The Bioclipse project is a

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mo ...

-based,

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

, visual platform for chemo- and

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

based on the

Eclipse An eclipse is an astronomical event that 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 c ...

Rich Client Platform (RCP). It 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 update A patch is a set of changes to a computer program or its supporting data designed to update, fix, or improve it. This includes fixing security vulnerabilities and other bugs, with such patches usually being called bugfixes or bug fixes. Patche ...

s, 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 The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. It is available for Windows, Linux, Unix, and macOS. It is free and open-source software distributed un ...

(CDK) plugin to provide a chemoinformatic backend, a

Jmol Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry. It is written in ...

plugin for 3D-visualization of molecules, and a

BioJava BioJava is an open-source software project dedicated to provide Java tools to process biological data.VS Matha and P Kangueane, 2009, ''Bioinformatics: a concept-based introduction'', 2009. p26 BioJava is a set of library functions written in the p ...

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 ( sv, Uppsala universitet) is a public research university in Uppsala, Sweden. Founded in 1477, it is the oldest university in Sweden and the Nordic countries still in operation. The university rose to significance during ...

, 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, Germany. Education Steinbeck received his ...

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''; nl, Universiteit Leiden) is a public research university in Leiden, Netherlands. The university was founded as a Protestant university in 1575 by William, Prince of Orange, as a reward to the city o ...

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

Karolinska Institutet The Karolinska Institute (KI; sv, Karolinska Institutet; sometimes known as the (Royal) Caroline Institute in English) is a research-led medical university in Solna within the Stockholm urban area of Sweden. The Karolinska Institute is consist ...

and

Maastricht University Maastricht University (abbreviated as UM; nl, Universiteit Maastricht) is a public research university in Maastricht, Netherlands. Founded in 1976, it is the second youngest of the thirteen Dutch universities. In 2021, 22,383 students studied at ...

. 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 that is one of the core technologies of the World Wide Web, alongside HTML and CSS. As of 2022, 98% of websites use JavaScript on the client side for webpage behavior, of ...

and Groovy. 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 is a social web site for researchers sharing research objects such as scientific workflows. The myExperiment website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of workfl ...

.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