CCV Bioinformatics Workshop

Tue, October 18, 2011
9:00am - 12:00pm
BioMed B13

Register at http://training.brown.edu/user/reg.php?eventID=6454

Join the Center for Computation and Visualization for a workshop on using bio-informatics applications on CCV's high-performance computing systems.

9:00-9:40 Mark Howison: "Bioinformatics Applications on Oscar" [PDF]

I will give an overview of the various bioinformatics applications available on Oscar, CCV's compute cluster. Then I will demonstrate how to run these programs through the Oscar batch system, using BLAST, mpiBLAST, bowtie, and RAxML as specific examples.

9:40-10:15 Christoph Schorl: "The role of the Genomics Core Facility in Next Generation Sequencing" [PDF]

10:15-10:30 [Coffee Break]

10:30-11:30 Casey Dunn: "Practical Computing for Biologists" [PDF]

I'll be doing some exercises from the book I wrote with Steve Haddock, Practical Computing for Biologists. To follow along, you will need to have a text editor that supports regular expressions (sometimes called grep). Recommended editors include:

  • TextWrangler for OS X
  • JEdit for Linux and Windows (Requires that a Java runtime environment also be installed)
  • NotePad++ for Windows

11:30-12:00 Lingsheng Dong: "Chip-Seq and RNA-Seq" [PDF]