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. 2015 Mar 1;31(5):764-6.
doi: 10.1093/bioinformatics/btu712. Epub 2014 Oct 27.

Navigating Protected Genomics Data With UCSC Genome Browser in a Box

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Free PMC article

Navigating Protected Genomics Data With UCSC Genome Browser in a Box

Maximilian Haeussler et al. Bioinformatics. .
Free PMC article

Abstract

Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access.

Availability and implementation: Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/).

Figures

Fig. 1.
Fig. 1.
Data flow when accessing the UCSC Genome Browser website (A) versus the Genome Browser in a Box (B). In case (B) the custom track data does not leave the user’s PC and is not transmitted over the Internet

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References

    1. Afgan E., et al. . (2010) Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics, 21, S4. - PMC - PubMed
    1. Angiuoli S.V., et al. . (2011) CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics, 12, 356. - PMC - PubMed
    1. Gu Y.H., et al. (2007) UDT: UDP-based data transfer for highspeed wide area networks, Comput . Networks, 51, 1777–1799.
    1. Karolchik D.K., et al. (2014) The UCSC Genome Browser database: 2014 update. Nucleic Acids Res., 42, D764–D770. - PMC - PubMed
    1. Kent W.J., et al. (2002) The human genome browser at UCSC. Genome Res. , 12, 996–1006. - PMC - PubMed

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