Translating desktop success to the web in the cytoscape project

Dexter Pratt; Rudolf T Pillich; John H Morris

doi:10.3389/fbinf.2023.1125949

Translating desktop success to the web in the cytoscape project

Front Bioinform. 2023 Mar 23:3:1125949. doi: 10.3389/fbinf.2023.1125949. eCollection 2023.

Authors

Dexter Pratt¹, Rudolf T Pillich¹, John H Morris²

Affiliations

¹ Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, United States.
² Resource on Biocomputing, Visualization, and Informatics, University of California San Francisco, San Francisco, CA, United States.

Abstract

Cytoscape is an open-source bioinformatics environment for the analysis, integration, visualization, and query of biological networks. In this perspective piece, we describe our project to bring the Cytoscape desktop application to the web while explaining our strategy in ways relevant to others in the bioinformatics community. We examine opportunities and challenges in developing bioinformatics software that spans both the desktop and web, and we describe our ongoing efforts to build a Cytoscape web application, highlighting the principles that guide our development.

Keywords: bioinformatics; cytoscape; data visualisation; network biology; software development; systems biology.

Abstract

Grants and funding