Motivation: Network biology is widely used to elucidate mechanisms of disease and biological processes. The ability to interact with biological networks is important for hypothesis generation and to give researchers an intuitive understanding of the data. We present visJS2jupyter, a tool designed to embed interactive networks in Jupyter notebooks to streamline network analysis and to promote reproducible research.
Results: The tool provides functions for performing and visualizing useful network operations in biology, including network overlap, network propagation around a focal set of genes, and co-localization of two sets of seed genes. visJS2jupyter uses the JavaScript library vis.js to create interactive networks displayed within Jupyter notebook cells with features including drag, click, hover, and zoom. We demonstrate the functionality of visJS2jupyter applied to a biological question, by creating a network propagation visualization to prioritize risk-related genes in autism.
Availability and implementation: The visJS2jupyter package is distributed under the MIT License. The source code, documentation and installation instructions are freely available on GitHub at https://github.com/ucsd-ccbb/visJS2jupyter. The package can be downloaded at https://pypi.python.org/pypi/visJS2jupyter.
Contact: sbrosenthal@ucsd.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.
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