Sections
You are here: Home » Meet » OpenTox 2011 » Apply Bioclipse and OpenTox to modify Chemical Structure to remove Toxicity

Apply Bioclipse and OpenTox to modify Chemical Structure to remove Toxicity

Facilitated by Ola Spjuth

This activity will feature a hands-on session with Bioclipse and the Decision Support feature together with the recently developed OpenTox plugin. Participants will be given the chance to modifying chemical structures with the aim to overcome chemical liabilities. Also covered will be how to script OpenTox using the Bioclipse Scripting Language (BSL).

 

Links:

* Activity wiki page - http://wiki.bioclipse.net/index.php?title=OpenTox2011
* Bioclipse Decision Support - http://www.bioclipse.net/decision-support


Download and install Bioclipse

You can find download links on the Activity wiki page referenced above

 

Getting Started

  • Start Bioclipse
  • Open the Decision Support Perspective (menu: Window > Open perspective > other.. > Decision support)
  • Create a new sample data project (menu: File > New... > Project > Other > Sample data project)
  • In the Navigator, double-click on a 2D molecule to open the 2D editor
  • In the Decision Support View, click the "Run" button.
  • Inspect the results...

 

Additional information

In May 2011 we held an online tutorial session. You can download a recording of the tutorial at

http://opentox.org/data/documents/development/tutorialfiles/downloads/2011-05-25_Bioclipse-OpenTox-Integration.wmv

 

Scripting

If you are interested in learning how to use and develop scripts in Bioclipse to access OpenTox services, visit the following page:

http://chem-bla-ics.blogspot.com/2011/05/my-slides-for-this-afternoons-bioclipse.html

 

Evaluation Form

Complete the evaluation form following this link: Evaluation Form

Document Actions