Bioclipse-An open source workbench for chemo- and

bioinformatics

Ola SpjuthDept. Pharmaceutical Biosciences

Uppsala UniversitySweden

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

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

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

Background: Eclipse

• Originally designed as an IDE– Java– C++– Web– etc…

• Today: Universal tool platform– Plugin architecture– Everything is a plugin, even core modules

Eclipse: screenshot

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

Architecture

•Access data from a variety of sources

Basic features

• Load, retrieve, edit, convert, analyze, visualize, and save biological entities– Small molecules– Proteins– Sequences– Spectra– Scripts– Reactions– Many more…

Bioclipse basics

View

View

Editor

ConsoleProperties

View

• Display information to user

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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

Perspective

Wizard

• Ordered set of dialogs

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Menus

Menus

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Context menus

Work with molecules in 2D:JChemPaint plugin

Visualize molecules in 3D: Jmol plugin

Work with spectra: Spectrum plugin

Work with sequences: BioJava plugin

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.

CMLRSS plugin: Chemistry on the web

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)

The WSDbfetch Web Servicein Bioclipse

Supported Databases:emblemblsvaemblconemblannconemblcdsmedlinepdbrefseqrefseqphgbaseinterprouniprotuniparcuniref100uniref90uniref50jpo_prtepo_prtuspto_prtipi

Scripting capabilities

• Javascript-based (Mozilla Rhino)

• Write scripts for anything!– Open wizards– Calculations– Pipelining tasks– Web services

Scripting capabilities

Plugging into Bioclipse

• Add functionality via plugins– Visualizations– Algorithms– Interfaces

• Plugins can interact!

• User may select what plugins to install

Plugin dependencies

Current development

• Maintain and develop Bioclipse core

• Increase basic features

• Support more file formats

• Online update function

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

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)

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

Future projects

• Integrate more tools and features!

• Find areas where plugin interaction lead to new possibilities

• Connect to GRID services

Major back-ends

• Chemoinformatics: Chemistry Development Kit (CDK)

• Bioinformatics: BioJava

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

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

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