Local ICTS Mirror of UCSC Genome Browser
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Local ICTS Mirror of UCSC Genome Browser Lucas Van Tol : lucas-vantol@uiowa.edu, Gi-yung Ryu : gi-yung-ryu@uiowa.edu Institute for Clinical and Translational Science. UCSC Genome Browser

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The institute for clinical and translational science icts

Local ICTS Mirror of UCSC Genome BrowserLucas Van Tol: lucas-vantol@uiowa.edu, Gi-yungRyu: gi-yung-ryu@uiowa.eduInstitute for Clinical and Translational Science

  • UCSC Genome Browser

  • An up-to-date source for genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.

  • Provides a way to examine the data from many genomes, with extensive annotation tracks for various data types including known genes, predicted genes, SNPs, comparative multi-species analysis and much more.

  • Custom annotation tracks allow users to upload personal data for temporary use in the Genome Browser and Table Browser.

  • Table Browser provides a powerful and flexible graphical interface for querying and manipulating the data in the Genome Browser annotation database.

  • Mirroring Genome Browser

  • To facilitate and expedite the research of the University of Iowa Genomics community, ICTS plans to provide a local mirror of the UCSC Genome Browser.

  • ICTS has deployed a public Genome Browser which is accessible from The University of Iowa campus.

  • ICTS plans to provide private instances of the Genome Browser application to labs. These instances will only be accessible to authenticated users, ensuring the privacy of sensitive or unpublished data (such as custom tracks). Data in these instances will also not be subject to the custom track data retention restrictions.

  • We are in the early stages of deployment and welcome feedback on how the platform can be most useful.

  • UCSC Genome Browser Issues

  • There is no protection for private data.

  • Custom tracks are deleted after a period of time and no longer accessible.

  • Uploading large data sets takes a long time and sometimes times out because of slow network connectivity.

  • The latency introduced by using the offsite UCSC genome browser decreases productivity.

The Institute for Clinical and Translational Science (ICTS)

Home to the National Institutes of Health funded Clinical and Translational Science Award at the University of Iowa, dedicated to providing the synergy, resources, and experience necessary to enhance and accelerate the "bench to bedside" approach of biomedical knowledge by forging unique networks and developing new cures and treatments for disease, and help establish unique collaborations between clinicians, investigators, and community members.

public instance is deployed at