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This article is part of the supplement: Highlights of the 1st IEEE Symposium on Biological Data Visualization (BioVis 2011)

Open Access Research

HiTSEE KNIME: a visualization tool for hit selection and analysis in high-throughput screening experiments for the KNIME platform

Hendrik Strobelt1*, Enrico Bertini13, Joachim Braun2, Oliver Deussen123, Ulrich Groth2, Thomas U Mayer23 and Dorit Merhof123

Author Affiliations

1 Department of Computer Science, Konstanz University, Universitätsstr. 10, Konstanz, Germany

2 Konstanz Research School Chemical Biology, Konstanz University, Universitätsstr. 10, Konstanz, Germany

3 Interdisciplinary Center for Interactive Data Analysis, Modelling and Visual Exploration (INCIDE), Konstanz University, Universitätsstr. 10, Konstanz, Germany

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BMC Bioinformatics 2012, 13(Suppl 8):S4  doi:10.1186/1471-2105-13-S8-S4

Published: 18 May 2012

Abstract

We present HiTSEE (High-Throughput Screening Exploration Environment), a visualization tool for the analysis of large chemical screens used to examine biochemical processes. The tool supports the investigation of structure-activity relationships (SAR analysis) and, through a flexible interaction mechanism, the navigation of large chemical spaces. Our approach is based on the projection of one or a few molecules of interest and the expansion around their neighborhood and allows for the exploration of large chemical libraries without the need to create an all encompassing overview of the whole library. We describe the requirements we collected during our collaboration with biologists and chemists, the design rationale behind the tool, and two case studies on different datasets. The described integration (HiTSEE KNIME) into the KNIME platform allows additional flexibility in adopting our approach to a wide range of different biochemical problems and enables other research groups to use HiTSEE.