Difference between revisions of "Antimony"
From BioUML platform
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==Features overview== | ==Features overview== | ||
| − | Currently plugin is in | + | 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. | 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. | And for this purpose we need some additions for the antimony specification. | ||
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<table border="1" align="center" cellspacing="0" cellpadding="4"> | <table border="1" align="center" cellspacing="0" cellpadding="4"> | ||
<tr bgcolor="#999999"> | <tr bgcolor="#999999"> | ||
| − | <td> | + | <td> Are supported within an antimony </td> |
<td> Necessary additions in the antimony specification</td> | <td> Necessary additions in the antimony specification</td> | ||
</tr> | </tr> | ||
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<li>Opportunity to divide initial value and initial assignment</li> | <li>Opportunity to divide initial value and initial assignment</li> | ||
<li>Opportunity to change independently attributes "constant" and "boundary conditional",</li> | <li>Opportunity to change independently attributes "constant" and "boundary conditional",</li> | ||
| − | |||
</ul> | </ul> | ||
</td> | </td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td bgcolor="#999999">Antimony features which hadn't supported in | + | <td bgcolor="#999999">Antimony features which hadn't supported in beta-version</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td> | <td> | ||
<ul> | <ul> | ||
| − | <li> | + | <li>Can import only a diagram from the current collection,</li> |
| − | <li> | + | <li>The public port is created only if it is registered in a parameters model,</li> |
| − | + | <li>Some declarations don't supported: <i> DNA strand definitions, deletions</i>,</li> | |
| − | <li>Some declarations don't supported: <i> | + | |
<li>From symbol types only "species" and "compartment" are supported,</li> | <li>From symbol types only "species" and "compartment" are supported,</li> | ||
| − | <li>Reactions with interactions (inhibition, activation) don't use | + | <li>Reactions with interactions (inhibition, activation) don't use;</li> |
| − | + | ||
</ul> | </ul> | ||
</td> | </td> | ||
Revision as of 16:35, 31 October 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.
| Are supported within an antimony | Necessary additions in the antimony specification |
|
|
| Antimony features which hadn't supported in beta-version | |
|
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
