KNIME workflow tool

JChem Marvin KNIME extensions are also available [22]. The modules allow researchers to handle chemical structure data using ChemAxon s software tools such as Marvin, JChem and Standardizer within the open-source KNIME workflow environment. The KNIME platform provides a modular environment to visually create data flows, analyse and build predictive models. The JChem Extensions contain some nodes that are free of charge for general use. These nodes are called Marvin Family Nodes which include a set of nodes for structure conversion, Marvin Sketch , Marvin View and Marvin Space which offer sophisticated rendering capabilities for chemical structures. 

Initially, it was planned to implement a separate interactive front-end for the CIDB to allow for a native access to the database contents. However, our experience shows that such a front-end is rarely used in practice and that it is sufficient to provide access via workflow tools (e.g., Pipeline Pilot [6] and KNIME [7]). Extracts of the data are made available to end users through the project data marts described in Section 13.2.5. 

Workflow is the connection of sequential steps for data management and analysis in chemistry. There are several tools for creating a workflow or pipelines Aeeehys ipeline Pilot [11], IDBS Chemsense (Inforsense snite) [12], chemistry development kit (CDK) Tavema [13], KNIME [14] etc. 

KNIME stands for the Konstanz Information Miner and is a visualization platform for creating and editing data evaluation pipelines and workflows using certain features called as Node Repository . It is an open-source tool for creating chemical workflows and was developed by Prof. Michael Berthold [18]. KNIME is downloadable from www.knime.org. CDK chemistry project was incorporated in KNIME and was written in Java. It can work in integration with chemoinformatics software. 

The KNIME Workbench After accepting the path of the workspace, KNIME opens the KNIME workbench. The KNIME workbench includes a workflow editor where the user can create the workflows. The KNIME workbench was developed as an Eclipse Plug-in and many of its features are inherited from the Eclipse environment. The KNIME Workbench consists of a top menu, a tool bar and a few panels. Panels can be closed and moved arotmd (Figs. 9.5 and 9.6). 

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