this author SBML Level 3 Community members SBML Level 3 Community membersA complete list of members and affiliations appears in the Appendix 1Search for more papers by this author Author Information Sarah M Keating1,2,3,‡, Dagmar Waltemath4,‡, Matthias König5, Fengkai Zhang6, Andreas Dräger7,8,9, Claudine Chaouiya10,11, Frank T Bergmann3, Andrew Finney12, Colin S Gillespie13, Tomáš Helikar14, Stefan Hoops15, Rahuman S Malik-Sheriff2, Stuart L Moodie16, Ion I Moraru17, Chris J Myers18, Aurélien Naldi19, Brett G Olivier1,3,20, Sven Sahle3, James C Schaff21, Lucian P Smith1,22, Maciej J Swat23, Denis Thieffry19, Leandro Watanabe18, Darren J Wilkinson13,24, Michael L Blinov17, Kimberly Begley25, James R Faeder26, Harold F Gómez27, Thomas M Hamm7,8, Yuichiro Inagaki28, Wolfram Liebermeister29, Allyson L Lister30, Daniel Lucio31, Eric Mjolsness32, Carole J Proctor33, Karthik Raman34,35,36, Nicolas Rodriguez37, Clifford A Shaffer38, Bruce E Shapiro39, Joerg Stelling40, Neil Swainston41, Naoki Tanimura42, John Wagner43, Martin Meier-Schellersheim6, Herbert M Sauro22, Bernhard Palsson44, Hamid Bolouri45, Hiroaki Kitano46,47, Akira Funahashi48, Henning Hermjakob2, John C Doyle1, Michael Hucka *,1, , Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean-Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez-Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova and Jeremy Zucker 1Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA 2European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK 3BioQuant/COS, Heidelberg University, Heidelberg, Germany 4Medical Informatics, Institute for Community Health, University Medicine Greifswald, Greifswald, Germany 5Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany 6Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA 7Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany 8Department of Computer Science, University of Tübingen, Tübingen, Germany 9German Center for Infection Research (DZIF), Tübingen, Germany 10Aix-Marseille Université, CNRS, Centrale Marseille, Marseille, France 11Instituto Gulbenkian de Ciência, Oeiras, Portugal 12ANSYS UK Ltd, Milton Park, Oxfordshire, UK 13School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK 14Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE, USA 15Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA, USA 16Eight Pillars Ltd, Edinburgh, UK 17Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA 18Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA 19Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France 20SysBioLab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands 21Applied BioMath, LLC, Concord, MA, USA 22Department of Bioengineering, University of Washington, Seattle, WA, USA 23Simcyp (a Certara company), Sheffield, South Yorkshire, UK 24The Alan Turing Institute, British Library, London, UK 25California Institute of Technology, Pasadena, CA, USA 26Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA 27Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland 28Management & IT Consulting Division, Mizuho Information & Research Institute, Inc., Tokyo, Japan 29Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France 30Oxford e-Research Centre (OeRC), Department of Engineering Science, University of Oxford, Oxford, UK 31College of Sciences, NC State University, Raleigh, NC, USA 32Department of Computer Science, University of California, Irvine, CA, USA 33Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK 34Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India 35Initiative for Biological Systems Engineering (IBSE), IIT Madras, Chennai, India 36Robert Bosch Centre for Data Science and Artificial Intelligence (RBC-DSAI), IIT Madras, Chennai, India 37The Babraham Institute, Cambridge, UK 38Department of Computer Science, Virginia Tech, Blacksburg, VA, USA 39Department of Mathematics, California State University, Northridge, CA, USA 40Department of Biosystems Science and Engineering, SIB Swiss Institute of Bioinformatics, ETH Zürich, Basel, Switzerland 41Institute of Integrative Biology, University of Liverpool, Liverpool, UK 42Science Solutions Division, Mizuho Information & Research Institute, Inc., Tokyo, Japan 43IBM Research Australia, Melbourne, Vic., Australia 44Department of Bioengineering, University of California San Diego, La Jolla, CA, USA 45Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA 46The Systems Biology Institute, Tokyo, Japan 47Okinawa Institute of Science and Technology, Okinawa, Japan 48Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan ‡These authors contributed equally to this work *Corresponding author. Tel: +1 626 395 3418; E-mail: [email protected] Molecular Systems Biology (2020)16:e9110https://doi.org/10.15252/msb.20199110 Correction added on 4 September 2020, after first online publication: the symbol in row Distributions, column Specification was corrected to a checkmark PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Abstract Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution. Introduction Systems modeling and numerical simulations in biology can be traced to the mid-20th century. Though general theorizing about systems began earlier, the application of systems analysis to biolo
Referência(s)