Bioclipse Decision Support

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Bioclipse Project
Maintainer:Ola
Plugins path:net.bioclipse.ds.*
Status:Stable
Wiki page last updated:2014-03-19
Repo URL:http://github.com/bioclipse/bioclipse.ds

Aim

Ds-view.png

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

Ds single 400.png

Installation

  • Grab the latest Bioclipse release
  • Use the Install option in the main menu till install DS models

Usage

  • 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".
Ds multimol 400.png


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

  • Exact matches (InChI, molecular signature, and CDK fingerprint)
  • Near neighbours (CDK fingerprints)
  • QSAR models (libsvm with atom signatures) - classification and regression models
  • Structural alerts (SMARTS and Signatures)

Example of a custom DS implementation

Available Datasets

  • Ames Mutagenicity
  • CPDB Carcinogenicity
  • AHR inhibition

Model discovery

Made possible via looking up and invoking OpenTox services.

Model building

Early prototype exists in github (must be built from source), branch sdk.

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'.


Citing Bioclipse DS

Spjuth O, Eklund M, Ahlberg Helgee E, Boyer S, Carlsson L. 
Integrated decision support for assessing chemical liabilities. 
J Chem Inf Model. 2011 Aug 22;51(8):1840-7. 
doi: 10.1021/ci200242c. Epub 2011 Aug 5. PubMed PMID: 21774475.


Contact

ola(AT)bioclipse.net