Workshop Schedule

Date

Time

Session

Topic

Instructor

Location

8:15

8:45

Registration

 

LaRita, Jiang, Kevin, Juan

Avery

115

8:45

9:00

Welcome

Program overview

Juan

 

9:00

9:15

Welcome

Introduction to Bioinformatics Program in CSE

Stephen

 

9:15

9:30

Welcome

HCC facility and GALAXY

David

9:30

10:05

Talk 1

What can we do with RNA sequencing?

Steve

10:05

10:40

Talk 2

Omics Driven Cancer Research

Juan

 

10:40

11:00

Break

11:00

11:35

Talk 3

Identification of AGO3 associated miRNAs and computational prediction of their targets in Chlamydomonas reinhardtii

Adam

 

11:35

11:50

Discussion

Participant's research interests

All

 

28-Jul

12:00

13:00

Lunch

13:00

13:45

Lecture

Introduction to Next-generation Sequencing and Microarray I

Steve

 

13:45

14:15

Lecture

Introduction to Next-generation Sequencing and Microarray II

Steve

 

14:15

14:45

Lecture

Experimental Design

Juan

 

14:45

15:00

Break

15:00

15:45

Lab

Unix Account set-up

Juan, Jiang, Kevin

Avery 21

15:45

17:00

Lecture

Introduction to R and Unix

Juan, Jiang, Kevin

 

17:00

17:30

Help Session

Additional assistance

Jiang

 

8:30

9:00

Lecture

Introduction to NGS workflow and platform

Juan

Avery 21

9:00

9:30

Lecture

Genome sequencing QC, mapping, and assembly

Steve

 

9:30

10:45

Lab

Galaxy and command-line based tools

Jingchao, Juan

 

10:45

11:00

Break

11:00

11:30

Lecture

SNP calling and mutation identification

Juan

 

11:30

12:00

Lab

Galaxy

Jingchao

 

29-Jul

12:00

13:00

Lunch

13:00

13:45

Lecture

Structural variation detection (CNVs, translocation)

Chi

 

13:45

14:30

Lecture

Functional annotation ( resequencing vs new-species sequencing)

Juan

 

14:30

14:45

Break

14:45

16:45

Lab

Lab project: assembly of the given chromosome and annotation

 

 

16:45

17:00

Lab

Summary

Juan, Jingchao, Jiang, Kevin

 

17:00

17:30

Help Session

Additional assistance

Jiang

 

8:30

9:00

Lecture

Micorarray data preprocessing and normalization

Chi

Avery 21

9:00

9:30

Lecture

RNA-seq data preprocessing and expression summarization

Chi

 

9:30

10:30

Lab

Tools (e.g. Tophat and Cufflink)  and Galaxy

Jingchao, Juan

 

10:30

10:45

Break

10:45

11:15

Lecture

Differential expression analysis

Chi

 

11:15

12:00

Lab

Data analysis using Mev or command-line based scripts

Juan, Jiang, Kevin

 

30-Jul

12:00

13:00

Lunch

13:00

13:30

Lecture

Clustering analysis

Juan

 

13:30

14:30

Lab

Cluster, Java Tree View and Expander

Juan

 

14:30

14:45

Break

14:45

15:15

Lecture

Functional and pathway enrichment analysis

Juan

 

15:15

16:15

Lab

Cytoscape ( and DAVID/KOBAS)

Juan, Jiang, Kevin

 

16:15

17:00

Discussion

Wrap-up

Juan, Jiang, Kevin