gms | German Medical Science

66. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS), 12. Jahreskongress der Technologie- und Methodenplattform für die vernetzte medizinische Forschung e. V. (TMF)

26. - 30.09.2021, online

NDExEdit: a web tool for biological network visualization

Meeting Abstract

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  • Simone Mayer - Universität Augsburg, Augsburg, Germany
  • Florian Auer - Universität Augsburg, Augsburg, Germany
  • Frank Kramer - Universität Augsburg, Augsburg, Germany

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie. 66. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS), 12. Jahreskongress der Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V. (TMF). sine loco [digital], 26.-30.09.2021. Düsseldorf: German Medical Science GMS Publishing House; 2021. DocAbstr. 209

doi: 10.3205/21gmds116, urn:nbn:de:0183-21gmds1162

Published: September 24, 2021

© 2021 Mayer et al.
This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 License. See license information at



Networks are often used, either as a source or result, to represent complex relations in biological research. Information associated with the individual nodes or edges can go far beyond name and type, thus increasing its complexity. This information-rich data provides the opportunity for comprehensive visualization but requires powerful tools to achieve. With our NDExEdit web-app plain networks can be easily enhanced for presentation and publication by applying so-called “attribute-to-visual-mappings”, where a node’s or edge’s attribute translates to its visual representation.

A major challenge when working with networks is their distribution. Collaboration on the same resources requires specific infrastructure to avoid redundancies, or worse, the corruption of the data. A well-established solution is provided by the NDEx platform [1] where users can upload a network, share it with selected colleagues or make it publicly available. NDEx also holds the feature to provide your private networks solely to the reviewers of a submitted paper, to protect the data until publication. NDEx is tightly connected to Cytoscape [2], the most prominent desktop software for biological network analysis and visualization. Besides its support for large networks and its rich set of features, Cytoscape comes with overhead for quick results and a steep learning curve.

NDExEdit is an application where simple data-dependent visualization can be applied to biological networks within the browser. Existing attribute-to-visual-mappings can be removed or edited, and new mappings created. The statistics view assists by providing distribution and coverage charts for each attribute within the network. To investigate the network data without applying any changes the user can select certain elements or define matching criteria to be highlighted within the network. The web tool is designed to conform to the CX (Cytoscape Exchange) data model, which is used for data transmission by both Cytoscape and NDEx. The user can load a network directly from NDEx or use a local CX-file and export the modified network as a CX-, PNG- or JPEG-file.

Since installation of desktop clients is often restricted due to security concerns, a web-based software can close this gap and furthermore provides access through mobile devices. However, changes to a network’s data and algorithmic applications still require a powerful desktop client like Cytoscape. Also, a direct re-upload to the NDEx platform is restricted by the browser’s Cross-origin resource sharing (CORS) policy [3]. This could be resolved by either locally deploying NDExEdit in conjunction with a private NDEx server, or by development of a backend service for the upload. Future improvements include the latter, as well as an option to apply predefined visualization templates, such as SBGN [4], STRING [5] or Reactome [6], [7] layouts to a network.

Even though NDExEdit only allows visual adjustments to a network, the application illustrates the great potential of web-based solutions for biological research: Users with any operating system can work with NDExEdit without a requirement for installation or account. It narrows the gap between desktop clients to create, edit and beautify a network, and platforms to distribute them.

Code and demo are available at

The authors declare that they have no competing interests.

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


Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, et al. NDEx, the Network Data Exchange. cels. 2015 Oct 28;1(4):302–5.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov;13(11):2498–504.
Cross-Origin Resource Sharing (CORS) - HTTP MDN [Internet]. [cited 2021 May 7]. Available from: External link
Novère NL, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, et al. The Systems Biology Graphical Notation. Nat Biotechnol. 2009 Aug;27(8):735–41.
Snel B, Lehmann G, Bork P, Huynen MA. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 2000 Sep 15;28(18):3442–4.
Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, et al. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8;48(D1):D498–503.
Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, et al. Reactome enhanced pathway visualization. Bioinformatics. 2017 Nov 1;33(21):3461–7.