Difference between revisions of "Antimony"

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(→‎Composite model)
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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> Are supported antimony features </td>
+
<td> Supported Antimony features </td>
−
<td> Antimony features which hadn't supported in beta-version</td>
+
<td> Not supported in current version</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
 
<td>
 
<td>
 
<ul>
 
<ul>
−
<li>Creating and removal of species, compartments,</li>
+
<li>Creating and removing of species, compartments,</li>
 
<li>Putting nodes into parental compartments,</li>
 
<li>Putting nodes into parental compartments,</li>
−
<li>Changing initial values,</li>
+
<li>Initial values changing,</li>
−
<li>Creating and removal of reaction with reactants and products,</li>
+
<li>Creating and removing of reaction with reactants and products,</li>
−
<li>Editing kinetic laws of reactions,</li>
+
<li>Editing of reaction kinetic laws,</li>
−
<li>Creating, removal and editing of functions,</li>
+
<li>Creating, removing and editing of functions,</li>
−
<li>Creating, removal and editing of scalar and rate equations,</li>
+
<li>Creating, removing and editing of scalar and rate equations,</li>
−
<li>Mounting constant value for species and variables;</li>
+
<li>Declarating species and variables as constants;</li>
 
</ul>
 
</ul>
 
</td>
 
</td>
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<ul>
 
<ul>
 
        <li>Declaration <i>"DNA strand definitions"</i> isn't supported,</li>
 
        <li>Declaration <i>"DNA strand definitions"</i> isn't supported,</li>
−
        <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>
+
        <li>Reactions with interactions (inhibition, activation);</li>
 
</ul>
 
</ul>
 
</td>
 
</td>
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<ul>
 
<ul>
 
                                 <li>Algebraic rules</li>
 
                                 <li>Algebraic rules</li>
−
<li>Opportunity to divide initial value and initial assignment</li>
+
<li>Distinguishing between initial value and initial assignment with numerical value,</li>
−
<li>Opportunity to change independently attributes "constant" and "boundary conditional",</li>
+
<li>Independent management of "constant" and "boundary conditional" attributes,</li>
 
</ul>
 
</ul>
 
</td>
 
</td>
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[[File:Ports.png |thumb| Use parameters of subdiagram or synchronization for adding connection.]]
 
[[File:Ports.png |thumb| Use parameters of subdiagram or synchronization for adding connection.]]
  
−
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.
+
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 corresponds to the composite model. Main model will be created and it contains all models like model definitions.
  
 
         <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> Are supported antimony features </td>
+
<td> Supported Antimony features </td>
−
<td> Features which aren't supported in beta version</td>
+
<td> Not supported in current version</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
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<li>External models,</li>
 
<li>External models,</li>
 
<li>SubDiagrams,</li>
 
<li>SubDiagrams,</li>
−
<li>Replacing elements from different models;</li>
+
<li>Replacing species and parameters from different models;</li>
 
</ul>
 
</ul>
 
</td>
 
</td>
 
<td rowspan="4" valign="top" >
 
<td rowspan="4" valign="top" >
 
<ul>
 
<ul>
−
<li>Sign < * > for defining main model isn't supported,</li>
+
<li>Sign < * > for defining main model,</li>
−
<li>Replacing on elements which are located below in more than one level  
+
<li>Replacing of elements with more than one level of depth
 
<br><b>Example:</b> s1 is A.B.s2,</li>
 
<br><b>Example:</b> s1 is A.B.s2,</li>
−
<li>Replacing elements which have different types,</li>
+
                                <li>Replacing of elements other than species and parameters,</li>
−
                                 <li>Can import only diagram from the current collection,</li>
+
<li>Replacing of elements with different types,</li>
−
                                 <li>Declaration <i>"deletions"</i> isn't supported,</li>
+
                                 <li>Import models from other collections,</li>
−
                                 <li>Substitutional elements must be registered in model parameters;</li>
+
                                 <li>"Deletion" attributes,</li>
 +
                                 <li>Operating with submodel elements wich are not defined in model definition as ports explicitly;</li>
 
</ul>
 
</ul>
 
</td>
 
</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
−
<td bgcolor="#999999">New elements which we added in Antimony language</td>
+
<td bgcolor="#999999">New elements which we have added in Antimony language</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>

Revision as of 16:16, 14 November 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.

Supported Antimony features Not supported in current version
  • Creating and removing of species, compartments,
  • Putting nodes into parental compartments,
  • Initial values changing,
  • Creating and removing of reaction with reactants and products,
  • Editing of reaction kinetic laws,
  • Creating, removing and editing of functions,
  • Creating, removing and editing of scalar and rate equations,
  • Declarating species and variables as constants;
  • Declaration "DNA strand definitions" isn't supported,
  • From symbol types, only "species" and "compartment" are supported,
  • Reactions with interactions (inhibition, activation);
Necessary additions in the antimony specification
  • Algebraic rules
  • Distinguishing between initial value and initial assignment with numerical value,
  • Independent management of "constant" and "boundary conditional" attributes,

Composite model

Use model definition or external model for adding subdiagram.
Use parameters of subdiagram or synchronization for adding connection.

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 corresponds to the composite model. Main model will be created and it contains all models like model definitions.

Supported Antimony features Not supported in current version
  • Model definitions,
  • External models,
  • SubDiagrams,
  • Replacing species and parameters from different models;
  • Sign < * > for defining main model,
  • Replacing of elements with more than one level of depth
    Example: s1 is A.B.s2,
  • Replacing of elements other than species and parameters,
  • Replacing of elements with different types,
  • Import models from other collections,
  • "Deletion" attributes,
  • Operating with submodel elements wich are not defined in model definition as ports explicitly;
New elements which we have added in Antimony language
  • Prefix for different type ports:
    • contact: "a",
    • input: ">a",
    • output: "<a";

    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=5294"
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