• Share
  • Email
  • Embed
  • Like
  • Save
  • Private Content
Accessing and scripting CDK from Bioclipse

Accessing and scripting CDK from Bioclipse



Presentation held at the CDK workshop 2009.

Presentation held at the CDK workshop 2009.



Total Views
Views on SlideShare
Embed Views



1 Embed 3

http://www.slideshare.net 3



Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
Post Comment
Edit your comment
  • Major bug: JCP
  • JAX x 2006 Trophees du libre 2007

Accessing and scripting CDK from Bioclipse Accessing and scripting CDK from Bioclipse Presentation Transcript

  • Accessing and scripting CDK from Bioclipse Ola Spjuth [email_address] Dept. Pharmaceutical Biosciences Uppsala University, Sweden http://www.bioclipse.net http://bioclipse.blogspot.com
  • Contents
    • Introduction to Bioclipse
    • The use of CDK in Bioclipse
    • Scripting CDK in Bioclipse
    • Calculating CDK properties
    • Some ongoing Bioclipse projects
  • Before we start
    • Download latest Bioclipse now from Sourceforge
    • (see www.bioclipse.net for link)
    • Installation on lab computers does not work.
    • Please note:
    • We will be using a Beta in the workshop. Bioclipse 2.0 is scheduled for release in late May.
  • Bioclipse history
    • Prof. Wikberg’s group performed Proteochemometrics analyses:
    • Heterogeneous data, many different software, incompatible file formats
    • At the CDK workshop 2005 in Cologne, teamed up with Steinbeck et. al. to form the Bioclipse project.
    • Internationally awarded 3 times
  • Introduction to Bioclipse
    • Bioclipse is a Rich Client
      • Standalone app, not run in a browser
      • Today’s desktop computers and laptops are powerful
      • Also take advantage of online resources (e.g. data, services, HPC)
    • > Intuitive, native, responsive GUI
    • > Full integration with operating system
  • Introduction to Bioclipse
    • Bioclipse is a built on Eclipse Rich Client Platform
      • Previously an IBM project, now an Open Source project managed by the Eclipse Foundation (www.eclipse.org)
    • Every application is a set of plugins
      • Even core modules
    • Can be extended by adding more plugins
  • Component based architecture Bioclipse Proteochemometrics 2D 3D Data analysis Spectra Molecular dynamics
  • Getting Bioclipse
    • Download latest from Sourceforge (see www.bioclipse.net for link)
    • Unzip
    • Start
    Bioclipse welcome page contains tutorials and links
  • Software updates After installation and restart we have new functionality and more options!
  • Install Sample Data Menu: File > New… Use name: Sample Data
  • The Workspace
    • Place on the local hard disk managed by Bioclipse
      • Track changes
      • Drag and drop or cut and paste into it
    Project Folder File(s)
  • Toolbar Perspective bar Stacked views Welcome Jmol Editor Outline Navigator Properties Javascript Console The Bioclipse Workbench
  • Bioclipse basics
    • Open files in editors
      • Double-click the file
      • Chose editor: Right-click file > Open with…
    • Show views
      • Menu: Window -> Show View > Other..
    • Customize workbench
      • Change size and drag views and editors around
      • Edit preferences in menu: Window > Preferences
    • Help system
      • Menu: Help > Help contents
  • Cheat Sheets Step by step tutorials inside the Workbench Interactive with actions to perform Menu: Help > Cheat Sheets
  • Bioclipse domain objects
    • IBioObject All domain objects in Bioclipse (UID)
    • IMolecule All molecules implementations (must
    • provide SMILES and/or CML)
    • ICDKMolecule CDK implementation of IMolecule
    ISequence IBioJavaSequence
    • Enter commands in the Javascript Console
    Scripting Bioclipse Manager Method Parameter(s)
  • Scripting Bioclipse
    • List available managers:
    • help (or press Tab key)
  • Scripting Bioclipse
    • List methods in a manager:
    • help <manager name>
  • Scripting Bioclipse
    • Get help for a method:
    • help <manager name>.<method name>
    • Example: help cdk.loadMolecule
  • Some basic CDK commands in Bioclipse Don’t forget tab-completion!
  • I/O and GUI interaction 1) Type 2) Drag and drop
  • Cheminformatics I/O
    • Ways to load molecules:
    • cdk.loadMolecule(“/Project/file.mol”)
    • cdk.loadMolecule(“/full/path/to/file.mol”)
    • Load several molecules:
    • cdk.loadMolecules(“/Project/file.sdf”)
    • cdk.loadMolecules(“/full/path/to/file.sdf”)
  • Javascript Editor
    • Edit and launch scripts with .js extension
    Script: /Sample Data/Javascripts/extractsmilesAndMass.js Execute script
  • Gists
    • Gist = versioned script [ http://gist.github.com ]
      • Ideal for sharing scripts online
      • Find gists for Bioclipse:
        • http://delicious.com/tag/bioclipse+gist
      • Find gists for the workshop:
        • http://delicious.com/tag/bioclipse+gist+cdkws2009
    • Bioclipse has Gist support built-in:
