Difference between revisions of "BioNetGen"
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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> | ||
| + | <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! | ||
[[File:Bionetgen adding species.png|thumb|Scheme for species adding via BioNetGen]] | [[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]] | [[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 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 (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. Also BNG-attribute will be removed (new BNG-attribute will be added when the <i>"Apply BioNetGen"</i> button is pressed).<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 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> | ||
Revision as of 09:17, 26 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 one 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 (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 "Apply BioNetGen" button is pressed).
"Deploy diagram" 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).
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.
