Upcoming Topics

• Visualizing Genomes: Circos Plots

Past topics:

• Genome browers: Discovering biology through genomics
  Color slides (pdf)    B&W slide handouts (pdf)    custom tracks for exercises (zip)    Solutions to exercises (plain text)   
• Applications of short-read sequencing: RNA-Seq and ChIP-Seq
  Color slides (pdf)    B&W slide handouts (pdf)    Hands-on exercises (plain text)    data for exercises (zip)   
• Unix: going beyond the basics
  Color slides (pdf)    Hands-on (plain text)    sample1.txt    datasets.zip
• January 31, 2013 - An Introduction to Analyzing Big Data using Amazon Web Services
  Tutorial (pdf)      zipped folder with tutorial files
• January 17, 2013 - RNA-seq Analysis in Galaxy
  Color slides (pdf)  
  Hands-on (pdf)  
• December 6, 2012 - NGS: QC'ing and Mapping Reads
  Color slides (pdf)  
• November 8, 2012 - Analysis of ChIP-seq data in Galaxy
  Color slides (pdf)  
• Oct 18, 2012 - Unix Essentials
Unix Essentials(pdf)   Hands-on Exercises(pdf)    HBI.customCDF_v15.annotated.medianlog2ratio.rma.txt(txt)
• June 21, 2012 - Galaxy, a web based platform for bioinformatics analysis
  Color slides (pdf)  
• June 6, 2012 - Identifying and Aligning Homologs
  Color slides 1 per page  Color slides 6 per page
• March 26-29, 2012 - Unix, Perl, and Python short course
  Full materials - Slides and exercises
• Feb 15 2012 - Enrichment Analysis
  Color slides (pdf)
• December 1 2011 - RNA-seq: A practical guide to the analysis of differential gene expression
  Color slides (pdf)
• November 10 2011 - Assessing Sequence and Microarray Data Quality
  Slides (pdf) Commands (pdf)
• October 3, 4, 6 2011 - R/Bioconductor short course
  Full materials - Slides and exercises
• August 24 2011 - Papers2
  Color handout (pdf)   
• May 26 2011 - An introduction to R Graphics
  Color slides (pdf)    B&W handouts (pdf)    vignette    vignette commands    sample data files: 1 2 3
• April 14 2011 - Juggling Genome Coordinates
  Color slides (pdf)
• March 24 2011 - Analysis of next generation sequencing experiments with Galaxy
  Color slides (pdf)
• Feb 17 2011 - RNA-Seq Methods and Applications
  Color slides (pdf)
• January 13 2011 - Analysis of ChIP-seq experiments
  Color slides (pdf)
• December 2 2010 - Mapping Next Generation Sequence Reads
  Color slides (pdf)
• November 18 2010 - Integrative Genomics Viewer (IGV)
  Color slides (pdf)   
• November 4 2010 - Querying Biological Databases with SQL
  Color slides (pdf)   
• September 2010 - An introduction to R
  Color slides (pdf)    B&W handouts (pdf)    vignette    vignette commands    sample data    Biostatistics vs. Lab Research (video)   
• May 2010 - UCSC Genome Browser
  Color slides (pdf)    Handouts (pdf)   
• Apr 2010 - Visualizing Networks: Cytoscape
  Slides (pdf)   
• March 2010 - Gene list enrichment analysis
  Color slides (pdf)    Handouts (pdf)   
• Feb 2010 - BIOBASE Knowledge Library & Human Gene Mutation Database
Slides (pdf)   
• Jan. 2010 -UNIX
  Powerpoint Slides    Slides (pdf)    compressed files for class and exercises    exercises and answers   
• December 2009 - Galaxy
  Powerpoint Slides    Slides (pdf)   
• November 2009 - Creating Phylogenetic Trees with MEGA
  Slides (pdf)    MEGA Quick Start
• October 2009 - Searching for transcription factor binding sites with TRANSFAC
  Slides
• September 2009 - Getting the most out of Entrez
  Handout      
• June, 2009 - Introduction to ENSEMBL
  Slides      
• May 5, 2009 - Tools for Motif and Pattern Searching
  Slides (pdf)      
• March 24, 2009 - An Introduction to Protein Structure Viewers (esp. Swiss-PdbViewer)
  Slides       Demo topics       Detailed demo
• February 24, 2009 - An Introduction to GraphPad Prism - statistics and graphing software
  Slides
• January 22, 2009 & January 27, 2009 - Relational Databases for Biologists, Filemaker Pro and MySQL
  
• December 8, 2008 - Tips and Tricks with Excel
  Color Slides       Demo.xls
• November 20, 2008 - Cool BaRC Web Tools
  Slides       handout
• October 27, 2008 - Identifying and displaying differentially expressed genes
  Color slides       B&W slides (6/page)
• September 15, 2008 - GeneGo: Bioinformatics Technology for Systems Biology
• August 26, 2008 - Browsing the Genome
  Powerpoint Slides     handouts
• June 19, 2008 - Speed up your research with LSF
  Powerpoint Slides      sample commands for submitting mutiple jobs
• May 15, 2008 - Ingenuity's Pathway Analysis
• April 9, 2008 - CERF: Electronic Lab Notebook
• March 20, 2008 - Clustering and Displaying Microarray Data
  Powerpoint Slides       sample data matrix
• January 29, 2008 - Unix Tips and Tricks - Part 1
  Powerpoint Slides       exercises       solutions
• August 8, 2007 - Orthologous Gene Searching
  Powerpoint Slides
• January 18, 2007 - Matlab Statistics Toolbox
  Powerpoint Slides       sample data files
• October 12, 2006 - Overview of Genome Browsers
  PDF
  Useful site for UCSC Genome Browser slides and rVISTA slides OpenHelix.com
• May 24, 2006 - Tips for aligning and annotating multiple sequences
  PDF
• January 25, 2006 - What's New in BLAST?
  Powerpoint Slides
• December 13, 2005 - Tips and Tricks with Excel
  PDF
• October 27, 2005 - Beginning Perl PDF
• July 26, 2005 - Unix Basics
• January 25, 2005 - EMBOSS
• November 17, 2004 - Depositing Microarray Data into ArrayExpress
• October 27, 2004 - Gene Ontology for Large-scale Functional Analysis
• May 27, 2004 - WADE training
• April 27, 2004 - Swiss-PdbViewer