Schedule

Monday

8:00 Breakfast

1. Introductory Session
   1. Sponsors
   2. Workshop outcomes
   3. Participant introductions
   4. Group assignments
2. Exercises
   1. OSU HPC
   2. iPlant DE
   3. iPlant Atmosphere
   4. Synchronizing workspaces
   5. Quality analysis of an NGS data set
   6. Conversion and processing NGS reads
3. Break
4. Building workflows
   1. Bash scripting
   2. The iPlant DE

Tuesday

8:00 Breakfast

1. Lecture: Genome Assembly
2. Exercises
   1. Genome Assembly
3. Lunch
4. Lecture: Supercomputing
5. Exercises
   1. Functional analysis of SNPs
6. Student Presentations

Wednesday

8:00 Breakfast

1. Lecture: CoGE
2. Break
3. Exercises
   1. CoGE Tutorials
      1. Brassica (comparison to A. thaliana, Haibao Tang and Eric Lyons)
      2. Maize (comparison to other grasses, James Schnable and Eric Lyons)
4. Lunch
5. Student Presentations
6. Intro: Web service APIs
7. Exercises using iPlant REST API*
   1. Large-scale BLASTX analysis of short reads (instructor-led)
   2. Predicting ORFs from metagenomic assembly
   3. Taxonomic analysis using MetaPhlan

Thursday

8:00 Breakfast

1. iPlant Atmosphere: An Open Science Cloud
2. Introduction to Metagenomics with MEGAN
3. Hands-on with MEGAN in iPlant Atmosphere
4. Student presentations

Friday

8:00 Breakfast

1. Lecture: Transcriptomics
2. Hands-on: Differential expression analysis using the iPlant Discovery Environment
3. Comparative genomics of metagenomics-derived species with CoGE
4. Wrap-up