UCSC Genome Browser Workshops

• Times and Locations
• Tentative Agenda and Topics
• Instructors
  

The Open Source, publicly available UCSC Genome Browser is an important bioinformatics tool. A web-based, graphical genome viewer and tool suite, it is designed for rapid visualization, examination, and querying of biosequence data at many levels. It currently holds >40 vertebrate and selected invertebrate genomes available for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Researchers can call-out and customize a wide variety of annotated datasets ("data tracks") including mapping and sequencing, variations and repeats, phenotype and disease association, genes and gene prediction, mRNA and EST, expression, regulation, and comparative genomics. Data can be searched via text or sequence (BLAT).

As part of the Bioinformatics @ HSL series, the Health Science Libraries at the University of Buffalo is sponsoring a full-day, hands-on computer workshop introducing and covering the major features of the Browser, presented by instructors from OpenHelix.

The workshop is open to all UB communities (faculty, graduate students, post-doctoral fellows, medical fellows, physicians, staff, undergraduates with bioinformatics experience, etc.) on all UB campuses, including the South, North and Buffalo Niagara Medical campuses. You need not have any prior experience with the Browser, but it is suggested that registrants be familiar with sequence data or searches (BLAST, etc.) through experience, readings or coursework.

The workshop is FREE, but you must register (see below) to attend, choosing either a South Campus or Buffalo Niagara Medical. Registration is on a "first-come-first-serve" basis. Register early, as seating is limited.

Questions? Contact Diane Rein, Bioinformatics Liaison, Health Sciences Library, through email (drein@buffalo.edu) or telephone (829-5749).

Times and Locations:

September 21, 2011, 9:00 am - 4:00 pm: Buffalo Niagara Medical Campus, location to be announced
September 22, 2011, 9:00 am - 4:00 pm: SOUTH Campus, location to be announced

To register for either workshop, click here.

Tentative Agenda and Topics (subject to change):

• 9:00 - 10:30 AM: Introduction to the UCSC Genome Browser
•  perform basic text searches
• customize displays in genomic regions of interest
• using a sequence, find genomic regions of interest
• 10:30 -10:40 AM: Break
• 10:40 - Noon: UCSC Genome Browser Advanced Topics
• perform advanced searches
• export and download targeted data
• create custom tracks and annotate them
• visualizing genome-wide association  data
• Noon – 1:30 PM: Lunch on your own
• 1:30 – 2:30 PM: ENCODE data at UCSC Genome Browser
• foundations and background of the ENCODE project
• identify ENCODE data in the UCSC Genome Browser, and explore the data use policies
• available ENCODE data types and locating them
• interacting and downloading ENCODE
• 2:30 – 2:45 PM: Break
• 2:45 – 4:00 PM: World Tour of Genome Resources
• locate and access public bioinformatics resources in a variety of different categories
• quick overview to several specific resources, including:
• DGV (Database of Genomic Variants), a curated catalog of structural human variations to enable correlation of genomic variation with phenotypic data
• IntAct, a protein interaction database at the European Bioinformatics Institute (EBI)
• STRING (Search Tool for the Retrieval of Interacting Genes/Proteins), a database of known and predicted protein-protein interactions of both physical (direct) and functional (indirect) types
• MEME Suite, a suite of DNA or protein motif-based sequence search and analysis tools
• iHOP (Information Hyperlinked Over Proteins), a searchable database of text-mined gene and protein information extracted from PubMed  that organizes  hits into an hyperlinked, navigable hit list
• CMR (Comprehensive Microbial Resource)
• Ensembl (EBI’s genome browser)
• DAVID (Database for Annotation, Visualization and Integrated Discovery), web-based analysis tools that permit functional annotation of differentially expressed genes, including from large datasets and/or gene lists
• Galaxy, integrated set of sophisticated web-based  motif, alignment and statistical tools  to analyze, manipulate, experiment with, and share bioinformatics data
• Overview of OpenHelix resources and search interface

Instructors:

Warren (Trey) Lathe, PhD:
Prior to joining OpenHelix, Dr. Lathe was a bioinformatics researcher at the European Molecular Biology Laboratory (EMBL) in the Bork group. His research topics ranged from the evolution and regulation of bacterial genes to mapping Human SNPs to 3D protein structures. Dr. Lathe holds a Ph.D. from the University of Rochester in Molecular and Evolutionary Biology.

Mary E. Mangan, PhD:
Dr. Mangan of OpenHelix has broad experience in the field of bioinformatics. Most recently, she successfully founded and operated Biological Software Testing Services, Inc. This company provided software testing from a biological scientist's perspective for the bioinformatics industry. Prior to that, Dr. Mangan has been an Application Scientist and Scientific and Technical Liaison for Incyte Genomics and Proteome. Dr. Mangan holds a Ph.D. in Cell, Molecular and Developmental Biology from the University of Rochester, and performed post-doctoral research with The Jackson Laboratory Mouse Genome Informatics group.

Last update: 2 September, 2011

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