D880 Nucleic Acids Research, 2011, Vol. 39, Database issue 46 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package for all vertebrate species, as well as primate and placental mammal subsets. The SNP track contains over 26 million mappings of more than 23 million reference SNPs that have been mapped to the reference genome by dbSNP. This represents a signiﬁcant increase from the provisional hg19 mappings of build 130 (33). As we continue to migrate the bulk of our hg18 annotation tracks to the hg19 assembly, we encourage our contribu- tors to submit hg19-based data sets for inclusion in this effort. Tracks that are regularly updated on the mouse browsers include the International Gene Trap Consortium (IGTC) tracks (34) (updated monthly), the Mouse Genome Informatics MGI tracks (35), which show quantitative trait loci, phenotypes and alleles, and the IKMC Genes tracks (36), which show the genes targeted by the International Knockout Mouse Consortium for generating mouse embryonic stem cells containing a mutation in every gene in the mouse genome. Some of our regularly updated tracks appear on multiple browsers. These include the Consensus Coding Sequence (CCDS) (37) tracks, which were updated on the human and mouse genomes, the Mammalian Gene Collection (MGC) tracks (38) on the human, mouse, rat, cow and frog genomes, and the Ensembl Genes tracks (6), available on approximately 25 different organisms. RefSeq and mRNA tracks, which display aligned sequences from all organisms in GenBank (5), are updated nightly, and EST tracks are updated weekly. FUTURE DIRECTIONS We plan to incorporate several new features as well as exciting new variation and medical genomics data over the next year. We will also continue to add new and updated vertebrate and other selected model organism assemblies that have been deposited into GenBank. (Only assemblies registered and deposited at NCBI will be considered for hosting at UCSC, as stipulated in the Browser Genome Release Agreement instituted by NCBI, Ensembl, and UCSC.) By late 2010 we plan to release a utility that enables users to quickly search track names and descriptions. This tool will provide both simple and advanced search interfaces, with the advanced interface allowing users to further reﬁne their search criteria and search the metadata associated with ENCODE tracks (e.g. cell line, transcrip- tion factor, stage, etc.). Also by the end of 2010, users will be able to quickly access conﬁguration and navigation shortcuts on the Genome Browser image by right-clicking on the vertical bar to the left of a track. We are developing data hub support that will make it possible to view user-supplied data (such as BigWig, BigBed and BAM ﬁles) with the more sophisticated track display options currently used on other UCSC tracks such as composite tracks. We are also working on several improvements to the display of BAM ﬁles such as ﬁltering by ﬂag and density-wiggle view. We plan to enable data extraction from BAM ﬁle-based tracks via the Table Browser. We anticipate adding a number of new variation tracks, including data from the 1000 Genomes project as well as from dbVar, a new structural variation database at NCBI. We are currently working on browser display support for data stored in Variant Call Format (VCF; http://1000genomes.org/wiki/doku.php?id=1000_ genomes:analysis:vcf4.0), a format developed by the 1000 Genomes Project to represent variant data. Additionally we are discussing strategies for distinguishing SNPs annotated as ‘clinically associated’ by dbSNP in our SNP annotations, and looking into other stratiﬁcations of these data such as singly mapped versus multiply mapped. We plan to import additional personal genome variant tracks from the Pennsylvania State University Bioinformatics Genome Browser (http://main.genome- browser.bx.psu.edu/), including updated 1000 Genomes high-coverage trio variants as well as variants from ﬁve Khoisan and Bantu genomes (39) and a Paleo-Eskimo Saqqaq genome (40). We intend to add medical genomics data from the International Standards for Cytogenomic Arrays (ISCA) consortium (41). These data should help clinicians inter- pret array CGH results by aggregating the results of potentially thousands of cases from clinics all over the world in one place. The data will be released to dbGaP and dbVar at NCBI and then integrated into the browser for display in the context of our other content. Finally, we plan to offer cloud support for mirrors, providing a Genome Browser image that will enable labs to instantiate a browser for private use without the overhead of a local server (42) and supporting the simple construction of new Genome Browsers on novel genome sequences. CONTACTING US We have two public, moderated mailing lists for user support: genome@soe.ucsc.edu for general questions about the Genome Browser, and genome-mirror@soe .ucsc.edu for questions speciﬁc to the setup and mainten- ance of Genome Browser mirrors. Archives of both lists are searchable from our contacts page at http://genome .ucsc.edu/contacts.html. You may also reach us at genome-www@soe.ucsc.edu, the preferred address for inquiring about mirror site licenses and reporting server errors. Messages sent to this address are not archived in a publicly searchable location. ACKNOWLEDGEMENTS The authors would like to thank the many data contribu- tors whose work makes the Genome Browser possible, our Scientiﬁc Advisory Board for steering our efforts, our users for their consistent support and valuable feedback, and our outstanding team of system administrators: Jorge Garcia, Erich Weiler, Victoria Lin and Alex Wolfe.