    • gist.download(95755)
    • gist.download(84188,”/Virtual/glu.js”)
  • Example script: Download and visualize proteins Script: /Sample Data/Javascripts/dnaiso.js Gist: 95779
  • Multiple molecules Script: /Sample Data/Javascripts/multimol.js Gist: 95790
  • Scripting Jmol Jmol manager: jmol.spinOn() Run general Jmol script: jmol.run(“spin on”)
  • 2D coordinates
  • 3D coordinates
  • 2D/3D complete script Script: /Sample Data/Javascripts/gencoords.js Gist: 95755
  • Script JCP editing Script: /Sample Data/Javascripts/buildmol.js Gist: 96594
  • Balloon: Conformer generation
    • Generate 3D coordinates
    • res=balloon.generate3Dcoordinates(&quot;/Sample Data/2D structures/ATP.mol&quot;)
    • Generate 10 conformations
    • res=balloon.generate3Dconformations(&quot;/Sample Data/2D structures/ATP.mol&quot;, 10)
    • ui.open(res)
    • ui.open(res, &quot;jmol&quot;)
    • ui.open(res)
    [ http://web.abo.fi/~mivainio/balloon ]
  • Javascript in Javascript Console
    • Use Javascript mixed with Manager code!
    • var mols = cdk.loadMolecules(&quot;/Sample Data/SDF/Fragments2.sdf&quot;);
    • for (var i = 0; i < mols.size(); i++) {
    • js.print(mols.get(i).getSMILES() + &quot; &quot;);
    • }
    • Plugins add new managers and new commands
  • Calculating CDK properties (descriptors)
    • List descriptors:
    • qsar.getDescriptorIDs()
    • Calculate a descriptor:
    • qsar.calculate(IMolecule, descriptorID)
    • Descriptor IDs are from the Blue Obelisk Descriptor Ontology
    • http://blueobelisk.sourceforge.net
  • Calculating CDK properties Command: qsar.calculate( molecule, descriptor) Script: /Sample Data/Javascripts/qsar.js Gist: 95194
  • Calculating CDK properties: Multiple molecules, multiple descriptors Command: qsar.calculateNoParams( molecules, descriptors) Script: /Sample Data/Javascripts/qsar-multi.js Gist: 95189
  • Bridging JS to R
    • Bioclipse has an R-console
      • Menu: Window > Show View > Other > R-Console
    • Access JS variables with `myJSvariable`
  • Calculating CDK properties: QSAR project
    • Create New QSAR project
    • Menu: File > New… > QSAR Project
    QSAR Editor Cheat Sheet: QSAR Project
  • Use R on QSAR dataset
  • To sum up: What is Bioclipse?
    • Bioclipse is an intuitive workbench for end users in life science
    • Bioclipse is an advanced scriptable framework for power users
    • Bioclipse is a platform for rapid development and provisioning
  • Some ongoing Bioclipse projects
  • Speclipse: Spectrum analysis in Bioclipse More information: Stefan Kuhn and Dr. Christoph Steinbeck, EBI, UK
  • MetaPrint2D: Site-of-metabolism prediction Collaboration with Dr. Lars Carlsson, AstraZeneca, SE and Prof. Robert Glenn, Cambridge University, UK
  • Pharmacophores Collaboration with Dr. John Van Drie (Van Drie Research LLC) and Dr . Rajarshi Guha (Indiana University)
  • Brunn: High Throughput Screening Collaboration with Prof. Rolf Larsson, Dept Clinical Pharmacology, Uppsala University, Sweden www.brunn.sf.net More information: Jonathan Alvarsson, Uppsala University, Sweden
  • Data analysis Collaboration with Genetta Soft AB, Sweden. www.genettasoft.com
  • Bioclipse Licensing
    • Bioclipse: EPL - Eclipse public license
      • Flexible open source license
    • Plugins: Any license, even commercial
      • All plugins packaged with Bioclipse are free and open source
  • Acknowledgements
    • Dept. Pharmaceutical Biosciences, Uppsala University, Sweden
    • Prof. Jarl E. S. Wikberg
    • Dr. Egon Willighagen
    • Martin Eklund
    • Jonathan Alvarsson
    • Carl Mäsak
    • Eskil Anderssen
    • Annsofi Andersson
    • Arvid Berg
    • Bjarni Juliusson
    • Unilever Centre for Molecular Informatics, Univ. Cambridge, UK
    • Prof. Peter Murray-Rust
    • Prof. Robert Glen
    • Samuel Adams
    • Linnaeus Centre for Bioinformatics, Uppsala, Sweden
    • Dr. Erik Bongcam-Rudloff
    • Sofia Burvall
    • Eur opean Bioinformatics Institute, Hinxton, UK
    • Dr. Christoph Steinbeck
    • Stefan Kuhn
    • Dr. Gilleain Torrence
    • Cologne University Bioinformatics Centre (CUBIC), Germany
    • Dr. Tobias Helmus
    • Miguel Rojas
    • Thomas Kuhn
    • Dept Clinical Pharmacology, Uppsala University, Sweden
    • Prof. Rolf Larsson
    • Dr. Claes Andersson
    • Hanna Göransson
    • Ludwig-Maximilians-Universität, Munich, Germany
    • Dr. Johannes Wagener
    • Dept. Pharmaceutical Biosciences, Uppsala University, Sweden
    • Prof. Johan Åqvist
    • Dr. Martin Nervall
    • Göran Wallin
    • Global Safety Assessment, AstraZeneca, Mölndal Sweden
    • Dr. Scott Boyer
    • Dr. Lars Carlsson
    • Van Drie Research LLC, MA, US
    • Dr. John Van Drie
    • Indiana University, IN, USA
    • Dr. Rajarshi Guha
    • Others
    • Dr. Jerome Pansanel
    • … and all others for contributing code, feature requests, bug reports, proposals, and comments!
  • Thank you!
    • Ola Spjuth
    • [email_address]