The BIOCLIPSE project is a Java -based, open source , visual platform for chemo - and bioinformatics based on the Eclipse Rich Client Platform (RCP). It gained scripting functionality in 2009.
Like any RCP application, Bioclipse uses a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates , preferences, cross-platform deployment etc. Via its plugins, Bioclipse provides functionality for chemo- and bioinformatics, and extension points that easily can be extended by other, possibly proprietary, plugins to provide additional functionality.
The first stable release of Bioclipse includes a Chemistry Development Kit (CDK) plugin to provide a chemoinformatic backend, a Jmol plugin for 3D-visualization of molecules, and a BioJava plugin for sequence analysis. Recently, the R platform, using StatET, and OpenTox were added.
Bioclipse is developed as a collaboration between the
Proteochemometric Group, Dept. of Pharmaceutical Biosciences, Uppsala
University , Sweden, the
BIOCLIPSE SCRIPTING LANGUAGE
Bioclipse Scripting Language (BSL) is a scripting environment,
currently based on
* ^ https://sourceforge.net/projects/bioclipse/files/bioclipse/ * ^ Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, P. Murray-Rust , Christoph Steinbeck, Jarl E.S. Wikberg, Bioclipse: An open source workbench for chemo- and bioinformatics, BMC Bioinformatics, 2007, 8. doi :10.1186/1471-2105-8-59 * ^ Ola Spjuth, Jonathan Alvarsson, Arvid Berg, Martin Eklund, Stefan Kuhn, Carl Mäsak, Gilleain Torrance, Johannes Wagener, Egon L Willighagen, Christoph Steinbeck, and Jarl ES Wikberg, Bioclipse 2: A scriptable integration platform for the life sciences, BMC Bioinformatics, 2009, 10, doi :10.1186/1471-2105-10-397 *