BioNetGen - Revision history

Manikitos@yandex.ru: link fixed

2015-07-21T11:16:21Z

link fixed

Manikitos@yandex.ru: BioUML version used, features table corrected

2015-05-22T05:14:34Z

BioUML version used, features table corrected

Manikitos@yandex.ru at 04:52, 1 April 2014

2014-04-01T04:52:38Z

Manikitos@yandex.ru at 06:00, 20 March 2014

2014-03-20T06:00:40Z

Manikitos@yandex.ru: /* Features overview */

2014-03-17T04:18:39Z

‎Features overview

Manikitos@yandex.ru at 02:17, 26 November 2013

2013-11-26T02:17:11Z

Manikitos@yandex.ru at 09:47, 25 November 2013

2013-11-25T09:47:14Z

Manikitos@yandex.ru at 05:24, 25 November 2013

2013-11-25T05:24:39Z

Manikitos@yandex.ru: screenshots added

2013-11-25T05:23:29Z

screenshots added

Manikitos@yandex.ru at 01:19, 25 November 2013

2013-11-25T01:19:44Z

@@ Line 3: / Line 3: @@
 [[Biouml.plugins.bionetgen (plugin)|BioNetGen (BNG) plugin]] for [[BioUML]] {{BioUML current version}} aims to combine two representations of the rule based model in BioUML:
 * visual representation as BioUML {{Type link|diagram}} using special BNG-notation;
-* text-based representation using BioNetGen Language (BNGL)<ref> [http://bionetgen.org http://bionetgen.org] </ref><ref>[[BioNetGen diagram (file format)]]</ref>.
+* text-based representation using BioNetGen Language (BNGL)<ref> [http://bionetgen.org http://bionetgen.org] </ref><ref>[[BioNetGen language format]]</ref>.
 Plugin allows user to edit model both as BioUML {{Type link|diagram}} and BNG-text. Visual representation being changed BNG-text is updated on the fly.<br>
-Text changes are applied to the diagram on demand (after <i>"Apply BioNetGen"</i> button have been pressed).<br>
+Text changes are applied to the {{Type link|diagram}} on demand (after <i>"Apply BioNetGen"</i> button have been pressed).<br>
-Besides model representations synchronisation, also care is taken of preserving user diagram layout as well as BNG-text formatting (spaces, comments, etc.)<br>
+Besides model representations synchronisation, also care is taken of preserving user {{Type link|diagram}} layout as well as BNG-text formatting (spaces, comments, etc.)<br>
-<b>Please note:</b> text changes would be applied only after <i>"Apply BioNetGen"</i> button have been pressed. If diagram is changed before this button have been pressed, all changes in text will be lost!
+<b>Please note:</b> text changes would be applied only after <i>"Apply BioNetGen"</i> button have been pressed. If {{Type link|diagram}} is changed before this button have been pressed, all changes in text will be lost!
 [[File:Bionetgen adding species.png|thumb|Scheme for species adding via BioNetGen]]
 [[File:Bionetgen adding reaction rule.png|thumb|Scheme for reaction adding via BioNetGen]]
-It is allowed one to recreate appropriate BNG-text. If <i>"Recreate text"</i> button is pressed text will be recreated using diagram.<br>
+It is allowed one to recreate appropriate BNG-text. If <i>"Recreate text"</i> button is pressed text will be recreated using {{Type link|diagram}}.<br>
 <b>Note:</b> all text formatting and some of comments (which are not linked with existing nodes or variables) will be removed.<br>
-<i>"Deploy diagram"</i> button being pressed deployed model is generated. Deployed model corresponds to the model created by source BioNetGen using generate_network action. If there exists this action in the BNG-text BioUML use its parameterts otherwise default parameters are used. Source diagram will be substituted by deployed diagram (it will not be saved without pressing of the save button, and will have "_deployed" suffix in its name).<br>
+<i>"Deploy diagram"</i> button being pressed deployed model is generated. Deployed model corresponds to the model created by source BioNetGen using generate_network action. If there exists this action in the BNG-text BioUML use its parameterts otherwise default parameters are used. Source {{Type link|diagram}} will be substituted by deployed {{Type link|diagram}} (it will not be saved without pressing of the save button, and will have "_deployed" suffix in its name).<br>
-<b>Note:</b> source diagram won't be changed and won't be replaced.<br>
+<b>Note:</b> source {{Type link|diagram}} won't be changed and won't be replaced.<br>
 ==Features overview==

