A new online tutorial suite teaches users how to access the ENCyclopedia of DNA Elements (ENCODE) project data in the UCSC Genome Browser. The online tutorial, created by OpenHelix in conjunction with the UCSC Genome Bioinformatics Group at the University of California, Santa Cruz, can be viewed for free at http://www.openhelix.com/encode.
The ENCODE Project is an international consortium of researchers who are moving beyond the basic information of the reference genome sequence. Data generated using the newest genome sequencing technologies and numerous other strategies reveal variations, genes, non-coding transcripts, regulatory elements, genome structure, and more, providing extensive detail across the entire genome.
The ENCODE project is coordinated by the National Human Genome Research Institute (NHGRI), a division of the National Institutes of Health. The UCSC Genome Browser is the designated Data Coordination Center (DCC) for the ENCODE project and the official ENCODE data repository.
“The ENCODE project and data are crucial to ongoing genomics research and have already changed our understanding of the organization and function of the genome,” said Kate Rosenbloom, the ENCODE technical project manager at UCSC.
“New data are continually submitted to the Data Coordination Center before they appear in the literature. To maximize the impact on the broader biomedical community it is important to bring people up to speed quickly and efficiently on how to navigate the data,” Rosenbloom said.
The online narrated tutorial, which runs on just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders. In approximately 60 minutes, the tutorial examines aspects of the ENCODE project and data types and explores ways to access and learn about the ENCODE data available within the UCSC Genome Browser.
Combined with the OpenHelix tutorials on the search and display features of the UCSC Genome Browser, the ENCODE data will enable researchers to access cutting-edge data, including pre-publication information.
Rosenbloom said, “The OpenHelix tutorial suite will contribute greatly to our outreach and usability efforts for ENCODE.”
Besides introducing new users to the ENCODE project, the tutorial shows existing users new features and functionality, and it can serve as a reference tool to understand specific features.
In addition to the tutorial, users can also access useful training materials, including the animated PowerPoint slides that form the basis for the tutorial, a suggested script for the slides, slide handouts, and exercises. This can save a tremendous amount time and effort for teachers and professors to create classroom content.
About the UCSC Genome Bioinformatics Group
The UCSC Genome Bioinformatics Group is part of the Center for Biomolecular Science & Engineering (CBSE) at the University of California, Santa Cruz. Director and HHMI investigator David Haussler leads a team of scientists, engineers, and students in the study and comparative analysis of mammalian and model organism genomes. Research scientist Jim Kent heads the engineering team that develops and maintains the UCSC Genome Browser (http://genome.ucsc.edu). The UCSC Genome Bioinformatics Group continues to uphold its original mission to provide free, unrestricted public access to genomic data on the Web.
OpenHelix, LLC, (http://www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites, and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget ,and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.