This component describes our plans for the scientific, project, and personnel management of the UCSC Genome Browser team and resource, the dissemination of our software and data, and the training of our users. We place a high value on the benefits of a good management team and adherence to solid project processes and best practices. During the sixteen years since the inception of the Genome Browser resource, we have developed and fine-tuned many management methods and processes that we will continue to leverage in upcoming years, while learning about new tools and ideas that might benefit our team, and thus our users. We will continue to seek scientific guidance from our Genome Browser PIs, Scientific Advisory Board (SAB), and colleagues, which helps us to focus our work on efforts that best support our research community and to remain aware of upcoming challenges in the field. The UCSC Genome Browser website at https://genome.ucsc.edu/ is the main venue for disseminating the resources and data created through this grant. The assemblies and the data underlying the annotation tracks can be downloaded in bulk from the browser's downloads server and through queries from our Table Browser and Data Integrator. The Genome Browser software and Genome Browser in a Box (GBiB) product are available from our online web store, and the full suite of data manipulation bioinformatics tools can be obtained from our downloads server. The raw source code is available from our public GitHub repository. Even with 1.2 million hits per day to the Genome Browser website, we understand the importance of reaching out to new users as we simultaneously support our existing user base. To help prevent the many features of this mature resource from becoming overwhelming to new users, we offer a variety of instructional materials to help them learn about the data and tools. The website features online help documentation, user guides, and how-to videos, and we often post project information of public interest on our social media sites and home page. Our trainers conduct onsite workshops at institutions and scientific meetings tailored to the needs and experience level of each audience. Our help desk fields questions and feedback from new and advanced users alike.
We aim to keep our training and outreach methods current and relevant as we move into the next phase of this project.
| Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine et al. (2018) ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res 46:D718-D725 |
| 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 |
| GTEx Consortium (2018) Erratum: Genetic effects on gene expression across human tissues. Nature 553:530 |
| Dyke, Stephanie O M; Linden, Mikael; Lappalainen, Ilkka et al. (2018) Registered access: authorizing data access. Eur J Hum Genet 26:1721-1731 |
| Howard, Jonathan M; Lin, Hai; Wallace, Andrew J et al. (2018) HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo. Genome Res 28:689-698 |
| 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 |
Showing the most recent 10 out of 41 publications
