Hands-On Training Schedule
Wednesdays
1-3 pm
Falk Library Classroom 2 (upstairs)
Registration is NOT required.
September 9th: Literature Mining: InfoBoosters, Molecular Databases, & F1000Workspace
- This hands-on workshop will cover literature searching software, molecular databases, and tools to help quickly mine these resources for pertinent information. Participants will learn how to identify the most appropriate scientific articles as well as annotate them with results fetched from gene, protein, disease, and drug-related databases.
September 30th: Genome Navigation: UCSC Genome Browser
- This hands-on workshop will focus on a variety of genome biology resources. Participants will learn to (1) identify and retrieve 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), (3) construct complex queries and retrieve large-scale genome data (Table Browser), and (4) create custom genome browser tracks from users’ own uploaded data (UCSC Custom Track tool).
October 7th: Gene Regulation: TRANSFAC, NextBio, ENCODE
- This hands-on workshop provides an overview of resources and search strategies on transcriptional regulation. Emphasis will be given to databases, including TRANSFAC (transcription factors), Proteome (promoter sequences) and RegulomeDB (SNPs with known and predicted regulatory elements). Software that will be covered: BIOBASE Match to locate transcription factor binding sites present in a query sequence, UCSC Genome Browser to visualize the regulatory regions present in the human genome generated by the Encyclopedia of DNA Elements (ENCODE) project, and the HSLS licensed tool – NextBio Enterprise to mine microarray/RNA Seq data from the Gene Expression Omnibus (GEO) repository.
October 21st: Pathway Analysis: NIH DAVID & IPA
- This hands-on 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 NCBI 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 interactions and literature-curated gene/protein knowledgebases using pathway informatics software, including Ingenuity Pathway Analysis (IPA) and NIH DAVID.
November 4th: Genetic Variation & Cancer Mutation: dbSNP, COSMIC, & more
- This hands-on workshop focuses on human genetic variation and cancer mutation resources. It covers the basic concepts behind different forms of variations, introduces variation databases (dbSNP, ClinVar, OMIM, DGV, PheGenI, HGMD, NextBio, COSMIC, Broad Tumor Portal, ExAc Browser, RegulomeDb), suggests database searching strategies, and the use of bioinformatics tools for predictive functional analysis of mutations (EBI Variant Effect Predictor).
November 18th: RNA-seq Analysis: CLC Genomics Workbench
- This hands-on workshop will provide an introduction to RNA-seq analysis using the library-licensed CLC Genomics Workbench. Participants will learn how to (1) align RNA-seq data to a reference genome, (2) calculate known genes and transcript expressions, (3) perform differential expression analysis, and (4) discover novel exons.
These classes are approved for AMA Category 2 CME credit.