CDK-Taverna: an open workflow environment for cheminformatics

Thomas Kuhn; Egon L. Willighagen; Achim Zielesny; Christoph Steinbeck

doi:10.1186/1471-2105-11-159

CDK-Taverna: an open workflow environment for cheminformatics

Thomas Kuhn, Egon L. Willighagen, Achim Zielesny, Christoph Steinbeck^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

37 Citations (Web of Science)

Abstract

Background: Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone.

Results: Here we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry Development Kit (CDK) resulting in a open source workflow solution for cheminformatics. We have implemented more than 160 different workers to handle specific cheminformatics tasks. We describe the applications of CDK-Taverna in various usage scenarios.

Conclusions: The combination of the workflow engine Taverna and the Chemistry Development Kit provides the first open source cheminformatics workflow solution for the biosciences. With the Taverna-community working towards a more powerful workflow engine and a more user-friendly user interface, CDK-Taverna has the potential to become a free alternative to existing proprietary workflow tools.

Original language	English
Article number	159
Number of pages	11
Journal	BMC Bioinformatics
Volume	11
DOIs	https://doi.org/10.1186/1471-2105-11-159
Publication status	Published - 29 Mar 2010
Externally published	Yes

Keywords

SOURCE JAVA LIBRARY
DEVELOPMENT KIT CDK
CHEMICAL MARKUP
WEB
XML

Access to Document

10.1186/1471-2105-11-159

Cite this

@article{2bac4632864849b9b3a7565435ab5dca,

title = "CDK-Taverna: an open workflow environment for cheminformatics",

abstract = "Background: Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone.Results: Here we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry Development Kit (CDK) resulting in a open source workflow solution for cheminformatics. We have implemented more than 160 different workers to handle specific cheminformatics tasks. We describe the applications of CDK-Taverna in various usage scenarios.Conclusions: The combination of the workflow engine Taverna and the Chemistry Development Kit provides the first open source cheminformatics workflow solution for the biosciences. With the Taverna-community working towards a more powerful workflow engine and a more user-friendly user interface, CDK-Taverna has the potential to become a free alternative to existing proprietary workflow tools.",

keywords = "SOURCE JAVA LIBRARY, DEVELOPMENT KIT CDK, CHEMICAL MARKUP, WEB, XML",

author = "Thomas Kuhn and Willighagen, {Egon L.} and Achim Zielesny and Christoph Steinbeck",

year = "2010",

month = mar,

day = "29",

doi = "10.1186/1471-2105-11-159",

language = "English",

volume = "11",

journal = "BMC Bioinformatics",

issn = "1471-2105",

publisher = "BioMed Central Ltd",

}

TY - JOUR

T1 - CDK-Taverna

T2 - an open workflow environment for cheminformatics

AU - Kuhn, Thomas

AU - Willighagen, Egon L.

AU - Zielesny, Achim

AU - Steinbeck, Christoph

PY - 2010/3/29

Y1 - 2010/3/29

N2 - Background: Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone.Results: Here we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry Development Kit (CDK) resulting in a open source workflow solution for cheminformatics. We have implemented more than 160 different workers to handle specific cheminformatics tasks. We describe the applications of CDK-Taverna in various usage scenarios.Conclusions: The combination of the workflow engine Taverna and the Chemistry Development Kit provides the first open source cheminformatics workflow solution for the biosciences. With the Taverna-community working towards a more powerful workflow engine and a more user-friendly user interface, CDK-Taverna has the potential to become a free alternative to existing proprietary workflow tools.

AB - Background: Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone.Results: Here we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry Development Kit (CDK) resulting in a open source workflow solution for cheminformatics. We have implemented more than 160 different workers to handle specific cheminformatics tasks. We describe the applications of CDK-Taverna in various usage scenarios.Conclusions: The combination of the workflow engine Taverna and the Chemistry Development Kit provides the first open source cheminformatics workflow solution for the biosciences. With the Taverna-community working towards a more powerful workflow engine and a more user-friendly user interface, CDK-Taverna has the potential to become a free alternative to existing proprietary workflow tools.

KW - SOURCE JAVA LIBRARY

KW - DEVELOPMENT KIT CDK

KW - CHEMICAL MARKUP

KW - WEB

KW - XML

U2 - 10.1186/1471-2105-11-159

DO - 10.1186/1471-2105-11-159

M3 - Article

VL - 11

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

M1 - 159

ER -