Software and Services

Bioclipse

Bioclipse is a free and open source workbench for the life sciences which is equipped with features for storing, querying, analyzing and visualizing primarily chemical compounds (such as drugs) but also biological entities (such as sequences and proteins). With intuitive user interfaces, Bioclipse enables researchers to easily access complex technologies and advanced mathematical and statistical methods, prioviding a graphical workbench with built-in help system and tutorials in a wide range of areas.

Bioclipse website: www.bioclipse.net

Bioclipse wiki: www.wiki.bioclipse.net

Selected publications on Bioclipse:

Bioclipse: An open source workbench for chemo- and bioinformatics
Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JE.
BMC Bioinformatics 2007, 8:59 doi:10.1186/1471-2105-8-59

Bioclipse 2: A scriptable integration platform for the life sciences
Spjuth O, Alvarsson J, Berg A, Eklund M, Kuhn S, Mäsak C, Torrance G, Wagener J, Willighagen EL, Steinbeck C, Wikberg JE.
BMC Bioinformatics 2009, 10:397 doi:10.1186/1471-2105-10-397

Open source drug discovery with bioclipse
Spjuth O, Carlsson L, Alvarsson J, Georgiev V, Willighagen E, Eklund M.
Curr Top Med Chem. 2012;12(18):1980-6.

Bioclipse-R: integrating management and visualization of life science data with statistical analysis
Spjuth O, Georgiev V, Carlsson L, Alvarsson J, Berg A, Willighagen E, Wikberg JE, Eklund M.
Bioinformatics. 2013 Jan 15;29(2):286-9. doi: 10.1093/bioinformatics/bts681.

 

Bioclipse Decision Support

Bioclipse DS is a flexible framework for working with predictive models in Bioclipse. Or particular focus for our research group is to further develop Bioclipse to simplify in the building, sharing, and usage of predictive models in drug discovery.

Plugin description: http://wiki.bioclipse.net/index.php?title=Bioclipse_Decision_Support

Selected publications:

Integrated decision support for assessing chemical liabilities.
Spjuth O, Eklund M, Ahlberg Helgee E, Boyer S, Carlsson L.
J Chem Inf Model. 2011 Aug 22;51(8):1840-7. doi: 10.1021/ci200242c

Computational toxicology using the OpenTox application programming interface and Bioclipse
Willighagen EL, Jeliazkova N, Hardy B, Grafström RC, Spjuth O.
BMC Res Notes. 2011 Nov 10;4:487. doi: 10.1186/1756-0500-4-487

A unified proteochemometric model for prediction of inhibition of cytochrome p450 isoforms
Lapins M, Worachartcheewan A, Spjuth O, Georgiev V, Prachayasittikul V, Nantasenamat C, Wikberg JE.
PLoS One. 2013 Jun 17;8(6):e66566. doi: 10.1371/journal.pone.0066566

 

Metaprint2D

Metaprint2D is a method to predict site-of-metabolism based on circular fingerprints. The method is very fast – a SOM-prediction takes about 50 ms per chemical structure and is available from within Bioclipse.

Plugin description: http://wiki.bioclipse.net/index.php?title=MetaPrint2D

Reference:

Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse
Carlsson L, Spjuth O, Adams S, Glen RC, Boyer S.
BMC Bioinformatics. 2010 Jul 1;11:362. doi: 10.1186/1471-2105-11-362.

Involvements