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6. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Author

Hucka, Michael, primary, Bergmann, Frank T., additional, Chaouiya, Claudine, additional, Dräger, Andreas, additional, Hoops, Stefan, additional, Keating, Sarah M., additional, König, Matthias, additional, Novère, Nicolas Le, additional, Myers, Chris J., additional, Olivier, Brett G., additional, Sahle, Sven, additional, Schaff, James C., additional, Sheriff, Rahuman, additional, Smith, Lucian P., additional, Waltemath, Dagmar, additional, Wilkinson, Darren J., additional, and Zhang, Fengkai, additional

Published
2019
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7. The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core

Author

Gauges Ralph, Rost Ursula, Sahle Sven, Wengler Katja, and Bergmann Frank T.

Subjects
Internationality, Proteome, Systems Biology, Datasets as Topic, Information Storage and Retrieval, Data processing, computer science, computer systems, Guidelines as Topic, Documentation, General Medicine, Models, Biological, Biological Ontologies, Computer Graphics, Animals, Humans, Programming Languages, TP248.13-248.65, Biotechnology, Signal Transduction
Abstract

SummaryMany software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded.The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.

Published
2015

8. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2

Author

Bergmann, Frank T., Cooper, Jonathan, Le Novere, Nicolas, Nickerson, David, and Waltemath, Dagmar

Subjects
Internationality, Systems Biology, Data processing, computer science, computer systems, Datasets as Topic, Information Storage and Retrieval, Guidelines as Topic, Documentation, General Medicine, Models, Biological, Biological Ontologies, Programming Languages, TP248.13-248.65, Biotechnology
Abstract

Summary The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines.This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

Published
2015

9. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Author

Hucka, Michael, primary, Bergmann, Frank T., additional, Dräger, Andreas, additional, Hoops, Stefan, additional, Keating, Sarah M., additional, Le Novère, Nicolas, additional, Myers, Chris J., additional, Olivier, Brett G., additional, Sahle, Sven, additional, Schaff, James C., additional, Smith, Lucian P., additional, Waltemath, Dagmar, additional, and Wilkinson, Darren J., additional

Published
2018
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13. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

Author

Hucka, Michael, primary, Bergmann, Frank T., additional, Dräger, Andreas, additional, Hoops, Stefan, additional, Keating, Sarah M., additional, Le Novère, Nicolas, additional, Myers, Chris J., additional, Olivier, Brett G., additional, Sahle, Sven, additional, Schaff, James C., additional, Smith, Lucian P., additional, Waltemath, Dagmar, additional, and Wilkinson, Darren J., additional

Published
2018
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17. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Author

Hucka, Michael, primary, Bergmann, Frank T., additional, Dräger, Andreas, additional, Hoops, Stefan, additional, Keating, Sarah M., additional, Le Novère, Nicolas, additional, Myers, Chris J., additional, Olivier, Brett G., additional, Sahle, Sven, additional, Schaff, James C., additional, Smith, Lucian P., additional, Waltemath, Dagmar, additional, and Wilkinson, Darren J., additional

Published
2015
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