gms | German Medical Science

63. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS)

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie

02. - 06.09.2018, Osnabrück

NDExR and Cytoscape: interactive and automated visualization of biological networks using R

Meeting Abstract

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  • Florian Auer - Universitätsmedizin Göttingen, Göttingen, Deutschland
  • Frank Kramer - Universitätsmedizin Göttingen, Göttingen, Deutschland
  • Tim Beißbarth - Universitätsmedizin Göttingen, Göttingen, Deutschland

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie. 63. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS). Osnabrück, 02.-06.09.2018. Düsseldorf: German Medical Science GMS Publishing House; 2018. DocAbstr. 218

doi: 10.3205/18gmds087, urn:nbn:de:0183-18gmds0877

Published: August 27, 2018

© 2018 Auer et al.
This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 License. See license information at



Network models form a simple and flexible way of representing diverse associations within complex systems, and its applications are well-established in a wide range of fields in biology [1], [2], [3]. Within a common bioinformatics workflow data integration, network analysis and visualization accompany each other [4], [5], and comprise fundamental challenges of combining various tools. Implementation of fully automated pipelines enhances the intricacy of such tasks furthermore [6].

Using standard technologies, we demonstrate a course from data acquisition to the finished visualization, and options to achieve the individual sub tasks. Thereby the network data exchange (NDEx) platform [7], [8] and the Cytoscape project [9], and appendant R [10], form the core components.

We use our R package ndexr [11] to retrieve networks from the public NDEx platform, and also to store the results for later collaboration and publication. Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks. Beside the graphical interface, the latest release offers a RESTful interface [12], [13] and R packages [14], [15] providing access to it.

Along an exemplary bioinformatics workflow, we demonstrate how the single steps can be performed not only interactively, but also in a fully automated manner. Each step can be done using Cytoscape or R, or a combination of both: Controlling Cytoscape remotely from within R. Starting at an interactive analysis we move towards automation, illustrating the interchangeability and flexibility of the different approaches.

The authors declare that they have no competing interests.

The authors declare that an ethics committee vote is not required.

This contribution has already been published [16].


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