Download - Bioclipse
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Bioclipse-An open source workbench for chemo- and
bioinformatics
Ola SpjuthDept. Pharmaceutical Biosciences
Uppsala UniversitySweden
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What is Bioclipse?
• Workbench for life-science– Chemo- and bioinformatics
• Integration platform– Easy to integrate/extend functionality using
powerful plugin architecture
• Development environment– Inherit existing functionality
• Deployment framework– Spread your algorithms
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The Bioclipse project
• Objectives:– Provide a free, open source platform for
application development in life-science– Integrate as much functionality as possible
into a user-friendly workbench
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Implementation
• Type of application: Rich client– Responsive GUI– Make use of desktop computer
• Main programming language: Java– Platform independence– Existing components in bioinformatics
• Release for Windows, Linux, and Mac OS X
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Background: Eclipse
• Originally designed as an IDE– Java– C++– Web– etc…
• Today: Universal tool platform– Plugin architecture– Everything is a plugin, even core modules
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Eclipse: screenshot
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Bioclipse architecture
• Built on Eclipse Rich Client Platform (RCP)– Minimal set of Eclipse plugins to develop a
complete software application
• Powerful plugin-architecture– Everything is a plugin
• Extension points– Points that plugins can extend– Exist for almost anything– You can define new points
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Architecture
•Access data from a variety of sources
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Basic features
• Load, retrieve, edit, convert, analyze, visualize, and save biological entities– Small molecules– Proteins– Sequences– Spectra– Scripts– Reactions– Many more…
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Bioclipse basics
View
View
Editor
ConsoleProperties
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View
• Display information to user
• User might interact QuickTime™ and aTIFF (LZW) decompressor
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Editor
• Load/Save life cycle
• Undo/redo
• Cut and paste
• Text-based– Syntax highlighting– Code completion
• Graphical objects
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PDB Editor
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2D Editor
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Perspective
• Set of Views, menus, and editors with their relative position and sizes
• Can be changed• Saved between sessions• Examples
– Chemoinformatics perspective– Bioinformatics perspective– Spectrum perspective
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Perspective
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Wizard
• Ordered set of dialogs
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Menus
Menus
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Context menus
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Work with molecules in 2D:JChemPaint plugin
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Visualize molecules in 3D: Jmol plugin
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Work with spectra: Spectrum plugin
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Work with sequences: BioJava plugin
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CMLRSS plugin: Chemistry on the web
• Reader for chemical information in feeds using CML (Chemical Markup Language)
• Supports the formats: RSS 1.0, RSS 2.0, Atom 0.3, Atom 1.0
• Access structures/spectra/sequences published on the web– Blogs, databases etc.
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CMLRSS plugin: Chemistry on the web
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Web service support
• General Web service mechanism
• Example of Web services– WSDBFetch at EBI for retrieving proteins,
sequences from various databases– SubLoc for subcellular predictions– Alignments (BLAST, ClustalW)
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The WSDbfetch Web Servicein Bioclipse
Supported Databases:emblemblsvaemblconemblannconemblcdsmedlinepdbrefseqrefseqphgbaseinterprouniprotuniparcuniref100uniref90uniref50jpo_prtepo_prtuspto_prtipi
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Scripting capabilities
• Javascript-based (Mozilla Rhino)
• Write scripts for anything!– Open wizards– Calculations– Pipelining tasks– Web services
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Scripting capabilities
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Plugging into Bioclipse
• Add functionality via plugins– Visualizations– Algorithms– Interfaces
• Plugins can interact!
• User may select what plugins to install
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Plugin dependencies
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Current development
• Maintain and develop Bioclipse core
• Increase basic features
• Support more file formats
• Online update function
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Ongoing projects
• Structure-activity analysis– Descriptor calculation– Dataset/matrix editing– Interface with R for analysis
• Taverna interoperability– Run workflows from within Bioclipse– Visualize results from Taverna
• Computer aided structure elucidation
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Ongoing projects
• Local database persistence– Molecular libraries– Substructure searching– Virtual screening– Pharmacology– Drug screening data management– Interaction modeling
• New asynchronous Web services (XMPP)• Microarrays (Base 2.0)
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Ongoing projects
• Molecular dynamics (Ghemical, using JNI)• Systems biology (SBML)• Text mining (Oscar3)• Mass spectrometry (Mascot, other)• Reaction modeling• Semantic publishing (SciML)• Data analysis (R, Matlab, Java, 3’rd party)• More Web services
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Future projects
• Integrate more tools and features!
• Find areas where plugin interaction lead to new possibilities
• Connect to GRID services
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Major back-ends
• Chemoinformatics: Chemistry Development Kit (CDK)
• Bioinformatics: BioJava
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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
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Bioclipse Workshop 2007
• May 23-25, 2007, BMC, Uppsala• Lectures and hands-on labs to demonstrate the features of
Bioclipse, the power of the plugin architecture, and how to integrate new features into the framework.
• Participation in the workshop is free of charge.
• Workshop homepage:– http://teacher.bmc.uu.se/BioclipseWS07
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Acknowledgements
Dept. Pharmaceutical Biosciences, Uppsala University, Sweden
Prof. Jarl E. S. Wikberg
Martin Eklund
Jonathan Alvarsson
Dept of Chemistry, Molecular Informatics, Cambridge University
Prof. Peter Murray-Rust et al (CML)
Linnaeus Centre for Bioinformatics, Uppsala University and SLU, Sweden
Dr. Eric Bongcam-Rudloff
Sofia Burvall
Cologne University Bioinformatics Centre (CUBIC), Germany
Prof. Christoph SteinbeckEgon WillighagenTobias HelmusStefan KuhnMiguel RojasThomas Kuhn
OthersJohannes Wagener (Web services, scripting)Jerome Pansanel (Chemical structures)Rob Schellhorn (Ghemical)
… and all others for contributing code, feature requests, bug reports, proposals, and comments
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Bioclipse
www.bioclipse.net
Bioclipse: An open source workbench for chemo- and bioinformaticsOla Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E.S. WikbergBMC Bioinformatics 2007, 8:59