Antimony - Revision history

Manikitos@yandex.ru: BioUML version used, minor fixes

2015-07-21T11:08:43Z

BioUML version used, minor fixes

Buharov@DevelopmentOnTheEdge.com at 10:24, 22 May 2014

2014-05-22T10:24:04Z

Buharov@developmentontheedge.com: /* Composite model */

2013-11-15T10:21:07Z

‎Composite model

Axec@dote.ru at 09:56, 14 November 2013

2013-11-14T09:56:32Z

Axec@dote.ru at 09:16, 14 November 2013

2013-11-14T09:16:42Z

Buharov@developmentontheedge.com: /* Composite model */

2013-11-13T11:50:19Z

‎Composite model

Buharov@developmentontheedge.com: /* Features overview */

2013-11-13T11:49:16Z

‎Features overview

Buharov@developmentontheedge.com: /* Composite model */

2013-11-13T11:48:33Z

‎Composite model

Buharov@developmentontheedge.com: /* Features overview */

2013-11-13T11:36:23Z

‎Features overview

Buharov@developmentontheedge.com: /* Composite model */

2013-11-13T11:32:58Z

‎Composite model

@@ Line 1: / Line 1: @@
 ==Antimony plugin==
 [[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]] {{BioUML current version}} aims to combine two representations of mathematical model (particularly - SBML model):
 <ul>
-<li>visual representation as BioUML-diagram using extended SBGN notation
+<li>visual representation as BioUML {{Type link|diagram}} using extended SBGN notation
 <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>
@@ Line 9: / Line 9: @@
 Plugin allows user to edit model both visually and as text.
 If visual repesentation is changed - antimony text is updated on the fly.<br>
-Text changes are applied to the diagram on demand (after pressing "Apply Antimony" button).<br>
+Text changes are applied to the {{Type link|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.)
 <br>
-<b>Please note:</b> antimony changes will be applied to the diagram only after "Apply Antimony" button is pressed.
+<b>Please note:</b> antimony changes will be applied to the {{Type link|diagram}} only after "Apply Antimony" button is pressed.
-If you change diagram before you press this button, all changes in text will be lost!
+If you change {{Type link|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]]

@@ Line 115: / Line 115: @@
 	</tr>
 	</table>
 == References==

@@ Line 67: / Line 67: @@
 [[File:SubDiagram.PNG |thumb| Use model definition or external model for adding subdiagram.]]
 [[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 corresponds to the composite model. Main model will be created and it contains all models like model definitions.

@@ Line 80: / Line 80: @@
 				<li>Model definitions,</li>
 				<li>External models,</li>
-				<li>SubDiagrams,</li>
+				<li>Submodels,</li>
 				<li>Replacing species and parameters from different models;</li>
 			</ul>

@@ Line 26: / Line 26: @@
 	<table  border="1" align="center"  cellspacing="0" cellpadding="4">
 	<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>
 		<td>
 			<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>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>
 		</td>
@@ Line 45: / Line 45: @@
 			<ul>
 			        <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>
 		</td>
@@ Line 57: / Line 57: @@
 		<ul>
                                  <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>
 		</td>
@@ Line 68: / Line 68: @@
 [[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">
 	<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>
@@ Line 81: / Line 81: @@
 				<li>External models,</li>
 				<li>SubDiagrams,</li>
-				<li>Replacing elements from different models;</li>
+				<li>Replacing species and parameters from different models;</li>
 			</ul>
 		</td>
 		<td rowspan="4" valign="top" >
 			<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>
-				<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>
 			</ul>
 		</td>
 	</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>

@@ Line 91: / Line 91: @@
 						<br><b>Example:</b> s1 is A.B.s2,</li>
 				<li>Synchronizing elements which have different types,</li>
-				<li>Defining a model into subdiagrams or other model definitions,</li>
+                                <li>Can import only diagram from the current collection,</li>
-				<li>Adding propagation ports;</li>
 			</ul>
 		</td>