Department of IT-Infrastructure for Translational Medical Research, Faculty of Applied Computer Science, University of Augsburg, Augsburg, Germany.
PLoS Comput Biol. 2022 Jun 8;18(6):e1010205. doi: 10.1371/journal.pcbi.1010205. eCollection 2022 Jun.
Networks are a common methodology used to capture increasingly complex associations between biological entities. They serve as a resource of biological knowledge for bioinformatics analyses, and also comprise the subsequent results. However, the interpretation of biological networks is challenging and requires suitable visualizations dependent on the contained information. 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. A further challenge when working with networks is their distribution. Within a typical collaborative workflow, even slight changes of the network data force one to repeat the visualization step as well. Also, just minor adjustments to the visual representation not only need the networks to be transferred back and forth. 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 where users can upload a network, share it with selected colleagues or make it publicly available. NDExEdit is a web-based application where simple changes can be made to biological networks within the browser, and which does not require installation. With our tool, plain networks can be enhanced easily for further usage in presentations and publications. Since the network data is only stored locally within the web browser, users can edit their private networks without concerns of unintentional publication. 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. 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.
网络是一种常用的方法，用于捕获生物实体之间日益复杂的关联。它们是生物信息学分析的生物知识资源，也是后续结果的组成部分。然而，生物网络的解释具有挑战性，需要根据包含的信息进行适当的可视化。该领域用于可视化生物网络的最突出的软件是 Cytoscape，这是一个桌面建模环境，还包括许多用于分析的功能。在使用网络时，另一个挑战是它们的分布。在典型的协作工作流程中，即使网络数据发生微小变化，也需要重复可视化步骤。此外，对视觉表示的微小调整不仅需要来回传输网络。对同一资源的协作需要特定的基础设施来避免冗余，或者更糟糕的是，数据的损坏。NDEx 平台提供了一个成熟的解决方案，用户可以在该平台上上传网络，与选定的同事共享网络，或者将其公开。NDExEdit 是一个基于网络的应用程序，用户可以在浏览器中对生物网络进行简单的更改，并且无需安装。使用我们的工具，可以轻松增强普通网络，以便在演示和出版物中进一步使用。由于网络数据仅存储在 Web 浏览器的本地，用户可以在不担心意外发布的情况下编辑他们的私人网络。该网络工具旨在符合 Cytoscape Exchange (CX) 格式作为数据模型，该格式用于 Cytoscape 和 NDEx 这两个工具的数据传输。因此，修改后的网络可以直接导出到 NDEx 平台，或保存为兼容的 CX 文件，以及标准的图像格式，如 PNG 和 JPEG。
