Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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

Free PMC article

Navigating Protected Genomics Data With UCSC Genome Browser in a Box

Maximilian Haeussler et al. Bioinformatics. .
Free PMC article


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 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 (


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

Similar articles

  • The UCSC Table Browser data retrieval tool.
    Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. Karolchik D, et al. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6. doi: 10.1093/nar/gkh103. Nucleic Acids Res. 2004. PMID: 14681465 Free PMC article.
  • The UCSC Genome Browser.
    Karolchik D, Hinrichs AS, Kent WJ. Karolchik D, et al. Curr Protoc Bioinformatics. 2009 Dec;Chapter 1:Unit1.4. doi: 10.1002/0471250953.bi0104s28. Curr Protoc Bioinformatics. 2009. PMID: 19957273 Free PMC article.
  • Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.
    Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Raney BJ, et al. Bioinformatics. 2014 Apr 1;30(7):1003-5. doi: 10.1093/bioinformatics/btt637. Epub 2013 Nov 13. Bioinformatics. 2014. PMID: 24227676 Free PMC article.
  • UCSC genome browser tutorial.
    Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. Zweig AS, et al. Genomics. 2008 Aug;92(2):75-84. doi: 10.1016/j.ygeno.2008.02.003. Epub 2008 Jun 2. Genomics. 2008. PMID: 18514479 Review.
  • UCSC genome browser: deep support for molecular biomedical research.
    Mangan ME, Williams JM, Lathe SM, Karolchik D, Lathe WC 3rd. Mangan ME, et al. Biotechnol Annu Rev. 2008;14:63-108. doi: 10.1016/S1387-2656(08)00003-3. Biotechnol Annu Rev. 2008. PMID: 18606360 Review.
See all similar articles

Cited by 21 articles

See all "Cited by" articles


    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

Publication types