Outcome of the Bioclipse Autumn Worskop 2006

The Bioclipse Autumn Workshop 2006 in Cologne has just ended; 3 full days of presentations, demos, discussions, and hacking sessions. Check out the outcome and highlights on the wiki, but I feel that I must mention the new Bioclipse plugin bc_rhino which brings scripting capability (Javascript) into the Bioclipse workbench! Johannes Wagener (edrin) will be working on a general Web service feature using scripts, which in my opinion could be extremely powerful.

I’d like to thank Christoph Steinbeck and the CUBIC crew for a very nice and productive workshop and hope to be able to welcome you all in Uppsala for the Bioclipse Spring Workshop 2007!


Bioclipse 1.0 released

The Bioclipse team is proud to announce the release
of Bioclipse 1.0.

Bioclipse is a free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc. The major features of version 1.0 are:

* Import and export in various file formats
* Visual editing of molecular 2D-structures
* 3D-visualization of molecules and proteins
* Editing and visualization of sequences and features (DNA, RNA, proteins etc)
* Graphing and editing of various types of spectra, e. g. NMR, MS
* Retrieval of resources (sequences, proteins, etc) from public data repositories
* Scripting of 3D-visualizations with syntax highlighting and content assistance
* PDB-editor with syntax highlighting for working with PDB files
* CMLRSS-viewer for downloading chemical content published on the web using RSS-feeds
* Integrated, searchable help-system
* Hierarchical view of molecular and macromolecular substructures and calculation of chemical properties* Connection with external programs, e. g. PyMol

Bioclipse is a rich client, which means it is run on your local computer but also gives the possibility to communicate with servers for data retrieval and computational services. The powerful plugin architecture is based on Eclipse, and results in a responsive, integrated user interface designed for simple and intuitive operations that at the same time is easy to extend with custom functionality.

There is much ongoing work with Bioclipse and new features are constantly added. Please visit the Bioclipse Wiki in order to get the latest information regarding the development.

Bioclipse is available for download from Sourceforge.

Thanks to all developers who have made this release possible!


Bioclipse 0.9.10 released

After a major cleanup of jars and testdata, as well as some bug fixes we decided to release Bioclipse 0.9.10, which has a dramatically smaller archive size of ~40 Mb. Available from Sourceforge.


Bioclipse 0.9.9 released

Bioclipse 0.9.9 has been released as the last pre-1.0 version. The download is available from Sourceforge [1]. We would appreciate everyone to test this version and report bugs to the sourceforge project site [2]. Version 1.0 is scheduled for release on August 11th.

Bioclipse homepage: www.bioclipse.net

[1] Bioclipse downloads
[2] Bioclipse bug reports


Bioclipse 0.9.2 released

Today, Bioclipse 0.9.2 was released. The new version includes (apart from numerous bugfixes) the following additions:
  • Updated PDB-parsing
  • A new PDBEditor for visualization of PDB-files with highlighting and code completion
  • New help topics
Download the release from SourceForge. Bioclipse is now ready for some serious testing and please report any errors using the SF bugtracker.

Bioclipse homepage
Bioclipse wiki
Getting Started Tutorial


Bioclipse 0.9.1 released


Bioclipse [1] version 0.9.1 was released today for Linux and Windows, containing bugfixing and updates according to the Wiki [2]. Files are available from Sourceforge [3].

Please report any errors using the SF bugtracker.

[1] Bioclipse homepage
[2] Bioclipse roadmap towards 1.0
[3] Bioclipse downloads


Bioclipse double slam at JAX 2006

What a day! Bioclipse wins not only the 3'rd prize in JAX Innovation awards 2006 (http://www.jax-award.com/) but also the Audience Award!

I'd personally like to thank all developers and contributors of Bioclipse as well as all the included components (CDK, JChempaint, Jmol, CML, and Biojava) without whom this project would not have been possible.

The award money will be used to fund meetings, workshops, and other events supporting the development of Bioclipse.


Bioclipse nominated for the JAX Innovation Award 2006

Bioclipse has been nominated as one of the ten candidates for the JAX Innovation ward 2006. The first prize will be awarded to the most innovative projects based on Java and Eclipse. The award ceremony takes place in Wiesbaden May 10th at the JAX 2006 conference, and me and Christoph Steinbeck will be there representing Bioclipse.

Link: http://jax-award.com/



Bioclipse 0.9.0 released

Bioclipse v. 0.9.0 (linux, windows) is now available from SourceForge. The new release features:
  • Molecular management using CDK
  • Molecular editing in 2D using JChemPaint
  • Molecular visualization in 3D using Jmol
  • Spectra visualization
  • Sequence management and visualization using BioJava
  • CMLRSS newsreader

+ and much more exciting features!

Note: This is a feature freeze for v. 1.0 and from now on only bugfixes will be contributed.

To get started, see the Getting Started Tutorial

Please see the Bioclipse wiki for more information on the development.


Bioclipse 0.8.1 released

Finally I managed to create packages for Linux, Windows and Mac. Bioclipse 0.8.1 includes the new CMLRSS plugin, properties for ChemObjects (such as bonds, atoms in the ChemObjectTree) and fixes several bugs. Download from Sourceforge and simply unzip (creates a "bioclipse" directory). Needs Java 1.5 to run, and if you have multiple Java installed you need to add the following line to the file "bioclipse.ini":

-vm /path/to/java1.5/bin/java

The current version has not been tested on Mac (as we have no machines for testing), so please report to me if it runs (or not) and what VM you used.

See the Bioclipse website and Bioclipse Wiki for more information about the project.

.../Ola Spjuth


Bioclipse 0.8.0 linux released

Today, Bioclipse v. 0.8.0 was released. Unfortunately it is only available for linux (gtk, x86) due to problems with the latest Eclipse version. We hope to have a Windows version out soon.

The new version is fully functional but is in no way to consider stable. Nevertheless it has all basic functionality such as molecular browsing, 2D-editing (using JchemPaint), 3D-visualization (using Jmol), spectrum analysis and visualization, CML-support and much more. See the Bioclipse Wiki for more information and tutorials.

The release is available from Sourceforge.

Ola Spjuth