Difference between revisions of "Antimony"
Ilya Kiselev (Talk | contribs) |
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[[File:SubDiagram.PNG |thumb| Use model definition or external model for adding subdiagram.]] | [[File:SubDiagram.PNG |thumb| Use model definition or external model for adding subdiagram.]] | ||
[[File:Ports.png |thumb| Use parameters of subdiagram or synchronization for adding connection.]] | [[File:Ports.png |thumb| Use parameters of subdiagram or synchronization for adding connection.]] | ||
+ | [[File:CompositDiagram.png |thumb| Visual (SBGN) and text-based (Antimony) representations of composite model.]] | ||
In the beta-version plugin new declarations were added for working with composite models. If antimony text contains few models or declarations outside model then this text corresponds to the composite model. Main model will be created and it contains all models like model definitions. | In the beta-version plugin new declarations were added for working with composite models. If antimony text contains few models or declarations outside model then this text corresponds to the composite model. Main model will be created and it contains all models like model definitions. |
Revision as of 17:21, 15 November 2013
Contents |
Antimony plugin
Antimony plugin for BioUML 0.9.6 aims to combine two representations of mathematical model (particularly - SBML model):
- visual representation as BioUML-diagram using extended SBGN notation
- text-based representation using Antimony language[1].
Plugin allows user to edit model both visually and as text.
If visual repesentation is changed - antimony text is updated on the fly.
Text changes are applied to the diagram on demand (after pressing "Apply Antimony" button).
Besides model representations syncrhonisation, we also try to presereve user diagram layout as well as antimony text format (spaces, comments, etc.)
Please note: antimony changes will be applied to the diagram only after "Apply Antimony" button is pressed.
If you change diagram before you press this button, all changes in text will be lost!
Features overview
Currently plugin is in beta version, some features of antimony aren't supported. Also we want to achieve full synchronization between antimony and sbml-model in BioUML. And for this purpose we need some additions for the antimony specification.
Supported Antimony features | Not supported in current version |
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Necessary additions in the antimony specification | |
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Composite model
In the beta-version plugin new declarations were added for working with composite models. If antimony text contains few models or declarations outside model then this text corresponds to the composite model. Main model will be created and it contains all models like model definitions.
Supported Antimony features | Not supported in current version |
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New elements which we have added in Antimony language | |
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References
- ↑ Smith, L.P., Bergmann, F.T., Chandran, D. Sauro, M.H. Antimony: a modular model definition language. Bioinformatics, 2009, 25(18): 2452-2454. doi:10.1093/bioinformatics/btp401