Hands-On Training Schedule
Wednesdays
1-3 pm
Falk Library Classroom 2 (upstairs)
Registration is NOT required.
May 13th: Genome Browsers
- This workshop will focus on a variety of genome biology resources. Participants will learn to (1) identify and retrieve organism’s whole genome sequence information by searching databases (NCBI Genome, Integrated Microbial Genome), (2) navigate genome sequences and extract information from annotated genome data (UCSC Genome Browser, NCBI MapViewer), (3) construct complex queries and retrieve large-scale genome data (Table Browser), and (4) create custom genome browser track from users’ own uploaded data (UCSC Custom Track tool).
June 10th: Gene Regulation Resources
- This hands-on workshop provides an overview of resources and search strategies on transcriptional regulation. Special emphasis will be given on databases, including BioBase TRANSFAC, GenomeTrax, and RegulomeDB, and software such as Biobase Match, HaploReg, UCSC Genome browser to visualize the regulatory regions present in the human genome generated by the Encyclopedia of DNA Elements (ENCODE) project, and the recently licensed library tool – NextBio Enterprise to mine microarray data from the Gene Expression Omnibus (GEO) repository.
July 8th: Pathway Analysis Tools
- This workshop introduces open access and commercial biological pathway informatics tools. First we will learn how to mine a list of differentially expressed genes associated with a disease of interest by searching the Gene Expression Omnibus (GEO) using the library-licensed tool NextBio. Then we will focus on uncovering the biology hidden behind the extracted gene list by searching protein-protein interaction and literature curated gene/protein knowledge bases using pathway informatics software, including Ingenuity Pathways Analysis (IPA) and NIH DAVID.
August 12th: SNPs & Genetic Variation
- This hands-on workshop features genetic variation resources and will focus on Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs). It covers the basic concepts behind different forms of genetic variations, introduction to variation databases (dbSNP, OMIM, DGV, PheGenI, HGMD, GenomeTrax, NextBio), database searching strategies, and the use of bioinformatics tools for predictive functional analysis of mutations.
These classes are approved for AMA Category 2 CME credit.