This is a brief overview of new features that we introduced in this version:

• Preferences
• Look & feel
• ODE solver for stiff problems
• User interface for rules and events
• Performance improvements
• Bug fixing

Please note: the document is under construction.

Preferences

From a programmer´s view point
will be described latter

From a user´s view point
You can press preferences button     in the workbench toolbar and Preferences dialog will be open.

• Java simulation engine, output directory - specifies output directory where the simulation engine will store the generated code.
• MATLAB simulation engine, output directory - specifies output directory where the simulation engine will store the generated code.
• Look and feel - possible look and feel that can be used.
• Look and feel theme - if look and feel supports themes you can select one of them to be used by the workbench.

Additionally many dialogs stores their preferences, for example directory that was used last time in preferences, but this properties are hidden in Preferences dialog.

Look and feel

Currently BioUML workbench allows user to specify his favorite look and feel and theme (if selected look and feel supports themes) using Preferences described above. There is special extension poit that allows to add new look and feels and their themes. List of look and feels that are available in default installation of BioUML workbench are shown in the figure above.

BioUML workbench version 0.7.0 (alpha)

This is a brief overview of main features that we introduced in this version:

	Eclipse runtime for plug-ins management
	Ontology diagram type
	Reaction concept refactoring
	HTML description for diagram
	Legend for diagram types
	Systems Biology Markup Language support

Eclipse runtime for plug-ins management

The main change in BioUML architecture is using of Eclipse platform to provide BioUML workbench extensibility as well as seamless integration with other tools for systems biology. 

BioUML workbench now is a plugin-based application framework. It consists from a core runtime kernel that supports 'plug-ins' and a set of plug-ins that support database access, diagram editing, and simulation for different complex systems.

A plug-in is a structured component that describes itself to the system using a XML-based manifest file (plugin.xml).  We use Eclipse runtime to start the workbench and dynamically discover plug-ins. The platform maintains a registry of installed plug-ins and the function they provide.

Functionality is added to BioUML workbench using a common extension model.

Extension points are well-defined function points in the system that can be extended by plug-ins. When a plug-in contributes an implementation for an extension point, we say that it adds an extension to the platform. Plug-ins can define their own extension points, so that other plug-ins can integrate tightly with them.

Further details:
   extension points
   plug-ins (will be available soon)

Ontology diagram type

We have introduced new diagram type for ontological description of some biological process or system. This diagram type is also convenient as overview.
 

Reaction concept update

BioUML user guide provides a description of new approach.

HTML description for diagram

Now arbitrary HTML text can be associated with the diagram as its description. BioUML workbench provides simple editor to edit the description as HTML or plain text.

Legend for diagram types

Now each diagram type should provide a legend that describes visual syntax used by the diagram.

Special tab show the diagram legend as HTML text.

  Issue Online Request for Proposal .