Difference between revisions of "Antimony"

From BioUML platform
Jump to: navigation, search
(→‎Features overview)
(→‎Composite model)
Line 67: Line 67:
  
 
==Composite model==
 
==Composite model==
 +
 +
In the beta-version plugin a new declarations were added for working with composite models.
 +
 +
<table  border="1" align="center"  cellspacing="0" cellpadding="4">
 +
<col width="400" valign="top">
 +
<col width="400" valign="top">
 +
<tr bgcolor="#999999">
 +
<td> Are supported within an antimony </td>
 +
<td> Antimony features which hadn't be supported in beta-version</td>
 +
</tr>
 +
<tr>
 +
<td>
 +
<ul>
 +
<li>Model definitions,</li>
 +
<li>External models,</li>
 +
<li>SubDiagrams,</li>
 +
<li>Synchronization elements from different models;</li>
 +
</ul>
 +
</td>
 +
<td rowspan="4" valign="top" >
 +
<ul>
 +
<li>Defining main model using sign "*"</li>
 +
<li>Synchronizing elements which are located below in more than one level
 +
<br><b>Example:</b> s1 is A.B.s2;</li>
 +
<li>Synchronizing elements which have different types;</li>
 +
</ul>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td bgcolor="#999999">New elements which we added in Antimony language</td>
 +
</tr>
 +
<tr>
 +
<td>
 +
<ul>
 +
<li>Prefix for different type ports
 +
<br><b>Example:</b> model nameModel(a,&lt;b,&gt;c);</li>
 +
</ul>
 +
</td>
 +
</tr>
 +
</table>
  
 
== References==
 
== References==

Revision as of 16:43, 31 October 2013

Contents

Antimony plugin

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):

  • 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!

Scheme for compartment adding via Antimony
Scheme for species adding via Antimony

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
  • Creating and removal of species, compartments,
  • Putting nodes into parental compartments,
  • Changing initial values,
  • Creating and removal of reaction with reactants and products,
  • Editing kinetic laws of reactions,
  • Creating, removal and editing of functions,
  • Creating, removal and editing of scalar and rate equations,
  • Mounting constant value for species and variables;
  • Algebraic rules
  • Opportunity to divide initial value and initial assignment
  • Opportunity to change independently attributes "constant" and "boundary conditional",
Antimony features which hadn't supported in beta-version
  • Can import only diagram from the current collection,
  • The public port is created only if it is registered in a parameters model,
  • Some declarations don't supported: DNA strand definitions, deletions,
  • From symbol types only "species" and "compartment" are supported,
  • Reactions with interactions (inhibition, activation) don't use;

Composite model

In the beta-version plugin a new declarations were added for working with composite models.

<col width="400" valign="top"> <col width="400" valign="top">
Are supported within an antimony Antimony features which hadn't be supported in beta-version
  • Model definitions,
  • External models,
  • SubDiagrams,
  • Synchronization elements from different models;
  • Defining main model using sign "*"
  • Synchronizing elements which are located below in more than one level
    Example: s1 is A.B.s2;
  • Synchronizing elements which have different types;
New elements which we added in Antimony language
  • Prefix for different type ports
    Example: model nameModel(a,<b,>c);

References

  1. ↑ 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

See also

Retrieved from "https://wiki.biouml.org/index.php?title=Antimony&oldid=5266"
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox