Workshop: World Tour of Genome Browser and Galaxy of Analysis Tools

Would like to just announce that Mary and I will be giving an all-day hands-on workshop on Tuesday, November 2nd, 2010 in Washington DC (my home town), right before the ASHG conference (where we will also be). The title of the workshop is A World Tour of Genome Browsers and a Galaxy of Analysis Tools. We’ll be covering UCSC Genome and Table Browsers, an overview of other genome browsers, BioMart, Galaxy and a tour of genome resources and how to find them. For more information on location, cost, topics you can continue reading here. There are workshops on UCSC and Galaxy at ASHG  for attendess (which we will be at, but Bob, Anton and others will be doing), but those have sold out and filled up. We are offering this workshop for those who would like to learn these topics and more, both DC residents and ASHG attendees.

To purchase a seat and register, go to our upcoming workshops page.

Workshop: The World of Genome Browsers and the Galaxy of Analysis Tools

OpenHelix is offering a full day hands-on computer workshop introducing genome browsers, advanced genome searching and an introduction to analysis using Galaxy. The workshop is hands-on with both a follow-along lecture section and hands-on exercises, as well as time for questions and answers. This workshop will be offered in Washington DC on Tuesday November 2, 2010 from 9am to 5pm. Cost for full day workshop is USD $395.95 and lunch, snacks and beverages are provided. See below for more details and to register.

The day’s agenda:

Morning 9:00am-12:15pm
*Introduction to the UCSC Genome Browser. This section will cover the topics needed to effectively use this powerful, free, publicly-accessible tool, including: basic functionality of Genome Browser searching and BLAT use. The UCSC Genome Browser includes dozens of species genomes and a wealth of annotation data for a complete genomic context to such information as expression, gene structure, comparative analysis and more.

*Advanced searching using the UCSC Table Browser and custom tracks. A introduction to advanced searching of the genomics database using the Table Browser and an introduction to creating custom annotation tracks. The UCSC Table Browser provides a way to query and extract the data from many genomes, with extensive annotation for various data types including known genes, predicted genes, SNPs, comparative multi-species analysis and much more. Obtain large lists of genes, SNPs, or any other features of interest, or display your own data, using the tools underlying the UCSC Genome Browser.

Working Lunch (provided) 12:15-1:30

*A World Tour of Genome Resources. A 30 minute introduction to a sample of the thousands of publicly available genomic resources for the researcher, how to find them and learn how to use them.

Afternoon 1:30pm-5pm
*Overview of Genome Browsers. In this section we introduce, compare and contrast additional genome browsers including Ensembl, IMG, GBrowse and more. Several major genome web browsers are widely used to search, retrieve, and display genome information for human and numerous other species. Here we introduce Ensembl, Map Viewer, UCSC Genome Browser, and the Integrated Microbial Genomes (IMG) browser. We also introduce the GBrowse software system, which is the framework for many additional genome browsers. Biomedical researchers need to be aware of these resources and be able to access the data available within.

*Introduction to BioMart. An introduction to advanced searching of genome data using the BioMart search interface. BioMart is a publicly available open source tool for the management and querying of many types of biological data. It is widely used around the world for various projects. As a component of the GMOD (Generic Model Organism Database) suite of tools, many projects and individuals contribute to the development of BioMart.

*Introduction to Galaxy. This introduction will assist the researcher in using Galaxy to analyze genomics data. Galaxy is an excellent online genome analysis tool that combines the power of existing genome annotation databases with a simple web portal with a variety of tools and algorithms, to enable users to search remote resources, combine data from independent queries, prepare, manipulate and analyze the data using a large suite of analysis tools. A history workflow is created for every analysis providing a record ensuring reproducibility of results, and the opportunity to share workflows with other Galaxy users.


“The World of Genome Browsers and the Galaxy of Analysis Tools,” a seminar and hands-on computer workshop presented by OpenHelix, LLC.

When and Where:

Washington, DC: MicroTek @ 1101 Vermont Ave. NW, Suite 300, Washington DC 20005.

November 2, 2010. 9am to 5pm.


Anyone interested in an introduction to genome browsers and resources. Requires basic knowledge of genomic/biological concepts. No programming skills required.


USD $395.95. Lunch and snacks are provided. Participants receive complete slide and exercise handouts and printed Quick Reference Cards. Seating is limited, register as soon as possible.

Contact Information: by email or toll-free phone (within US) 1-888-861-5051

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