Keating, Sarah M;
Waltemath, Dagmar;
Koenig, Matthias;
Zhang, Fengkai;
Draeger, Andreas;
Chaouiya, Claudine;
Bergmann, Frank T;
... Hucka, Michael; + view all
(2020)
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Molecular Systems Biology
, 16
(8)
, Article e9110. 10.15252/msb.20199110.
Preview |
Text
SBML Level 3 an extensible format for the exchange and reuse of biological models.pdf - Other Download (2MB) | Preview |
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.
| Type: | Article |
|---|---|
| Title: | SBML Level 3: an extensible format for the exchange and reuse of biological models |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.15252/msb.20199110 |
| Publisher version: | https://doi.org/10.15252/msb.20199110 |
| Language: | English |
| Additional information: | This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third-party material in this article are included in the Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
| Keywords: | Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, computational modeling, file format, interoperability, reproducibility, systems biology, SYSTEMS BIOLOGY, MARKUP LANGUAGE, SIMULATION, STANDARDS, SOFTWARE, INFORMATION, ENVIRONMENT, ANNOTATION, REPOSITORY, ONTOLOGY |
| UCL classification: | UCL |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10158982 |
Archive Staff Only
 |
View Item |
