Antimony
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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.
Are supported antimony features | Antimony features which hadn't supported in beta-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 correspond composite model. Main model will be created and it contains all models like model definitions.
Are supported within an antimony | Features which aren't supported in beta version |
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New elements which we 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