User documentation

Getting started with Bioclipse

Online help (from latest Bioclipse release)

Bioclipse blog


Scientific publications

  • O. Spjuth, M. Eklund, and J.E.S. Wikberg. An Information System for Proteochemometrics, CDK News, Vol. 2/2, 2005.
  • O. Spjuth, T. Helmus, E. Willighagen, S. Kuhn, M. Eklund, J. Wagener, P. Murray-Rust, C. Steinbeck, and J.E.S. Wikberg. Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinformatics, 2007, 8:59.
  • J. Wagener, O. Spjuth, E. L. Willighagen, and J. E. S. Wikberg. Xmpp for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. BMC Bioinformatics, 2009, 10:279.
  • O. Spjuth, J. Alvarsson, A. Berg, M. Eklund, S. Kuhn, C. Mäsak, G. Torrance, J. Wagener, E.L. Willighagen, C. Steinbeck, and J.E.S. Wikberg. Bioclipse 2: A scriptable integration platform for the life sciences. BMC Bioinformatics, 2009, 5:397
  • O. Spjuth, E.L. Willighagen, R. Guha, M. Eklund, and J.E.S. Wikberg. Towards interoperable and reproducible QSAR analyses: Exchange of data sets. Journal of Cheminformatics 2010, 2:5 doi:10.1186/1758-2946-2-5
  • L. Carlsson, O. Spjuth, S. Adams, R. C. Glen, and S. Boyer. Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2d and Bioclipse.BMC Bioinformatics 2010, 11:362 doi:10.1186/1471-2105-11-362
  • O. Spjuth. Bioclipse - integration of data and software in the life sciences. Doctoral Thesis, Uppsala University, 2009. ISBN 978-91-554-7633-5.

Articles in popular magazines

  • O. Spjuth. Using Bioclipse to integrate bioinformatics functionality, EMBNet News, March 13(1), 2005.
  • Bioclipse: Eine visuelle Ope-Source-Platform fûr Chemo- und Bioinformatik, JavaMagazine, 8, 2006.
  • O. Spjuth, J. Alvarsson, and D. Krachtus. Bioclipse 2.0: Life Science setzt auf die Staerken von Eclipse., Eclipse Magazine, 4, 2009.
  • O. Spjuth, and J. Alvarsson. Bioclipse 2: Towards integrated biocheminformatics, EMBNet News 15(3), 2009.

Developer documentation
The Bioclipse Wiki is the main resource for developers with numerous tutorials how to develop and extend Bioclipse are available. Developers hang out daily on the IRC channel \#bioclipse on where they exchange ideas and answer each others questions.