The Bioclipse project is a

Java Java is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea (a part of Pacific Ocean) to the north. With a population of 156.9 million people (including Madura) in mid 2024, proje ...

-based,

open-source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentrali ...

, visual platform for chemo- and

bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

based on the

Eclipse An eclipse is an astronomical event which occurs when an astronomical object or spacecraft is temporarily obscured, by passing into the shadow of another body or by having another body pass between it and the viewer. This alignment of three ...

Rich Client Platform (RCP).

About

Biclipse gained scripting functionality in 2009, and a command line version in 2021. 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.

Product

The first stable release of Bioclipse includes a Chemistry Development Kit (CDK) plugin to provide a chemoinformatic backend, a

Jmol Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. It is an open-source Java viewer for chemical structures in 3D. The name originated from ''Jva (the programming language) + olcules, and also the m ...

plugin for 3D-visualization of molecules, and a

BioJava BioJava is an open-source software project dedicated to providing Java tools for processing biological data.VS Matha and P Kangueane, 2009, ''Bioinformatics: a concept-based introduction'', 2009. p26 BioJava is a set of library functions written i ...

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 Uppsala University (UU) () is a public university, public research university in Uppsala, Sweden. Founded in 1477, it is the List of universities in Sweden, oldest university in Sweden and the Nordic countries still in operation. Initially fou ...

, Sweden, the

Christoph Steinbeck Christoph Steinbeck (born 1966 in Neuwied) is a German chemist and has a professorship for analytical chemistry, cheminformatics and chemometrics at the Friedrich-Schiller-Universität Jena in Thuringia. Education Steinbeck received his PhD ...

Group at the

European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wel ...

, and the Analytical Chemistry Department at

Leiden University Leiden University (abbreviated as ''LEI''; ) is a Public university, public research university in Leiden, Netherlands. Established in 1575 by William the Silent, William, Prince of Orange as a Protestantism, Protestant institution, it holds the d ...

, but also includes extensions developed at other academic institutes, including the

Karolinska Institutet The Karolinska Institute (KI; ; sometimes known as the (Royal) Caroline Institute in English) is a research-led medical university in Solna within the Stockholm urban area of Sweden and one of the foremost medical research institutes globally. ...

and

Maastricht University Maastricht University (abbreviated as UM; ) is a public university, public research university in Maastricht, Netherlands. Founded in 1976, it is the second youngest of the thirteen List of universities in the Netherlands, Dutch universities. In ...

. The development is backed up by the International Bioclipse Association.Uppsala University Pressmedelanden: ''Dubbla utmärkelser för IT/bioteknik-system''

Bioclipse Scripting Language

The Bioclipse Scripting Language (BSL) is a scripting environment, currently based on

JavaScript JavaScript (), often abbreviated as JS, is a programming language and core technology of the World Wide Web, alongside HTML and CSS. Ninety-nine percent of websites use JavaScript on the client side for webpage behavior. Web browsers have ...

and

Groovy ''Groovy'' (or, less commonly, ''groovie'' or ''groovey'') is a slang colloquialism popular during the 1960s and 1970s. It is roughly synonymous with words such as "excellent", "fashionable", or "amazing", depending on context. History The word ...

. 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.

References

External links

{{Chemistry software Free bioinformatics software Cheminformatics Java platform software Free chemistry software Bioinformatics companies Chemotherapy