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New developments on the cheminformatics open workflow environment CDK-Taverna

Andreas Truszkowski1, Kalai Vanii Jayaseelan2, Stefan Neumann3, Egon L Willighagen4, Achim Zielesny1 and Christoph Steinbeck2*

Author Affiliations

1 Institute for Bioinformatics and Cheminformatics, University of Applied Sciences of Gelsenkirchen, Recklinghausen, Germany

2 Chemoinformatics and Metabolism, European Bioinformatics Institute (EBI), Cambridge, UK

3 GNWI - Gesellschaft fuer naturwissenschaftliche Informatik mbH, Oer-Erkenschwick, Germany

4 Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden

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Journal of Cheminformatics 2011, 3:54  doi:10.1186/1758-2946-3-54

Published: 13 December 2011

Abstract

Background

The computational processing and analysis of small molecules is at heart of cheminformatics and structural bioinformatics and their application in e.g. metabolomics or drug discovery. Pipelining or workflow tools allow for the Lego™-like, graphical assembly of I/O modules and algorithms into a complex workflow which can be easily deployed, modified and tested without the hassle of implementing it into a monolithic application. The CDK-Taverna project aims at building a free open-source cheminformatics pipelining solution through combination of different open-source projects such as Taverna, the Chemistry Development Kit (CDK) or the Waikato Environment for Knowledge Analysis (WEKA). A first integrated version 1.0 of CDK-Taverna was recently released to the public.

Results

The CDK-Taverna project was migrated to the most up-to-date versions of its foundational software libraries with a complete re-engineering of its worker's architecture (version 2.0). 64-bit computing and multi-core usage by paralleled threads are now supported to allow for fast in-memory processing and analysis of large sets of molecules. Earlier deficiencies like workarounds for iterative data reading are removed. The combinatorial chemistry related reaction enumeration features are considerably enhanced. Additional functionality for calculating a natural product likeness score for small molecules is implemented to identify possible drug candidates. Finally the data analysis capabilities are extended with new workers that provide access to the open-source WEKA library for clustering and machine learning as well as training and test set partitioning. The new features are outlined with usage scenarios.

Conclusions

CDK-Taverna 2.0 as an open-source cheminformatics workflow solution matured to become a freely available and increasingly powerful tool for the biosciences. The combination of the new CDK-Taverna worker family with the already available workflows developed by a lively Taverna community and published on myexperiment.org enables molecular scientists to quickly calculate, process and analyse molecular data as typically found in e.g. today's systems biology scenarios.

Graphical abstract