Difference between revisions of "BioNetGen"
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==BioNetGen plugin== | ==BioNetGen plugin== | ||
[[File:bionetgen demo.png|thumb|Visual (SBGN) and text-based (BioNetGen) representations of the rule based model in BioUML]] | [[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]] | + | [[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; | * 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 | + | * 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> | 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 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 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 {{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 {{Type link|diagram}} won't be changed and won't be replaced.<br> | ||
==Features overview== | ==Features overview== | ||
| − | Currently plugin is in | + | 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" | {| border="1" cellpadding="4" cellspacing="0" align="center" | ||
|- | |- | ||
! style="background:#efefef;" | Features which are supported within plugin | ! style="background:#efefef;" | Features which are supported within plugin | ||
| − | ! style="background:#efefef;" | Features of the BioNetgen which are not supported in the | + | ! style="background:#efefef;" | Features of the BioNetgen which are not supported in the current version |
|- | |- | ||
| | | | ||
| − | * 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 properties editing of reactions with reactants and products; | ||
* Creating, removal and editing of variables' initial assignment (scalar rate equation); | * Creating, removal and editing of variables' initial assignment (scalar rate equation); | ||
| + | * Labels usage for parameters, seed species, reaction rules and observables; | ||
* Deploying diagram. | * Deploying diagram. | ||
| | | | ||
| − | * | + | * Compartments; |
| − | * | + | * User defined functions; |
* Nf and stochastic simulations; | * Nf and stochastic simulations; | ||
| − | |||
* Expressions usage in observable definition. | * Expressions usage in observable definition. | ||
|} | |} | ||
Latest revision as of 18:16, 21 July 2015
Contents |
[edit] BioNetGen plugin
BioNetGen (BNG) plugin for BioUML 2023.3 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 recreate appropriate BNG-text. If "Recreate text" button is pressed text will be recreated using diagram.
Note: all text formatting and some of comments (which are not linked with existing nodes or variables) will be removed.
"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.
[edit] Features overview
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.
| Features which are supported within plugin | Features of the BioNetgen which are not supported in the current version |
|---|---|
|
|
Note: plugin also does not support changing of the species' initial value in the actions block.
