Last week, dozens of papers were published by the ENCODE (ENCyclopedia of DNA Elements) project, capping a long effort of a worldwide consortia to build a comprehensive parts list of functional elements in the human genome. What can be lost in the press coverage and sometimes heated discussion of the results is the critical value of the ENCODE data to individual researchers, labs and smaller research projects working in a wide variety of fields.
However, to access and study the ENCODE data, researchers need to know how to do so within the UCSC Genome Browser. OpenHelix has released a new online tutorial suite that teaches users how to access the ENCODE data in the UCSC Genome Browser. The online tutorial, created by OpenHelix in conjunction with the UCSC Bioinformatics Group can be viewed for free at http://www.openhelix.com/ENCODE2.
The online narrated tutorial, which runs in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The approximately 60 minute tutorial examines aspects of the ENCODE project and data types, and explores ways for you 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.
The tutorial can be used by new users to introduce them to ENCODE, for previous users to view new features and functionality, or simply as a reference tool to understand specific features.
Also available free (up to 30 cards shipped free in the U.S) is a Quick Reference Card (QRC). The QRC gives an overview of the site and many ways to access and view ENCODE data within the UCSC Genome Browser with screen shots and callouts of the various features and functions. You can order the card at www.openhelix.com/cgi/qrcOrder.cgi.
In addition to the tutorial and QRC, users can also access useful training materials including the animated PowerPoint slides used as a basis for the tutorial, 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.
In addition to the ENCODE tutorial suite, OpenHelix offers over 100 tutorial suites on some of the most powerful and popular bioinformatics and genomics tools available on the web. Some of the tutorials suites are freely available through support from the resource providers. The whole catalog of tutorials suites is available through a subscription. Users can view the tutorials and download the free materials at www.openhelix.com/free.
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials, web seminars, and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix also is contracted by resource providers to provide comprehensive, long-term training and outreach programs. Further information can be found on www.openhelix.com or by calling 1-888-861-5051.
EDIT: 10/12/12: The OpenHelix contract for the ENCODE DCC at UCSC has ended and the DCC Center has now transitioned to a group at Stanford. The new DCC group has chosen to take in-house the training and outreach OpenHelix performed and chose not to fund the sponsorship of the tutorials. However, we have worked with the UCSC Bioinformatics group and the ENCODE tutorial is again freely available until February 2013.