High-Throughput Biology - From Sequence to Networks 2019

High-Throughput Data Analysis

  Day 1   Day 2
  Monday, March 11   Tuesday, March 12
7:30 *Breakfast* 7:30 *Breakfast*
9:00 Welcome (Michelle) 9:00 Module 4: Small-Variant Calling and Annotation (Mathieu)
9:30 Module 1: Introduction to High-Throughput Sequencing (Sara Goodwin)    
10:30 *Coffee Break* 10:00 *Coffee Break*
11:00 Module 2: Data Visualization (Heather Gibling) 10:30 Module 4 Lab
11:45 Module 2 Lab 11:30 Module 5: Structural Variant Calling (Mathieu Bourgey)
12:30 *Lunch* 12:30 *Lunch*
1:30 Module 3: Genome Alignment (Mathieu) 1:30 Module 5 Lab
2:30 Connecting to the Cloud (Zhibin) 2:15 Module 6: De Novo Assembly (Jared Simpson)
3:00 *Coffee Break* 3:00 *Coffee Break*
3:30 Module 3 Lab 3:30 Module 6 Lab
5:30 *Dinner* 5:30 *Dinner*
7:00 *Welcome Reception* 7:00 Optional: Integrated Assignment

RNA-Seq Data Analysis

  Day 3   Day 4
  Wednesday, March 13   Thursday, March 14
7:30 *Breakfast* 7:30 *Breakfast*
9:00 Module 7: Introduction to RNA Sequencing (Malachi Griffith) 9:00 Module 9: Expression and Differential Expression (Christopher Miller)
10:00 *Coffee Break* 10:00 *Coffee Break*
10:30 Module 7 Lab 10:30 Module 9 Lab
12:30 *Lunch* 12:00 *Lunch*
1:30 Module 8: RNA-Seq Alignment and Visualization (Christopher Miller) 1:00 Module 10: Reference Free Alignment (Malachi Griffith)
    2:00 Module 11: Isoform Discovery and Alternative Expression (Kelsy Cotto)
3:00 *Coffee Break* 3:30 *Coffee Break*
3:30 Module 8 Lab 4:00 Module 11 Lab
5:30 *Dinner* 5:30 *Dinner*
7:00 Optional: Integrated Assignment 7:00 Optional: Integrated Assignment

Pathway and Network Analysis

  Day 5   Day 6   Day 7
  Friday, March 15   Saturday, March 16   Sunday, March 17
7:30 *Breakfast* 7:30 *Breakfast* 7:30 *Breakfast*
9:00 Module 12: Introduction to Pathway and Network Analysis (Jüri Reimand) 9:00 Module 15: More depth on network and pathway + Cytoscape Enrichment map (Veronique Voisin) 9:00 Module 17: Regulatory Network Analysis (Michael Hoffman)
10:00 *Coffee Break* 10:00 *Coffee Break* 10:30 *Coffee Break*
10:30 Module 13: Finding Over-Represented Pathways 10:30 Module 15 Lab: Cytoscape/Enrichment Map 11:00 Module 17 Lab
11:30 Module 13 Lab (Jüri Reimand)        
12:30 *Lunch* 12:30 *Lunch* 12:30 Survey and Closing Remarks
1:30 Module 13 Lab - Continued 1:30 Module 16: Gene Function Prediction (Quaid Morris) 1:00 Optional: Integrated Assignment to 3:00pm (Veronique Voisin)
2:00 Module 14: Network Visualization and Analysis with Cytoscape and Reactome (Robin Haw)        
3:15 *Coffee Break* 3:00 *Coffee Break*    
3:45 Module 14 Lab: De novo subnetwork clustering analysis- Reactome 3:30 Module 16 Lab: geneMANIA    
5:30 *Pizza Dinner (Hershey)* 5:30 *Banquet Dinner*    
7:00 Optional: Integrated Assignment 7:00 *Banquet*    
9:00 Dance Party with DJ (Bush Hall)