Creating chemo- & bioinformatics workflows, further developments within the CDK-Taverna Project

The CDK-Taverna project aims at building an open-source pipelining solution through combination of different open-source projects such as Taverna [1], the Chemistry Development Kit (CDK) [2] and Bioclipse [3]. 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, modi-fied and tested without the hassle of implementing it into a monolithic application. Current developments in CDK-Taverna focus on a soft computing framework which allows a flexible use of dif-ferent methods from, for example, the WEKA [4] library. Here, properties of chemical substances may be calculated using descriptors from the QSAR / QSPR package of the Chemistry Development Kit (CDK). Further, a reaction enumeration algorithm for combinato-rial chemistry based on existing methods of the Chemistry Development Kit is being developed. This algorithm allows for the enumeration of a reaction given that reac-tants and products are provided as “Markush ” structures.

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