Day Zero: “Preparing the Workshop”

• Questionnaire: Please answer as soon as possible
• Login and Open an account
• Material to prepare the workshop
• i-Plant Tutorials

Day One: Thursday December 17, 2015

• 8:30-9:00 Overview of iPlant 
• 9:00-9:45 Introduction to iPlant Discovery Environment (DE) 
• 9:45-10:30 Data Management and Collaborating with the iPlant Data Store 
• 10:30-11:00 Coffee-Break
• 11:00-12:00 Setting up an Analysis Pipeline in the DE 
• 12:00-13:00 RNASeq processing 
• 13:00-14:00 LUNCH (light lunch in the room)
• 14:00-15:00 Examining Differential Expression in an RNA-Seq Dataset 
• 15:00-16:00 Introduction to Atmosphere Cloud Computing 
• 16:00-16:15 Coffee-Break
• 16:15-17:15 iPlant Data Store: Expanded use 

Day Two: Friday December 18, 2015

• 8:30-10:30 Track one: Genome management, visualization, and analyses (Eric Lyons)
  • Genome Management and Visualization (with CoGe)
  • Comparative Genomics (with CoGe)
  • RNASeq/SNP pipelines (with CoGe)
• 8:30-10:30 Track two: Computational virtualization (Nirav Merchant, 3h)
  • Intro to virtualization
  • Full virtual machines: Atmosphere (OpenStack)
  • Container technology: Docker (Deploying tools in DE)
• 10:30-11:00 Coffee-Break
• 11:00-13:00 Visualization of RNA-Seq Data with R in Atmosphere — covered in CoGe workshop
• 13:00-14:00 LUNCH (light lunch in the room)
• 14:00-16:00 Tools for Association Analysis –GWAS Pipeline 
• 16:00-16:15 Coffee-Break 
• 16:15-17:15 Tools and Tool integration –Advanced Phylogenetics
• 17:15-18:30 Other topics for last discussion:
  • Genome Assembly with ALLPATHS 
  • Genome Annotation – MAKER 
  • Getting started with iPlant Foundation API 
• 20:00-23:00  Workshop Dinner (all participants are invited to  http://www.hoteltorremayor.cl/)