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PBrowse: A web-based platform for real-time collaborative exploration of genomic data

By Peter S Szot, Andrian Yang, Xin Wang, Uwe Röhm, Koon Ho Wong, Joshua W.K. Ho

Posted 05 Aug 2016
bioRxiv DOI: 10.1101/068049 (published DOI: 10.1093/nar/gkw1358)

Summary: The central task of a genome browser is to enable easy visual exploration of large genomic data to gain biological insight. Most existing genome browsers were designed for data exploration by individual users, while a few allow some limited forms of collaboration among multiple users, such as file sharing and wiki-style collaborative editing of gene annotations. Our work's premise is that allowing sharing of genome browser views instantaneously in real-time enables the exchange of ideas and insight in a collaborative project, thus harnessing the wisdom of the crowd. PBrowse is a parallel-access real-time collaborative web-based genome browser that provides both an integrated, real-time collaborative platform and a comprehensive file sharing system. PBrowse also allows real-time track comment and has integrated group chat to facilitate interactive discussion among multiple users. Through the Distributed Annotation Server protocol, PBrowse can easily access a wide range of publicly available genomic data, such as the ENCODE data sets. We argue that PBrowse, with the re-designed user management, data management and novel collaborative layer based on Biodalliance, represents a paradigm shift from seeing genome browser merely as a tool of data visualisation to a tool that enables real-time human-human interaction and knowledge exchange in a collaborative setting. Availability: PBrowse is available at http://pbrowse.victorchang.edu.au, and its source code is available via the open source BSD 3 license at http://github.com/VCCRI/PBrowse. Supplementary Information: Supplementary video demonstrating collaborative feature of PBrowse is available in https://www.youtube.com/watch?v=ROvKXZoXiIc.

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