Bioclipse Decision Support

From BioclipseWiki

Contents 1 Aim 2 Installation and Usage 3 Architecture 4 Available implementations 5 Available Datasets 6 Support 7 Contact

Aim

Provide tools for decision support when editing chemical structures in Bioclipse for defined endpoints.

Installation and Usage

• Grab the latest Bioclipse-devel release.
• Install the Bioclipse Decision Support feature from the devel-update site
• Open the Decision Support Perspective
• Open a molecule in JChemPaint for 2D editing
• Click "Run" in the local toolbar of the Decision Support View.
• Fore more help, see the Bioclipse help (available from the Help menu inside the Bioclipse workbench) under topic "Bioclipse Decision Support".

Architecture

Extension point: id=net.bioclipse.decisionsupport

A sample extension looks like this (taken from the plugin net.bioclipse.ds.bursi):

  <extension
        point="net.bioclipse.decisionsupport">
        
        <endpoint
              id="net.bioclipse.ds.mutagenicity"
              description="Ability to induce mutations to DNA"
              icon="icons/radioactive.png"
              name="Mutagenicity">
        </endpoint>
        
     <test
           id="bursi.sdflookup.exact"
           name="Bursi exact matches"
           endpoint="net.bioclipse.ds.mutagenicity"
           class="net.bioclipse.ds.impl.SDFPosNegExactMatchFP"
           propertycalculator="Bursi Exact Match"
           informative="true"
           reportmodel="net.bioclipse.ds.impl.report.ExactMatchReportModel">
           <resource name="file"
                 path="data/cas_4337_noH_props.sdf">
           </resource>
           <parameter name="responseProperty" value="Ames test categorisation" />
           <parameter name="positiveValue" value="mutagen" />
           <parameter name="negativeValue" value="nonmutagen" />
     </test>

Available implementations

• Database lookups (Exact and Nearest Neighbors)
• Smarts searching

Available Datasets

• Bursi Ames Mutagenicity

Support

• Mailing list: Please use bioclipse-devel.
• Bugs: Please report bugs using the Bioclipse Bugzilla available at http://bugs.bioclipse.net and please use the product 'Bioclipse2' and component 'Decision Support'.

Contact

ola(AT)bioclipse.net