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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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JBrowse Connect: A server API to connect JBrowse instances and users
Eric Yao1,2, Robert Buels1, Lincoln Stein3
1Department of Bioengineering, Stanley Hall, University of California, Berkeley, California, United States of America.
Plos Computational Biology
|August 19, 2020
Summary
JBrowse Connect enhances the JBrowse genome browser for developers, enabling live messaging, notifications, and in-browser analyses like BLAST searches and primer design. This expansion streamlines bioinformatics workflows and data visualization.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- The JBrowse genome browser is a widely used tool for visualizing genomic data.
- Developers require advanced functionalities for integrating complex analyses and real-time data updates within genome browsers.
Purpose of the Study:
- To introduce JBrowse Connect, an extensible module for the JBrowse genome browser.
- To enable dynamic features such as live messaging, notifications, and user-initiated heavy-duty analyses directly within the browser interface.
Main Methods:
- Development of JBrowse Connect as an optional expansion for the JBrowse genome browser.
- Implementation of modules for executing BLAST searches (leveraging NCBI Blast+) and running the Primer3 service.
- Integration with web servers and optional managed Galaxy instances for flexible analysis execution.
Main Results:
- JBrowse Connect facilitates live messaging and notifications for new annotation tracks.
- Users can initiate and track complex analyses, including BLAST searches and primer design, directly within JBrowse.
- Results are displayed contextually within the genome browser, enhancing data interpretation.
Conclusions:
- JBrowse Connect significantly expands the capabilities of the JBrowse genome browser for developers and researchers.
- The module streamlines bioinformatics workflows by integrating analysis tools and providing real-time feedback.
- JBrowse Connect is available under open-source licenses, promoting widespread adoption and further development.
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