Tutorials and Short Courses
Tutorials For Analyzing Quantitative 'Omic Data
2009-2010
Tutorial Organizer: Aditi Hazra
After an initial offering of this tutorial series last spring, the Program in Quantitative Genomics (PQG) will offer a monthly tutorial series on computational tools for analyzing genomic and proteomic data throughout the school year.
This tutorial series will cover basic Genome Browser navigation, overview of Galaxy queries, and an introduction to other analytic tools for genomics. The Spring 2009 series covered microarray analysis, PLINK, MaCH, PYTHON, and PERL.
All of the classes will be located in Kresge LL6, which has individual computers located at each workstation.
Participation is open to the HSPH community, but RSVP is not required. You must have a Harvard login and password to use the computers, otherwise you must contact Shaina Andelman at sandelma@hsph.harvard.edu to obtain a temporary login prior to class.
Upcoming Tutorial
Monday, November 23, 2009
3:30-5:30 PM, Kresge LL6Paul Bain
Topic: Genome Browsing with EnsemblEnsembl provides unified access to genomic information and annotation for more than 50 eukaryotic species. Learn how to find gene and genomic-related information, from splice sites to SNPs and more. We'll also explore the data mining tool BioMart that provides access to Ensembl data in bulk, with hands-on exercises.
Additional Dates
December 14, 2009
3:30-5:30 PM, Kresge LL6
Pierre R. Bushel - State-of-the-art Biological Processes Enrichment Using Gene OntologyJanurary 25, 2010
3:30-5:30 PM, Kresge LL6
Pyne Saumyadipta- Introduction to FLAME
February 22, 2010
3:30-5:30 PM, Kresge LL6
Speaker TBA
March 22, 2010
3:30-5:30 PM, Kresge LL6
Speaker TBA
April 26, 2010
3:30-5:30 PM, Kresge LL6
Speaker TBA
May 10, 2010
3:30-5:30 PM, Kresge LL6
Speaker TBA
Past Tutorials
Monday, October 26, 2009
3:30-5:30 PM Kresge LL6Ross Lazarus, MBBS MPH
Associate Professor, Harvard Medical School
Director of Bioinformatics, Channing Laboratory"An Introduction to the Galaxy Genomics Workbench"
Galaxy is a popular and flexible open-source analysis platform, designed to support and encourage persistent, reproducible and shareable genomics research. Requiring only a standards-compliant web browser, the free public server at Penn State offers transparent integration with familiar model organism and public human data sources such as BioMart and the UCSC, together with a flexible set of tools for text file manipulation, combined with specialized tools such as intersection operations on interval data. While a skilled informatician can readily program these steps using a scripting language, Galaxy has the advantage of requiring minimal user training, and more importantly, of organizing and retaining every step, parameter setting and intermediate dataset from every analysis in a persistent, shareable and reproducible 'history'. Some of these basic and widely applicable features will be illustrated in this tutorial/demonstration, and a preview of tools currently under development for QC and analysis of commodity whole genome statistical genetics and microarray expression data will be provided.
By the end of the session, attendees will be familiar with some simple, but widely applicable basic Galaxy tools and features that may prove to be useful in their own research, and will be ready to begin to explore some of the more specialized Galaxy capabilities such as the creation and sharing of complex workflows, and the rapidly growing suite of next-gen sequencing tools.