TheBioclipseproject is aJava-based,open-source,visual platform forchemo- andbioinformaticsbased on theEclipseRich Client Platform (RCP).[2][3]
 | |
| Developer(s) | The Bioclipse Project |
|---|---|
| Initial release | 17 November 2005[1] |
| Stable release | 2.6.2 (November 4, 2016)[±] |
| Preview release | 2.6.2 RC (April 15, 2016)[±] |
| Type | Cheminformatics,bioinformatics |
| License | Eclipse Public License |
| Website | www |
About
editBiclipse gained scripting functionality in 2009,[4]and a command line version in 2021.[5]
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 deploymentetc. Via its plugins, Bioclipse provides functionality for chemo- and bioinformatics, and extension points that easily can be extended by other, possibly proprietary,pluginsto provide additional functionality.
Product
editThe first stable release of Bioclipse includes aChemistry Development Kit(CDK) plugin to provide a chemoinformatic backend, aJmolplugin for 3D-visualization of molecules, and aBioJavaplugin for sequence analysis. Recently, theRplatform, using StatET,[6]and OpenTox were added.[7]
Bioclipse is developed as a collaboration between the Proteochemometric Group, Dept. of Pharmaceutical Biosciences,Uppsala University,Sweden, theChristoph SteinbeckGroup at theEuropean Bioinformatics Institute,and the Analytical Chemistry Department atLeiden University,but also includes extensions developed at other academic institutes, including theKarolinska InstitutetandMaastricht University.[8]The development is backed up by the International Bioclipse Association.[9]
Bioclipse Scripting Language
editThe Bioclipse Scripting Language (BSL) is a scripting environment, currently based onJavaScriptandGroovy.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, onMyExperiment.org. Bioclipse defines a number of core data types that managers support, allowing information to be used between these managers.
References
edit- ^"Bioclipse - Browse /Bioclipse at SourceForge.net".
- ^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
- ^Hasan, Mehedi (2023-01-24)."20 Best Bioinformatics Tools for Linux Systems".UbuntuPIT.Retrieved2023-09-14.
- ^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
- ^Willighagen, Egon (23 June 2021)."Bacting: a next generation, command line version of Bioclipse".Journal of Open Source Software.6(62): 2558.Bibcode:2021JOSS....6.2558W.doi:10.21105/joss.02558.
- ^Spjuth, O.; Georgiev, V.; Carlsson, L.; Alvarsson, J.; Berg, A.; Willighagen, E.; Wikberg, J. E. S.; Eklund, M. (2012)."Bioclipse-R: Integrating management and visualization of life science data with statistical analysis".Bioinformatics.29(2): 286–289.doi:10.1093/bioinformatics/bts681.PMC3546796.PMID23178637.
- ^Willighagen, E. L.; Jeliazkova, N.; Hardy, B.; Grafström, R. C.; Spjuth, O. (2011)."Computational toxicology using the OpenTox application programming interface and Bioclipse".BMC Research Notes.4:487.doi:10.1186/1756-0500-4-487.PMC3264531.PMID22075173.
- ^"Bioclipse Labs".Archived fromthe originalon 2011-07-20.Retrieved2010-02-02.
- ^Uppsala University Pressmedelanden:Dubbla utmärkelser för IT/bioteknik-systemArchivedAugust 8, 2007, at theWayback Machine