@@ Line 1: / Line 1: @@
 ==BioNetGen plugin==
 [[File:bionetgen demo.png|thumb|Visual (SBGN) and text-based (BioNetGen) representations of the rule based model in BioUML]]
-[[Biouml.plugins.bionetgen (plugin)|BioNetGen (BNG) plugin]] for [[BioUML]] 0.9.6 aims to combine two representations of the rule based model in BioUML:
+[[Biouml.plugins.bionetgen (plugin)|BioNetGen (BNG) plugin]] for [[BioUML]] {{BioUML current version}} aims to combine two representations of the rule based model in BioUML:
 * visual representation as BioUML {{Type link|diagram}} using special BNG-notation;
 * text-based representation using BioNetGen Language (BNGL)<ref> [http://bionetgen.org http://bionetgen.org] </ref><ref>[[BioNetGen diagram (file format)]]</ref>.
@@ Line 18: / Line 18: @@
 ==Features overview==
-Currently plugin is in alpha version, so some features of the BioNetGen aren't supported. Also we want to achieve full synchronisation between BioNetGen and plugin.
+Currently plugin is in beta version, so some features of the BioNetGen aren't supported. Also we want to achieve full synchronisation between BioNetGen and plugin.
 {| border="1" cellpadding="4" cellspacing="0" align="center"
@@ Line 32: / Line 32: @@
 * Deploying diagram.
+|
-* Functions;
+* Compartments;
 * Nf and stochastic simulations;
 * Expressions usage in observable definition.

@@ Line 11: / Line 11: @@
 [[File:Bionetgen adding species.png|thumb|Scheme for species adding via BioNetGen]]
 [[File:Bionetgen adding reaction rule.png|thumb|Scheme for reaction adding via BioNetGen]]
-It is allowed one to remove connection with current version of BNG-text. To do it <i>"Remove connection"</i> button should be pressed. If this button is pressed text is recreated using diagram.<br>
+It is allowed one to recreate appropriate BNG-text. If <i>"Recreate text"</i> button is pressed text will be recreated using diagram.<br>
-<b>Note:</b> all text formatting and some of comments (which are not linked with existing nodes or variables) will be removed. Also BNG-attribute will be removed (new BNG-attribute will be added when the <i>"Apply BioNetGen"</i> button is pressed).<br>
+<b>Note:</b> all text formatting and some of comments (which are not linked with existing nodes or variables) will be removed.<br>
 <i>"Deploy diagram"</i> button being pressed deployed model is generated. Deployed model corresponds to the model created by source BioNetGen using generate_network action. If there exists this action in the BNG-text BioUML use its parameterts otherwise default parameters are used. Source diagram will be substituted by deployed diagram (it will not be saved without pressing of the save button, and will have "_deployed" suffix in its name).<br>
 <b>Note:</b> source diagram won't be changed and won't be replaced.<br>

@@ Line 23: / Line 23: @@
 |-
 ! style="background:#efefef;" | Features which are supported within plugin
-! style="background:#efefef;" | Features of the BioNetgen which are not supported in the alpha-version
+! style="background:#efefef;" | Features of the BioNetgen which are not supported in the current version
 |-
+|
@@ Line 29: / Line 29: @@
 * Creating, removal and properties editing of reactions with reactants and products;
 * Creating, removal and editing of variables' initial assignment (scalar rate equation);
 * Deploying diagram.
+|
 * Functions;
 * Nf and stochastic simulations;
 * Expressions usage in observable definition.
 |}

@@ Line 26: / Line 26: @@
 |-
+|
-* Creating, removal and properties editing of species, molecules, molecule components, observables;
+* Creating, removal and properties editing of species, molecules, molecule components, observables, molecule types;
 * Creating, removal and properties editing of reactions with reactants and products;
 * Creating, removal and editing of variables' initial assignment (scalar rate equation);
 * Deploying diagram.
+|
 * Functions;
 * Nf and stochastic simulations;

@@ Line 11: / Line 11: @@
 It is allowed to remove connection with current version of BNG-text. To do it <i>"Remove connection"</i> button should be pressed. If this button is pressed text is recreated using diagram.<br>
 <b>Note:</b> all text formatting and some of comments will be removed. Also BNG-attribute will be removed.<br>
-<i>"Deploy"</i> button being pressed deployed model is generated. Source diagram will be substituted by deployed diagram (it will not be saved without pressing of the save button, and will have "_deployed" suffix in its name).<br>
+<i>"Deploy diagram"</i> button being pressed deployed model is generated. Source diagram will be substituted by deployed diagram (it will not be saved without pressing of the save button, and will have "_deployed" suffix in its name).<br>
 <b>Note:</b> source diagram won't be changed and won't be replaced.<br>
 [[File:Bionetgen adding species.png|thumb|Scheme for species adding via BioNetGen]]