Difference between revisions of "Antimony"
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Ilya Kiselev (Talk | contribs) |
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<h2>Antimony plugin</h2> | <h2>Antimony plugin</h2> | ||
| − | + | [[File:Antimony demo.png|thumb|Visual (SBGN) and text-based (Antimony) representations of SBML model in BioUML]] | |
| − | + | ||
Antimony plugin for BioUML 0.9.6 aims to combine two representations of mathematical model (particularly - SBML model): | Antimony plugin for BioUML 0.9.6 aims to combine two representations of mathematical model (particularly - SBML model): | ||
<ul> | <ul> | ||
<li>visual representation as BioUML-diagram using extended SBGN notation | <li>visual representation as BioUML-diagram using extended SBGN notation | ||
| − | <li>text-based representation using Antimony language. | + | <li>text-based representation using Antimony language<ref>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}}</ref>. |
</ul> | </ul> | ||
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. | + | If visual repesentation is changed - antimony text is updated on the fly.<br> |
| − | Text changes are applyed to the diagram on demand. | + | 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.) | ||
| − | |||
| − | |||
[[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]] | ||
| + | |||
| + | <h2>Features overview</h2> | ||
| + | |||
| + | 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. | ||
| + | |||
| + | <table border="1" align="center" cellspacing="0" cellpadding="4"> | ||
| + | <tr bgcolor="#999999"> | ||
| + | <td> Supported within an antimony </td> | ||
| + | <td> Necessary additions in the antimony specification</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td> | ||
| + | <ul> | ||
| + | <li>Creating and removal of species, compartments,</li> | ||
| + | <li>Putting nodes into parental compartments,</li> | ||
| + | <li>Changing initial values,</li> | ||
| + | <li>Creating and removal of reaction with reactants and products,</li> | ||
| + | <li>Editing kinetic laws of reactions,</li> | ||
| + | <li>Creating, removal and editing of functions,</li> | ||
| + | <li>Creating, removal and editing of scalar and rate equations,</li> | ||
| + | <li>Mounting constant value for species and variables;</li> | ||
| + | </ul> | ||
| + | </td> | ||
| + | <td rowspan="3" valign="top" > | ||
| + | <ul> | ||
| + | <li>Algebraic rules</li> | ||
| + | <li>Opportunity to divide initial value and initial assignment</li> | ||
| + | <li>Opportunity to change independently attributes "constant" and "boundary conditional",</li> | ||
| + | <li>"Delay" for events;</li> | ||
| + | </ul> | ||
| + | </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td bgcolor="#999999">Antimony features which hadn't supported in alfa-version</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td> | ||
| + | <ul> | ||
| + | <li>Import statements don't supported,</li> | ||
| + | <li>All declarations must be inside only one model,</li> | ||
| + | <li>Model can't have parameters,</li> | ||
| + | <li>Some declarations don't supported: <i>imported models, DNA strand definitions, synchronizations, deletions, display names</i>,</li> | ||
| + | <li>From symbol types only "species" and "compartment" are supported,</li> | ||
| + | <li>Reactions with interactions (inhibition, activation) don't use,</li> | ||
| + | <li>Also events and initial assignments work incorrectly;</li> | ||
| + | </ul> | ||
| + | </td> | ||
| + | </tr> | ||
| + | </table> | ||
| + | <References/> | ||
Revision as of 14:02, 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.)
File:Species.png
Scheme for species adding via Antimony
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 |
|
|
| Antimony features which hadn't supported in alfa-version | |
|
- ↑ 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
