BioNetGen

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BioNetGen plugin

Visual (SBGN) and text-based (BioNetGen) representations of the rule based model in BioUML

BioNetGen (BNG) plugin for BioUML 2016.4 aims to combine two representations of the rule based model in BioUML:

  • visual representation as BioUML Type-diagram-icon.png diagram using special BNG-notation;
  • text-based representation using BioNetGen Language (BNGL)[1][2].

Plugin allows user to edit model both as BioUML Type-diagram-icon.png diagram and BNG-text. Visual representation being changed BNG-text is updated on the fly.
Text changes are applied to the Type-diagram-icon.png diagram on demand (after "Apply BioNetGen" button have been pressed).
Besides model representations synchronisation, also care is taken of preserving user Type-diagram-icon.png 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 Type-diagram-icon.png diagram is changed before this button have been pressed, all changes in text will be lost!

Scheme for species adding via BioNetGen
Scheme for reaction adding via BioNetGen

It is allowed one to recreate appropriate BNG-text. If "Recreate text" button is pressed text will be recreated using Type-diagram-icon.png 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 Type-diagram-icon.png diagram will be substituted by deployed Type-diagram-icon.png diagram (it will not be saved without pressing of the save button, and will have "_deployed" suffix in its name).
Note: source Type-diagram-icon.png diagram won't be changed and won't be replaced.

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
  • 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);
  • Labels usage for parameters, seed species, reaction rules and observables;
  • Deploying diagram.
  • Compartments;
  • User defined functions;
  • Nf and stochastic simulations;
  • Expressions usage in observable definition.


Note: plugin also does not support changing of the species' initial value in the actions block.

References

  1. http://bionetgen.org
  2. BioNetGen language format

See also

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