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An ogive graph is sometimes called a cumulative frequency polygon. It is one type of frequency polygon that shows cumulative frequency. In other words, the cumulative percentages are added to the graph from left to right. An ogive graph plots cumulative frequency on the vertical y-axis and class boundaries along the horizontal x-axis. It’s very similar to a histogram; only instead of rectangles, an ogive displays a single point where the top right of the rectangle would be. Creating this...
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Interactive network visualization in Jupyter notebooks: visJS2jupyter.

Sara Brin Rosenthal1, Julia Len1, Mikayla Webster1

  • 1Department of Medicine, Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA.

Bioinformatics (Oxford, England)
|October 3, 2017
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Summary
This summary is machine-generated.

visJS2jupyter enables interactive biological network visualization within Jupyter notebooks, streamlining analysis and promoting reproducible research for disease mechanism discovery.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Network biology is crucial for understanding disease mechanisms and biological processes.
  • Interactive visualization aids hypothesis generation and data comprehension in biological networks.

Purpose of the Study:

  • To introduce visJS2jupyter, a novel tool for embedding interactive networks in Jupyter notebooks.
  • To facilitate streamlined network analysis and enhance reproducible research in computational biology.

Main Methods:

  • visJS2jupyter leverages the vis.js JavaScript library for interactive network creation.
  • The tool integrates seamlessly within Jupyter notebook cells, offering features like drag, click, hover, and zoom.
  • It supports key biological network operations such as network overlap and gene set propagation.

Main Results:

  • Demonstrated the utility of visJS2jupyter by visualizing network propagation to prioritize autism risk genes.
  • Interactive networks are generated directly within Jupyter notebooks for immediate analysis.
  • The tool enhances the intuitive understanding of complex biological network data.

Conclusions:

  • visJS2jupyter effectively integrates interactive network visualization into the Jupyter environment.
  • The tool promotes reproducible research by enabling direct analysis and visualization of biological networks.
  • It offers a valuable resource for researchers in network biology and computational genomics.