Accéder directement au contenu Accéder directement à la navigation
Article dans une revue

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

Littérature citée [104 références]  Voir  Masquer  Télécharger

https://hal.inrae.fr/hal-02924909
Déposant : Wolfram Liebermeister <>
Soumis le : vendredi 28 août 2020 - 15:01:52
Dernière modification le : mardi 22 septembre 2020 - 11:00:15

Fichier

Keating_2020_SBML Level 3.pdf
Fichiers éditeurs autorisés sur une archive ouverte

Licence


Distributed under a Creative Commons Paternité 4.0 International License

Identifiants

Citation

Sarah Keating, Frank Bergmann, Tomáš Helikar, Rahuman Malik‐sheriff, Ion Moraru, et al.. SBML Level : an extensible format for the 3 exchange and reuse of biological models. Molecular Systems Biology, EMBO Press, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩. ⟨hal-02924909⟩

Partager

Métriques

Consultations de la notice

144

Téléchargements de fichiers

123