Overview

This plug-in allows customer to use models in SBML format from BioUML workbench. The plugin is part of standard distributive of BioUML workbench. We have packed all models from SBML Model Repository into SBML model repository module that can be downloaded from the site and imported into BioUML workbench.

SBML diagram view in BioUML workbench and results of its simulation
(big picture)

Special module type is used to store SBML models. Unlike other BioUML modules SBML module type has not 'Data' section. These is due to that all information about species and reactions is defined inside SBML model files.

Special diagram type is used to show SBML models as diagrams. This diagram type is very similar with BioUML standard pathway simulation diagram and we use the same graphic notation.

These diagram type can be used for model simulation using MATLAB plug-in. The plugin will generate MATLAB files and starts MATLAB engine for model simulation and results visualization (see plugin user guide for more details).

While SBML model do not provides information about diagram layout some very simple layout algorithm is used for initial species and reactions layout.

The user can customize the layout and store it. For this purpose plugin defines its own extensions to store diagram layout data in <annotations> element.

Current plugin version is 0.7.0. It supports SBML level 1 version 1 format, however some features are not supported yet:

• rules - rules are ignored yet, some rules support will be available at BioUML version 0.7.5;
• unit list - plugin ignore unit list;
• functions - plugin does not support functions that can be used in kinetic low formulas;
• annotations - plugin does not support annotations provided by other software.

Further reading:

• What is SBML? - brief description of SBML and most essential links.
• User guide - describes the plug-in from the user view point.
• Implementation notes - describes classes that are used in plug-in, peculiarities and tricks how SBML models is mapped into BioUML internal model and vice versa as well as <biouml:> extensions to store diagram layout data in <annotations> element.
• SBML model repository module - we have packed all models from SBML Model Repository into one module that can be downloaded from the site and imported into BioUML workbench.