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

Abstract:

Systems biology has experienced dramatic growth in the number, size and complexity of computational models describing biology. To reproduce simulation results and reuse models, researchers need to exchange precise and unambiguous descriptions of model structure and meaning. SBML (the Systems Biology Markup Language) is a community-developed format for this purpose. The latest edition, called SBML Level 3, has a modular structure, with a core suited to representing reaction-based models, and packages that extend the core with features suited for a variety of model types. Examples include constraint-based models, reaction-diffusion models, logical network models, and rule-based models. SBML and its rich software ecosystem have transformed the way systems biologists build and interact with models, and has played an important role in increasing model interoperability and reuse over the past two decades. More recently, a rise of multiscale models of whole cells and organs, and new data sources such as single cells measurements and live imaging, have precipitated new ways of integrating data and models. SBML Level 3 provides the foundation needed to support this evolution.

Citation: Mol Syst Biol.

Date Published: 1st Jul 2020

URL: https://livermetabolism.com/paper/SBML_Keating2019.pdf

Registered Mode: imported from a bibtex file

Authors: SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, FT Bergmann, A Finney, CS Gillespie, T Helikar, S Hoops, RS Malik-Sheriff, SL Moodie, II Moraru, CJ Myers, A Naldi, BG Olivier, S Sahle, JC Schaff, LP Smith, MJ Swat, DT, L Watanabe, DJ Wilkinson, ML Blinov, K Begley, JR Faeder, HF Gómez, TM Hamm, Y Inagaki, W Liebermeister, AL Lister, D Lucio, E Mjolsness, CJ Proctor, K Raman, N Rodriguez, CA Shaffer, BE Shapiro, J Stelling, N Swainston, N Tanimura, J Wagner, M Meier-Schellersheim, HM Sauro, B Palsson, H Bolouri, H Kitano, Akira Funahashi, H Hermjakob, JC Doyle, M Hucka, SBML Community members

Help
help Creator
Creators
Not specified
Submitter
Citation
An error occurred whilst fetching the citation
Activity

Views: 121

Created: 27th Jul 2020 at 14:47

Last updated: 27th Jul 2020 at 15:02

help Attributions

None

Related items

Powered by
(v.1.10.1)
Copyright © 2008 - 2020 The University of Manchester and HITS gGmbH