The World of Genome Browsers and the Galaxy of Analysis Tools
Bellevue, WA (PRWEB) October 6, 2010
OpenHelix is offering a full day hands-on computer workshop introducing genome browsers, advanced genome searching, an introduction to analysis using Galaxy, and a overview of the publicly available bioinformatics and genomics resources available.
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. More details below; register at openhelix.com
The day's agenda:
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. An 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) 12:30-1:15
A World Tour of Genome Resources. A discussion of the number and breadth of publicly available bioscience resources available to researchers. It will include a tour of example resources, organized by categories such as Algorithms and Analysis tools, expression resources, genome browsers (General, Eukaryotic and Prokaryotic/Microbial), Literature and text mining resources, and resources focused on nucleotides, proteins, pathways, disease and variation. This main discussion will then lead into a discussion of how to find resources with the OpenHelix search interface, learning to use resources with OpenHelix tutorials, and a discussion of additional methods of learning about resources.
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.
November 2, 2010. 9 a.m. to 5 p.m.
Washington, DC: MicroTek @ 1101 Vermont Ave. NW, Suite 300, Washington DC 20005.
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/Registration: Register at openhelix.com/cgi/seminars.cgi?tab=6 or call1-888-861-5051
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.