This component describes our plans to develop, maintain, and extend the UCSC Genome Browser software, build and maintain genome browsers and annotations for species of biomedical interest, and integrate data from the scientific community that help interpret the functions of various genome regions. The UCSC Genome Browser has met the needs of the genomics and biomedical communities for over sixteen years while accommodating a dramatic increase in the volume of data and simultaneous users, supporting a wealth of new data types, and adapting to new computing platforms and displays. Our web-based tools garner over one million hits per day, and our Unix command-line tools are used in genomic analysis pipelines throughout the world. During the upcoming period we plan to expend more effort on maintaining and extending the Genome Browser software than on any other aim in this proposal. Highlights of our planned work include adding new displays to interpret personal genomes, developing displays that aggregate the increasing volumes of data, adding visualization support for chromatin conformation capture data and other data that cannot be easily shown in a linear, two-dimensional chromosome view, improving search capabilities of our databases and hubs, building a version targeted at mobile devices, and building browsers and displays that support single cell data. The Genome Browser database offers genomic data for nearly 100 organisms, many with multiple assemblies. The human and mouse genomes, which include the most recent assemblies from the Genome Reference Consortium, are the most richly annotated. We will continue to import new and updated assemblies, focusing on vertebrate genomes and with an emphasis on primates, animals used in scientific research, and animals that help extend coverage of the vertebrate phylogenetic tree. We intend to make it easier to build browsers and related tools on new genomes, automating the process when possible. We plan to map and compute annotations on patches issued between major releases of the human and mouse genomes to increase the usefulness of the patches to the scientific community. We will periodically evaluate multiple genome alignment software in search of a superior alternative to our existing pipeline. The genome framework is an ideal platform for integrating the research findings of a broad range of scientists. We plan to continue importing new data releases from projects that we currently support, in particular the GTEx and ENCODE projects, as well as incorporating new data from selected projects and papers recommended to us by our users, our scientific advisory board, and our funding agency. We will encourage the use of track hubs by external project groups and consortia for displaying their data sets in the browser. We also plan to integrate de-identified data into our public browser, and will coordinate with dbGAP to allow their authorized users to access specific, identifiable, private data sets in a secure manner on our site.
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| Casper, Jonathan; Zweig, Ann S; Villarreal, Chris et al. (2018) The UCSC Genome Browser database: 2018 update. Nucleic Acids Res 46:D762-D769 |
| Canver, Matthew C; Haeussler, Maximilian; Bauer, Daniel E et al. (2018) Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments. Nat Protoc 13:946-986 |
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| GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group et al. (2017) Genetic effects on gene expression across human tissues. Nature 550:204-213 |
| Saha, Ashis; Kim, Yungil; Gewirtz, Ariel D H et al. (2017) Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res 27:1843-1858 |
| Tyner, Cath; Barber, Galt P; Casper, Jonathan et al. (2017) The UCSC Genome Browser database: 2017 update. Nucleic Acids Res 45:D626-D634 |
| Vivian, John; Rao, Arjun Arkal; Nothaft, Frank Austin et al. (2017) Toil enables reproducible, open source, big biomedical data analyses. Nat Biotechnol 35:314-316 |
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