Overview: This workshop provides an introductory overview of important bioinformatics data analysis concepts related to genome sequencing, database techniques, structural biology, comparative genomics, next generation sequencing, such as RNA-Seq profiling, and small molecule/drug discovery.

Day 1 - Mon, July 23, 2012    [ Slides ]   [ Exercises ]

08:00 - 9:00 AM - Introduction to Bioinformatics and Important Databases
09:00-10:00 AM - Pairwise Sequence Alignments

10:00-10:30 AM - Break

10:30-11:00 AM - Multiple Sequence Alignments

11:00-12:30 PM - Sequence Similarity Searching

Day 2 - Tue, July 24, 2012    [ Slides1 ]   [ Slides2 ]   [ Slides3 ]   [ Exercises ]

02:00-03:00 PM - Phylogenetic Trees 

03:00-04:00 PM - Functional Gene Annotation Systems (Pfam, GO, Pathways)

04:00-04:30 PM - Break

04:30-05:30 PM - Introduction to R and Bioconductor

05:30-06:00 PM - Handling Genome Data in R

02:00-03:00 PM - Analysis of RNA-Seq Experiments

03:00-04:00 PM - Viewing Results in IGV Genome Browser

04:00-04:30 PM - Break 

04:30-05:00 PM - Introduction to Drug/Small Molecule Discovery

05:00-06:00 PM - Searching and Analyzing Small Molecules

- Internet access @ >5Mps

- Recent internet browser version (e.g. Firefox, Chrome or Safari)

- Cn3D: http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

- IGV (Integrative Genomics Viewer): http://www.broadinstitute.org/igv/

- R: http://www.r-project.org/

- RStudio: http://rstudio.org/

- To install the R libraries required for the course, run from within R the following two commands:

source("http://bioconductor.org/biocLite.R")

biocLite(c("Biostrings", "seqLogo", "GenomicRanges", "rtracklayer", "Rsamtools", "DESeq", "edgeR", "GOstats", "GO.db", "ath1121501.db", "ChemmineR"))