SBSI Visual

SBSIVisual is a desktop application whose primary purpose is to provide a user-friendly way to access SBSINumerics tools, databases and standard systems biology services. For simulations, the Copasi simulation library is bundled with SBSIVisual:

SBSIVisual features a robust plugin mechanism for integrating new functionality, based on the Eclipse plugin mechanism. These plugins enable SBSI to be customized for a particular project.
There are several plugins for SBSI now available for easy installation.

Currently, from version 1.3.0, we have integrated the Biopepa stochastic modelling framework into SBSIVisual, thus enabling stochastic modellers to access the optimization functionality provided by SBSI.

We are developing a set of plugins for SBSI. Below are some screenshots illustrating its functionality.

SBSI Visual workbench

Configuring optimization parameters

Viewing optimization results: comparing simulation with experimental data

Plugins

Several plugins are available for SBSIVisual to extend its functionality. All are available from the
Help->Install New Software...
menu in SBSIVisual. Click on a title below for more information about a particular plugin.

Plasmo

A plugin for the Plasmo database is now available for SBSIVisual.
This enables SBSI users to search, download models and upload modified versions of the model back to Plasmo in a seamless and integrated fashion.

To access the Plasmo plugin from SBSIVisual, just click on
Help->Install New Software...
menu and select the URL : sbsi - http://www.sbsi.ed.ac.uk/update
from the 'work with' drop-down list.

Select 'Plasmo' then follow the installation wizard, accepting defaults.

VisualBiology SBML editor

An alpha release of a native Eclipse-based SBML editor is now available.
This is a form based SBML editor. Currently it will accept only SBML in level 2 version 4, and does not yet support models that contain FunctionDefinitions or Events.

To access the VisualBiology plugin from SBSIVisual, just click on
Help->Install New Software...
menu and select the URL : sbsi - http://www.sbsi.ed.ac.uk/update
from the 'work with' drop-down list.

Select 'Visual Biology' then follow the installation wizard, accepting defaults.

When the application restarts, you can select an SBML file in your workspace and from the context menu, click
Open With->SBML editor.
The source-code for this project is on the SBSI Sourceforge project site.

SBMLEditor

A plugin for EBI's SBMLeditor is now available for SBSIVisual.
This enables SBSI users to edit SBML models more easily than via the XML directly.

To access the SBMLeditor plugin from SBSIVisual, just click on
Help->Install New Software...
menu and select the URL : sbsi - http://www.sbsi.ed.ac.uk/update
from the 'work with' drop-down list.

Select 'SBMLeditor' then follow the installation wizard, accepting defaults.

Rule Base

RuleBase is an Eclipse plugin for the Kappa modelling language which can also be installed into SBSIVisual.

To access the RuleBase plugin from SBSIVisual, just click on
Help->Install New Software...

Click 'add' at top-right corner as we need to add the Eclipse update site for plugins that kappa needs. Type 'eclipse' in the name field, and http://download.eclipse.org/eclipse/update in the 'URL' field, then OK.
Click the 'add' button again . In text box type 'Kappa' for name, http://eclipse.rulebase.org for URL, then OK.
Now in the 'work with' drop down choose the kappa update site you entered in step 2.
Select the 'Rule Studio for Rulebase' plugin, leave the branding feature unchecked. Make sure 'Contact all update sites during install' is also checked.
Now click next and follow prompts. After restart you should be able to do :
File->New->Other->Plectix->KappaFile
and access a 'Kappa perspective' from
Window->Show Perspective.

SED-ED visual SED-ML editor

The SED-ED editor is a visual editor to view, edit and annotate SED-ML files. More information is available in the SED-ED online documentation.

To access the SED-ED editor plugin from SBSIVisual, just click on
Help->Install New Software...
menu and select the URL : sbsi - http://www.sbsi.ed.ac.uk/update
from the 'work with' drop-down list.

Select 'SED-ED editor' then follow the installation wizard, accepting defaults.

Full Help information is available in the embedded Help pages for this plugin.

Parallel Dimension View (PD-View) plugin

The PD-View plugin provides a view of a parameter optimization search behaviour. To find out more please see our online documentation.

To access the PD-View plugin from SBSIVisual, just click on
Help->Install New Software...
menu and select the URL : sbsi - http://www.sbsi.ed.ac.uk/update
from the 'work with' drop-down list.

Select 'PD-View' then follow the installation wizard, accepting defaults.

Full Help information is available in the embedded Help pages for this plugin.

Stochastic simulation plugin ( new from 1.4.0 ! )

This plugin provides stochastic simulations for SBML models using the Fern stochastic simulation library. To find out more please see our online documentation.
Thanks to Florian Erhard for kindly agreeing to make this library available through SBSI.

To access the Fern plugin from SBSIVisual, just click on
Help->Install New Software...
menu and select the URL : sbsi - http://www.sbsi.ed.ac.uk/update
from the 'work with' drop-down list.

Select 'Fern stochastic simulations' then follow the installation wizard, accepting defaults.

Full Help information is available in the embedded Help pages for this plugin.

Step function plugin ( new from 1.4.0 ! )

This prototype plugin provides support for changing parameter regimes in an SBML model, and is particularly suitable for editing light:dark patterns in Circadian clock modelling. To find out more please see the our PDF tutorial.
Help->Install New Software...
menu and select the URL : sbsi - http://www.sbsi.ed.ac.uk/update
from the 'work with' drop-down list.

Select 'Step Function editor' then follow the installation wizard, accepting defaults.

Full Help information is available in the embedded Help pages for this plugin.