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      Extended LineSets: a visualization technique for the interactive inspection of biological pathways

      research-article
      1 , 1 ,
      BMC Proceedings
      BioMed Central
      5th Symposium on Biological Data Visualization
      10-11 July 2015
      Pathway Visualization, Hierarchical Inspection, Eliminating Node Redundancy, Line Sets, Interactive Visual Analysis

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          Abstract

          Background

          Biologists make use of pathway visualization tools for a range of tasks, including investigating inter-pathway connectivity and retrieving details about biological entities and interactions. Some of these tasks require an understanding of the hierarchical nature of elements within the pathway or the ability to make comparisons between multiple pathways. We introduce a technique inspired by LineSets that enables biologists to fulfill these tasks more effectively.

          Results

          We introduce a novel technique, Extended LineSets, to facilitate new explorations of biological pathways. Our technique incorporates intuitive graphical representations of different levels of information and includes a well-designed set of user interactions for selecting, filtering, and organizing biological pathway data gathered from multiple databases.

          Conclusions

          Based on interviews with domain experts and an analysis of two use cases, we show that our technique provides functionality not currently enabled by current techniques, and moreover that it helps biologists to better understand both inter-pathway connectivity and the hierarchical structure of biological elements within the pathways.

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          Most cited references13

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          A hierarchical O(N log N) force-calculation algorithm

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            Graph visualization and navigation in information visualization: A survey

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              VisANT: an online visualization and analysis tool for biological interaction data

              Background New techniques for determining relationships between biomolecules of all types – genes, proteins, noncoding DNA, metabolites and small molecules – are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems. Results We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package. VisANT is a freely available, open-source tool for researchers, and offers an online interface for a large range of published data sets on biomolecular interactions, including those entered by users. This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology. Conclusion VisANT has been developed to provide interactive visual mining of biological interaction data sets. The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is available at .
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                Author and article information

                Contributors
                Conference
                BMC Proc
                BMC Proc
                BMC Proceedings
                BioMed Central
                1753-6561
                2015
                13 August 2015
                : 9
                : Suppl 6
                : S4
                Affiliations
                [1 ]Department of Computer Science M/C 152, University of Illinois at Chicago, 851 S. Morgan, Room 1120, Chicago 60607-7053, IL, USA
                Article
                1753-6561-9-S6-S4
                10.1186/1753-6561-9-S6-S4
                4547339
                26361500
                e7c4a4ee-4b92-4c85-91f5-3c5214ac0ff6
                Copyright © 2015 Paduano et al.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                5th Symposium on Biological Data Visualization
                Dublin, Ireland
                10-11 July 2015
                History
                Categories
                Research

                Medicine
                pathway visualization,hierarchical inspection,eliminating node redundancy,line sets,interactive visual analysis

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