Difference between revisions of "Antimony"
Ilya Kiselev (Talk | contribs) |
Ilya Kiselev (Talk | contribs) |
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Plguin allows user to edit model both visually and as text. | Plguin allows user to edit model both visually and as text. | ||
If visual repesentation is changed - antimony text is updated on the fly.<br> | If visual repesentation is changed - antimony text is updated on the fly.<br> | ||
| − | Text changes are applyed to the diagram on demand (after pressing "Apply Antimony | + | Text changes are applyed to the diagram on demand (after pressing "Apply Antimony" button).<br> |
Besides model representations syncrhonisation, we also try to presereve user diagram layout as well as antimony text format (spaces, comments, etc.) | Besides model representations syncrhonisation, we also try to presereve user diagram layout as well as antimony text format (spaces, comments, etc.) | ||
| − | + | <br> | |
| + | <b>Please note:</b> antimony changes will be applyed 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! | ||
| + | <br> | ||
[[File:compartment antimony.png|thumb|Scheme for compartment adding via Antimony]] | [[File:compartment antimony.png|thumb|Scheme for compartment adding via Antimony]] | ||
[[File:species.png|thumb|Scheme for species adding via Antimony]] | [[File:species.png|thumb|Scheme for species adding via Antimony]] | ||
Revision as of 16:33, 11 September 2013
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].
Plguin 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 applyed 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 applyed 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 alpha 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 within an antimony | Necessary additions in the antimony specification |
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| Antimony features which hadn't supported in alfa-version | |
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- ↑ 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
