Bioclipse

Bioclipse -An open source workbench for chemo- and bioinformatics Ola Spjuth Dept. Pharmaceutical Biosciences Uppsala University Sweden

What is Bioclipse? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

The Bioclipse project ,[object Object],[object Object],[object Object]

Implementation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Background: Eclipse ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Bioclipse architecture ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Basic features ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Bioclipse basics View View Editor Console Properties

View ,[object Object],[object Object]

Editor ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Perspective ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Menus ,[object Object],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 ,[object Object],[object Object],[object Object],[object Object]

CMLRSS plugin: Chemistry on the web

Web service support ,[object Object],[object Object],[object Object],[object Object],[object Object]

The WSDbfetch Web Service in Bioclipse Supported Databases: embl emblsva emblcon emblanncon emblcds medline pdb refseq refseqp hgbase interpro uniprot uniparc uniref100 uniref90 uniref50 jpo_prt epo_prt uspto_prt ipi

Scripting capabilities ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Plugging into Bioclipse ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Current development ,[object Object],[object Object],[object Object],[object Object]

Ongoing projects ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Ongoing projects ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Future projects ,[object Object],[object Object],[object Object]

Major back-ends ,[object Object],[object Object]

Licensing ,[object Object],[object Object],[object Object],[object Object]

Bioclipse Workshop 2007 ,[object Object],[object Object],[object Object],[object Object],[object Object]

Acknowledgements ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Bioclipse ,[object Object],Bioclipse: An open source workbench for chemo- and bioinformatics Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E.S. Wikberg BMC Bioinformatics 2007, 8:59

Bioclipse

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Bioclipse