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SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML)

Nicolas Rodriguez, Marco Donizelli, Nicolas Le Novère
2007 BMC Bioinformatics  
The need to build a tool to facilitate the quick creation and editing of models encoded in the Systems Biology Markup language (SBML) has been growing with the number of users and the increased complexity  ...  SBMLeditor can be used as a module of the Systems Biology Workbench.  ...  Acknowledgements This work was supported by the European Molecular Biology Laboratory. Authors are grateful to Alex Golubev and Compugen for the development of SBW support.  ... 
doi:10.1186/1471-2105-8-79 pmid:17341299 pmcid:PMC1831489 fatcat:wgryily5avce7p6qbu7ex47vxu

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Michael Hucka, Andrew Finney, Stefan Hoops, Sarah Keating, Nicolas Le Novere
2007 Nature Precedings  
-2/version-3/ This release of the specification is available at http://sbml.org/specifications/sbml-level-2/version-3/release-1/ The list of known issues in all releases of SBML Level 2 Version 3 is available  ...  Notifications of new releases are broadcast on the mailing list sbml-announce@sbml.org The latest release of the SBML Level 2 Version 3 specification is available at http://sbml.org/specifications/sbml-level  ...  SBML is not static; we continue to develop and experiment with it, and we interact 19 with other groups who seek to develop similar markup languages.  ... 
doi:10.1038/npre.2007.58.1 fatcat:mgdu7fr4wjgprmo4nksfuihiji

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Michael Hucka, Andrew Finney, Stefan Hoops, Sarah Keating, Nicolas Le Novere
2007 Nature Precedings  
-2/version-3/ This release of the specification is available at http://sbml.org/specifications/sbml-level-2/version-3/release-1/ The list of known issues in all releases of SBML Level 2 Version 3 is available  ...  Notifications of new releases are broadcast on the mailing list sbml-announce@sbml.org The latest release of the SBML Level 2 Version 3 specification is available at http://sbml.org/specifications/sbml-level  ...  SBML is not static; we continue to develop and experiment with it, and we interact 19 with other groups who seek to develop similar markup languages.  ... 
doi:10.1038/npre.2007.58.2 fatcat:fpm75djjxjcwlcd3ogkbvbjjpq

Designing and encoding models for synthetic biology

L. Endler, N. Rodriguez, N. Juty, V. Chelliah, C. Laibe, C. Li, N. Le Novere
2009 Journal of the Royal Society Interface  
Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization.  ...  We give here an overview of the model creation and analysis processes as well as some software tools in common use.  ...  The authors are thankful to Dominic Tolle for discussions. This work was partly supported by the British Biotechnology and Biological Sciences Research Council.  ... 
doi:10.1098/rsif.2009.0035.focus pmid:19364720 pmcid:PMC2843962 fatcat:icdwnd2tcnazjpmfw4y4pomcvq

Towards a Complete Covering of SBML Functionalities [chapter]

Tommaso Mazza
Membrane Computing  
The Systems Biology Markup Language (SBML) is an attempt to overcome this issue and aims to simplify the exchange of information by imposing a standardized way of representing models.  ...  This work focuses on the translation of the Cyto-Sim simulation language (based on a discrete stochastic implementation of P systems) to SBML.  ...  that reflect the natural conceptual constructs used by modellers in the domain, SBML: Systems Biology Markup Language.  ... 
doi:10.1007/978-3-540-77312-2_22 dblp:conf/membrane/Mazza07 fatcat:j34wi3izs5hqbeio3xpdusigxe

A Liver-Centric Multiscale Modeling Framework for Xenobiotics

James P. Sluka, Xiao Fu, Maciej Swat, Julio M. Belmonte, Alin Cosmanescu, Sherry G. Clendenon, John F. Wambaugh, James A. Glazier, Edward E Schmidt
2016 PLoS ONE  
We have used standard modeling modalities at each of the three scales. In particular, we have used the Systems Biology Markup Language (SBML) to create both the wholebody and sub-cellular scales.  ...  Other studies focused on systems biology models of APAP metabolism and GSH homeostasis, such as [20] . developed an extended PBPK model of APAP metabolism in humans.  ...  Herbert Sauro's assistance in the use of the Systems Biology Workbench tools greatly facilitated the creation of both the PBPK and sub-cellular reaction kinetic models in SBML.  ... 
doi:10.1371/journal.pone.0162428 pmid:27636091 pmcid:PMC5026379 fatcat:uow7debu5bdo5b7dkukqzwxmcm