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Accessing and scripting CDK from Bioclipse
 

Accessing and scripting CDK from Bioclipse

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Presentation held at the CDK workshop 2009.

Presentation held at the CDK workshop 2009.

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  • Major bug: JCP
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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]
    www.bioclipse.net