Bioclipse
Encyclopedia
The Bioclipse project is a Java
-based, open source
, visual platform for chemo
- and bioinformatics
based on the Eclipse
Rich Client Platform (RCP). It recently gained scripting functionality.
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.
Bioclipse is developed as a collaboration between the Proteochemometric Group, Dept. of Pharmaceutical Biosciences, Uppsala University
, Sweden, the Steinbeck Group at the European Bioinformatics Institute
, and the Analytical Chemistry Department at Leiden University
, but also includes extensions developed at other academic institutes, including the Karolinska Institutet
. The development is backed up by the International Bioclipse Association.
. It extends the
scripting language with managers that wrap the functionality of third party libraries, as mentioned above. These scripts
thus provide means to make analyses in Bioclipse sharable, for example, on MyExperiment
.org. Bioclipse defines a number of core data types that managers support, allowing information to be used between these managers.
Java (programming language)
Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...
-based, open source
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
, visual platform for chemo
Cheminformatics
Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery...
- and bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
based on the Eclipse
Eclipse (software)
Eclipse is a multi-language software development environment comprising an integrated development environment and an extensible plug-in system...
Rich Client Platform (RCP). It recently gained scripting functionality.
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
Cross-platform
In computing, cross-platform, or multi-platform, is an attribute conferred to computer software or computing methods and concepts that are implemented and inter-operate on multiple computer platforms...
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
Chemistry Development Kit
The Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics. It is available for Windows, Unix, and Mac OS...
(CDK) plugin to provide a chemoinformatic backend, a Jmol
Jmol
Jmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...
plugin for 3D-visualization of molecules, and a BioJava
BioJava
The BioJava Project is an open source project dedicated to providing Java tools for processing biological data. This includes include objects for manipulating sequences, protein structures, file parsers, CORBA interoperability, DAS, access to AceDB, dynamic programming, and simple statistical...
plugin for sequence analysis.
Bioclipse is developed as a collaboration between the Proteochemometric Group, Dept. of Pharmaceutical Biosciences, Uppsala University
Uppsala University
Uppsala University is a research university in Uppsala, Sweden, and is the oldest university in Scandinavia, founded in 1477. It consistently ranks among the best universities in Northern Europe in international rankings and is generally considered one of the most prestigious institutions of...
, Sweden, the Steinbeck Group at the European Bioinformatics Institute
European Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
, and the Analytical Chemistry Department at Leiden University
Leiden University
Leiden University , located in the city of Leiden, is the oldest university in the Netherlands. The university was founded in 1575 by William, Prince of Orange, leader of the Dutch Revolt in the Eighty Years' War. The royal Dutch House of Orange-Nassau and Leiden University still have a close...
, but also includes extensions developed at other academic institutes, including the Karolinska Institutet
Karolinska Institutet
Karolinska institutet is a medical university in Solna within the Stockholm urban area, Sweden, and one of Europe's largest medical universities...
. The development is backed up by the International Bioclipse Association.
Bioclipse Scripting Language
The Bioclipse Scripting Language (BSL) is a scripting environment, currently based on JavaScriptJavaScript
JavaScript is a prototype-based scripting language that is dynamic, weakly typed and has first-class functions. It is a multi-paradigm language, supporting object-oriented, imperative, and functional programming styles....
. It extends the
scripting language with managers that wrap the functionality of third party libraries, as mentioned above. These scripts
thus provide means to make analyses in Bioclipse sharable, for example, on MyExperiment
MyExperiment
myExperiment is a social web site for researchers sharing Research Objects such as Scientific Workflows. The Website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of workflow systems, most notably Taverna, but also other tools such as...
.org. Bioclipse defines a number of core data types that managers support, allowing information to be used between these managers.