Received: NovemAccepted: Published: June 8, 2022Ĭopyright: © 2022 Auer et al. It allows us to import networks directly from the NDEx platform and apply changes to the visualization-including all types of mappings, one of which was briefly described above.Ĭitation: Auer F, Mayer S, Kramer F (2022) Data-dependent visualization of biological networks in the web-browser with NDE圎dit. We introduce NDE圎dit, a web-based solution for visualization changes to networks that conform to the CX data format. ![]() As of now these data-dependent modifications can only be made with a desktop client. Thus, our visualization is enriched with valuable information. ![]() Furthermore, we can change the visual appearance of our nodes and their interaction based on this information.įor example, if our network contains 20 nodes, that all interact with each other, but the strength of these interactions each range between 0 and 1, we can illustrate that by making the edges wider for strong interactions and slimmer for weak interactions. With established software solutions like Cytoscape we can add all the information we have about our nodes and their interaction to our data foundation. But the fact that the interaction between the two exists, may not be enough. For instance, if two proteins interact with each other during a certain process, the corresponding network would show two nodes connected by one edge. Relations in biological research are often visualized as networks. Therefore the modified network can be directly exported to the NDEx platform or saved as a compatible CX file, additionally to standard image formats like PNG and JPEG. The web tool is designed to conform to the Cytoscape Exchange (CX) format as a data model, which is used for the data transmission by both tools, Cytoscape and NDEx. Since the network data is only stored locally within the web browser, users can edit their private networks without concerns of unintentional publication. ![]() With our tool, plain networks can be enhanced easily for further usage in presentations and publications. NDE圎dit is a web-based application where simple changes can be made to biological networks within the browser, and which does not require installation. A well-established solution is provided by the NDEx platform where users can upload a network, share it with selected colleagues or make it publicly available. Collaboration on the same resources requires specific infrastructure to avoid redundancies, or worse, the corruption of the data. ![]() Also, just minor adjustments to the visual representation not only need the networks to be transferred back and forth. Within a typical collaborative workflow, even slight changes of the network data force one to repeat the visualization step as well. The most prominent software in the field for the visualization of biological networks is Cytoscape, a desktop modeling environment also including many features for analysis.Ī further challenge when working with networks is their distribution. However, the interpretation of biological networks is challenging and requires suitable visualizations dependent on the contained information. They serve as a resource of biological knowledge for bioinformatics analyses, and also comprise the subsequent results. Networks are a common methodology used to capture increasingly complex associations between biological entities.
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