Modular Explorer (MOE): A Web Application for Visualizing Time‐series Dynamic Networks

How to visualize complex dynamic networks is a tremendous challenge in many scientific areas. For example, biologists want to show the changes of various molecules across time. The engineers would like to track the numerous measurements of industrial systems. Some desktop applications such as Cytoscape, Matlab, and Gephi, may be suitable for a small network to produce static images. However, the static images are almost impossible to read when the network complexity increases. To create a useful tool for visualizing complex dynamic networks, we developed Modular Explorer (MOE) to ascertain the three most desirable features as follows: 1. Scientifically informative: Has an interactive environment, modular layout, and animation. 2. Flexible: Has enough design options with minimal programming experience required. 3. Sharable: Safe sharing via email, compatible with most computers/ smart phones. To illustrate the efficacy of MOE, we used a prion protein (Prp) replication and accumulation network. The authors integrated the global gene expression in the brains of eight distinct mouse strain‐prion strain combinations throughout the progression of the prion disease, and identified differentially expressed genes (DEGs) and pathways for different stages of the disease. A putative network was constructed based on the pooled DEGs primarily found in BL6 mice infected with infected prions across a time course of 6, 10, 14, 18, 20, and 22 weeks after inoculation. The DEGs shared by various prion‐mouse combinations were carefully distinguished. The original network was developed using Cytoscape and took tremendous time and effort to organize the layout and carefully modify the node size and font styles one by one. Using MOE, it is rather straightforward to construct the full interactive network in a few seconds by uploading nodes and links information, and yet have the dynamic slideshow and many other functions, such as search capability, gene description, and focused interactions. In this paper, we introduce an easy‐to‐use web application MOE with rich functions for dynamic network visualization. It was specifically designed to foster scientifically informative, flexible, and sharable visualization that is desired by many scientists. With this tool, one can save a lot of manual labor and have informative, interactive networks that can be displayed and shared freely. We are not aware of any similar products in existence. Support or Funding Information DISCLAIMERS: Research was conducted in compliance with the Animal Welfare Act and all other Federal Requirements. The views expressed are those of the authors and do not constitute endorsement by the U.S. Army.A six‐time‐point dynamic network representing prion replication and accumulation process reproduced from Fig 4 in Hwang et al . 2009. In all, 16 pathways represented in modules are involved in the network; the node color denotes the relative fold change of the gene expression (red‐upregulation, yellow‐no change, green‐downregulation). There are six prion‐mice combinations.