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SBML Level 3: an extensible format for the exchange and reuse of biological models

Sarah Keating 1 Frank Bergmann 2 Tomáš Helikar 3 Rahuman Malik‐sheriff 4 Ion Moraru 5 Martin Meier‐schellersheim 6 Richard Adams 7 Nicholas Allen 8 Bastian Angermann 6 Marco Antoniotti 9 Gary Bader 10 Jan Červený 11 Mélanie Courtot 12 Chris Cox 13 Piero Dalle Pezze 14 Emek Demir 15 William Denney 16 Harish Dharuri 17 Julien Dorier 18 Dirk Drasdo 19 Ali Ebrahim 20 Johannes Eichner 21 Johan Elf 22 Lukas Endler 23 Chris Evelo 24 Christoph Flamm 25 Ronan Mt Fleming 26 Martina Fröhlich 27 Mihai Glont 1 Emanuel Gonçalves 1 Martin Golebiewski 28 Hovakim Grabski 29 Alex Gutteridge 30 Damon Hachmeister 31 Leonard Harris 32 Benjamin Heavner 33 Ron Henkel 34 William Hlavacek 35 Bin Hu 36 Daniel Hyduke 37 Hidde Jong 38 Nick Juty 1 Peter Karp 39 Jonathan Karr 40 Douglas Kell 41 Roland Keller 42 Ilya Kiselev 43 Steffen Klamt 44 Edda Klipp 45 Christian Knüpfer 46 Fedor Kolpakov 43 Falko Krause 47 Martina Kutmon 24 Camille Laibe 1 Conor Lawless 48 Lu Li 49 Leslie Loew 5 Rainer Machne 50 Yukiko Matsuoka 51 Pedro Mendes 52 Huaiyu Mi 53 Florian Mittag 54 Pedro Monteiro 55 Kedar Nath Natarajan 56 Poul Mf Nielsen 57 Tramy Nguyen 58 Alida Palmisano 59 Jean‐baptiste Pettit 1 Thomas Pfau 60 Robert Phair 61 Tomas Radivoyevitch 62 Johann Rohwer 63 Oliver Ruebenacker 64 Julio Saez‐rodriguez 65 Martin Scharm 34 Henning Schmidt 34 Falk Schreiber 66 Michael Schubert 67 Roman Schulte 54 Stuart Sealfon 68 Kieran Smallbone 69 Sylvain Soliman 70 Melanie Stefan 71 Devin Sullivan 72 Koichi Takahashi 73 Bas Teusink 74 David Tolnay 71 Ibrahim Vazirabad 75 Axel Kamp 44 Ulrike Wittig 28 Clemens Wrzodek 42 Dagmar Waltemath 76 Finja Wrzodek 42 Ioannis Xenarios 18 Anna Zhukova 77 Jeremy Zucker 78 Matthias König 79 Fengkai Zhang 80 Andreas Dräger 81 Claudine Chaouiya 55 Frank Bergmann 65 Andrew Finney 82 Colin Gillespie 48 Stefan Hoops 83 Rahuman Malik-Sheriff 4 Stuart Moodie 84 Chris Myers 58 Aurélien Naldi 85 Brett Olivier 86 Sven Sahle 87 James Schaff 88 Lucian Smith 33 Maciej Swat 89 Denis Thieffry 90 Leandro Watanabe 91 Darren Wilkinson 48 Michael Blinov 5 Kimberly Begley 71 James Faeder 92 Harold Gómez 93 Thomas Hamm 42 Yuichiro Inagaki 94 Wolfram Liebermeister 95 Allyson Lister 96 Daniel Lucio 97 Eric Mjolsness 98 Carole Proctor 48 Karthik Raman 99 Nicolas Rodriguez 14 Clifford Shaffer 59 Bruce Shapiro 100 Joerg Stelling 93 Neil Swainston 101 Naoki Tanimura 94 John Wagner 102 Martin Meier-Schellersheim 80 Herbert Sauro 33 Bernhard Palsson 81 Hamid Bolouri 103 Hiroaki Kitano 104 Akira Funahashi 105 Henning Hermjakob 1 John Doyle 71 Michael Hucka 106
19 MAMBA - Modelling and Analysis for Medical and Biological Applications
Inria de Paris, LJLL (UMR_7598) - Laboratoire Jacques-Louis Lions
38 IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks
LAPM - Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble], Inria Grenoble - Rhône-Alpes, Institut Jean Roget
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 multi-scale 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 provides the foundation needed to support this evolution. 3
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Sarah Keating, Frank Bergmann, Tomáš Helikar, Rahuman Malik‐sheriff, Ion Moraru, et al.. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology, EMBO Press, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩. ⟨hal-02924909⟩

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