Difference between revisions of "BioNetGen"
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| − | ==BioNetGen | + | ==BioNetGen plugin== |
| − | BioNetGen (BNG) | + | [[Biouml.plugins.bionetgen (plugin)|BioNetGen (BNG) plugin]] for BioUML 0.9.6 aims to combine two representations of the rule based model in BioUML: |
* visual representation as BioUML-diagram using special BNG-notation; | * visual representation as BioUML-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 diagram (file format)]]</ref>. | ||
| − | + | Plugin allows user to edit model both as BioUML-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 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 diagram layout as well as BNG-text formatting (spaces, comments, etc.)<br> | ||
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==Features overview== | ==Features overview== | ||
| − | Currently | + | 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. |
{| border="1" cellpadding="4" cellspacing="0" align="center" | {| border="1" cellpadding="4" cellspacing="0" align="center" | ||
|- | |- | ||
| − | ! style="background:#efefef;" | Features which are supported within | + | ! 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 alpha-version | ||
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<br> | <br> | ||
| − | <b>Note:</b> | + | <b>Note:</b> plugin also does not support changing of the species' initial value in the actions block. |
==References== | ==References== | ||
Revision as of 14:10, 18 November 2013
Contents |
BioNetGen plugin
BioNetGen (BNG) plugin for BioUML 0.9.6 aims to combine two representations of the rule based model in BioUML:
- visual representation as BioUML-diagram using special BNG-notation;
- text-based representation using BioNetGen Language (BNGL)[1][2].
Plugin allows user to edit model both as BioUML-diagram and BNG-text. Visual representation being changed BNG-text is updated on the fly.
Text changes are applied to the diagram on demand (after "Apply BioNetGen" button have been pressed).
Besides model representations synchronisation, also care is taken of preserving user diagram layout as well as BNG-text formatting (spaces, comments, etc.)
Please note: text changes would be applied only after "Apply BioNetGen" button have been pressed. If diagram is changed before this button have been pressed, all changes in text will be lost!
It is allowed to remove connection with current version of BNG-text. To do it "Remove connection" button should be pressed. If this button is pressed text is recreated using diagram.
Note: all text formatting and some of comments will be removed. Also BNG-attribute will be removed.
"Deploy" 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).
Note: source diagram won't be changed and won't be replaced.
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.
| Features which are supported within plugin | Features of the BioNetgen which are not supported in the alpha-version |
|---|---|
|
|
Note: plugin also does not support changing of the species' initial value in the actions block.
