D760 Nucleic Acids Research, 2009, Vol. 37, Database issue including user-created custom tracks. This feature allows the user to quickly move to the left or right in the browser display to the next feature in a particular track, which is particularly useful for custom tracks with sparse coverage. We have also extended the custom track feature to two new data types. The bedGraph data type provides a simpliﬁed method for displaying quantitative data in the browser. The MAF data type allows users to upload multiple-alignment data to the browser as a custom track. This will prove to be especially useful as high- throughput sequencing methods become more widely adopted. The internal representation of custom tracks in the browser is now based on database tables on a dedicated machine rather than the previous ﬁle-based implementa- tion. This oﬀers a considerable speedup of the display, particularly when users revisit the browser in subsequent sessions. One of the most popular tools introduced to the Genome Browser in recent years is the session-saving function, which allows users to save and share multiple browser conﬁgurations for future use (4). Custom tracks that are associated with saved sessions in the browser now have increased longevity. Typically, custom tracks are kept on the Genome Browser for 48–72 h after the last access. However, when users associate the tracks with a saved session (the ‘Session’ link in the top navigation bar), an eﬀort is made to maintain the tracks for a minimum of several weeks. A related change now informs the user in the Session interface that there are custom tracks being saved, indicating the associated genome assembly. Because there are many browser settings and an unlim- ited number of combinations of tracks and display options, the Genome Browser uses browser cookies that persist from one visit to another to maintain the state of user sessions. This allows users to revisit the browser on subsequent days and resume a session without having to reestablish their session conﬁguration. Users frequently need to have more than one instance of the Genome Browser interface on their computer desktop simulta- neously. The browser now has a formal method of pre- venting these instances from interfering with one another. When a user spawns a new browser instance, the new session inherits all the settings of the original, but there- after maintains separate parameters, allowing independent browsing in several windows at once. Future directions UCSC will continue to add new vertebrate and selected invertebrate model organism assemblies and browsers to the GBD as the sequences become available. We are work- ing closely with NCBI and Ensembl to standardize the process for obtaining and distributing new sequence data to ensure that all centers are oﬀering the same versions. We expect to release a 44-species multiple alignment track for the 2 -coverage species project and an expanded mul- tiple alignment Conservation track for the latest human assembly. Data from the 1000 Genomes project will be incorporated into the variation annotations, and will include high-resolution maps of recombination hotspots. Several browser enhancements are planned, such as expanding the usability and conﬁgurability of our data- browsing tools, upgrading isPCR to allow users to query RNA space to align sequence separated by introns and adding support for custom tracks containing more than one type of data (mixed composite tracks). Within the next year we plan to release a new type of track that dis- plays user input directly on the Genome Browser via a wiki mechanism, which will allow experts on particular genes to post comments, data references and other infor- mation directly on the UCSC site. Finally, UCSC has been developing the capacity to display access-controlled med- ical data, e.g., HIV genomics and clinical data, in collab- oration with Global Solutions for Infectious Diseases. A new cancer genomics browser has been completed in collaboration with several research groups. We anticipate that a public version of it will be deployed after access and conﬁdentiality issues are resolved. ACKNOWLEDGEMENTS We would like to thank the many collaborators who have contributed data to our project, our Scientiﬁc Advisory Board for their valuable advice and recommendations, and our users for their feedback and support. We would also like to acknowledge the dedicated system administra- tors who have provided an excellent computing environ- ment: Jorge Garcia, Erich Weiler, Chester Manuel and Victoria Lin. FUNDING The National Human Genome Research Institute (1P41HG002371-08 to UCSC Center for Genomic Science, 2P41HG002371-08 ENCODE supplement to UCSC Center for Genomic Science, 1P41HG004568-01 UCSC ENCODE Data Coordination Center, a subcon- tract on 2U41 HG004269-02 to L.Stein for A Data Coordination Center for modENCODE and a subcon- tract on 1U54HG004555-01 to T.Hubbard for Integrated Human Genome Annotation; Generation of a Reference Gene Set); National Cancer Institute (Contract No. N01-CO-12400 for Mammalian Gene Collection); the Howard Hughes Medical Institute (to D.H.). T.W. is a Helen Hay Whitney fellow. Funding for open access charge: the Howard Hughes Medical Institute. Conﬂict of interest statement. R.M. Kuhn, D. Karolchik, A.S. Zweig, K. E. Smith, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, F. Hsu, A. S. Hinrichs, R. A. Harte, M. Diekhans, H. Clawson, G. P. Barber, D. Haussler and W.J. Kent receive royalties from the sale of UCSC Genome Browser source-code licenses to commercial entities. REFERENCES 1. Karolchik,D., Baertsch,R., Diekhans,M., Furey,T.S., Hinrichs,A., Lu,Y.T., Roskin,K.M., Schwartz,M., Sugnet,C.W., Thomas,D.J. et al. (2003) The UCSC genome browser database. Nucleic Acids Res., 31, 51–54.