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Upon completion of the course, please take moment to provide your thoughts on the class. Your feedback is greatly appreciated and will be used to help improve future education initiatives!

Wiki Markup\[[http://tinyurl.com/iihg-biocourse-feedback]\]

Bioinformatics Course "Cheat Sheet"

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Day 1: Wednesday, August 1

Location

Time

Title (click to listen to recording)

Instructor

Slides/Lab Instructions

Kelch Conference Room 1289 CBRB

8:00 am to 9:00 am

“The Magic of MPS” (1 hour)
*Recording contains first 3 Wed. Morning lectures conjoined

David Dimmock

Clinical Decision Making Based on Complete Genome Sequencing_Dimmock.pdf *Recording contains all Wed. Morning sessions conjoined

Kelch Conference Room 1289 CBRB

9:00 am to 9:30 am

Course Overview – Background, Goals for the Course, and Glossary of Terms (30 minutes)
*Recording contains first 3 Wed. Morning lectures conjoined

Eliot Shearer

IIHG-course-overview.pdf

Kelch Conference Room 1289 CBRB

9:30 am to 10:20 am

Next-Gen Sequencers Overview – Pros and Cons of each system; library preparation overview (50 minutes)
*Recording contains first 3 Wed. Morning lectures conjoined

Kevin Knudtson

Knudtson_GalaxyWorkshop_08012012.pdf

 

10:20 am to 10:40 am

Break 

 

 

Kelch Conference Room 1289 CBRB

10:40 am to 11:30 am

Experimental Design – The importance of filtering: inheritance models, segregation analysis, limitations and possibilities, etc. (50 minutes)

Richard Smith

The Importance of Filtering.pdf

Kelch Conference Room 1289 CBRB

11:30 am to 12:00 pm

Tour of the Genomics Core at the University of Iowa College of Medicine  (30 minutes)

Kevin Knudtson

 

EMRB Atrium

12:00 PM to 1:00 PM

Lunch


 

Hardin Information Commons

1:00 pm to 1:30 pm

Introduction to Data Analysis with MPS Data Sets (30 minutes)
*Recording contains into to lab session 1 as well

Ann Black

IIHG_Bioinformatics_Course.pdf

Hardin Information Commons

1:30 pm to 5:00 pm

Lab Session 1: Experimental Design for MPS Experiments – Using Galaxy to manipulate large data sets; creating a BED file for experimental design
*Recording contains into to Data Analysis and Lab 1 Intro

Lab instructors

Lab1_Instructions.pdf

Richard Smith’s home (11 Cherry Lane; 338-6404)

 6:00 PM to 8:00 PM

BBQ Dinner

 

 

Day 2: Thursday, August 2

Location

Time

Title (click to listen to recording)

Instructor

Slides/Lab Instructions

Kelch Conference Room 1289 CBRB

8:00 AM to 9:00 AM

Quality Check / Quality Assessment of MPS Data, Sequence Capture Assessment (60 minutes)
*Recording contains first two Thursday morning lectures

Andre Altmann

Lecture_20120802_Altmann_MPS_QC.pdf

Kelch Conference Room 1289 CBRB

9:00 AM to 9:50 AM

Read Alignment Algorithms (50 minutes)
*Recording contains first two Thursday morning lectures

Tom Bair

IIHG_Bioinformatics_Course_alignment.pdf

 

9:50 AM to 10:10 AM

Break 

 

 

Kelch Conference Room 1289 CBRB

10:10 AM to 11:10 AM

Variant Calling Algorithms – SNVs and indels, in pooled and non-pooled data sets ( 1 hour)
*Recording contains last two Thursday morning lectures

Andre Altmann

Lecture_20120802_Altmann_MPS_SNPcall.pdf

Kelch Conference Room 1289 CBRB

11:10 AM to 12:10 PM

Detecting Copy Number Variants with MPS Data (1 hour)
*Recording contains last two Thursday morning lectures

Alex S. Nord

ASN_CNV_20120731.pdf

EMRB Atrium

12:10 PM to 1:00 PM

Lunch


 

Hardin Information Commons

1:00 PM to 5:00 PM

Lab Session 2: QC/QA of MPS data, Read Alignment, Variant Calling

Lab Instructors

Lab II-handout.pdf



Dinner on your own.

 

 

Day 3: Friday, August 3

Location

Time

Title (click to listen to recording)

Instructor

 Slides/Lab Instructions

Kelch Conference Room 1289 CBRB

8:00 AM to 9:00 AM

Data Annotation and Filtering Overview (1 hour)
*Recording contains first two Friday morning lectures

Alex S. Nord

ASN_Filtering_20120803.pdf

Kelch Conference Room 1289 CBRB

9:00 AM to 9:50 AM

Data management and data storage issues when dealing with NGS data sets (50 minutes)
*Recording contains first two Friday morning lectures

Ben Rogers

BioinformaticsShortCourseDataManagementAndStorage.pptx

 

9:50 AM to 10:10 AM

Break

 

 

Kelch Conference Room 1289 CBRB

10:10 AM to 10:40 AM

Practical considerations for grants and budgets (30 minutes)
*Recording contains last two Friday morning lectures

Ben Darbro

BioinformaticsCourseTalk.pdf

Kelch Conference Room 1289 CBRB

10:40 AM to 11:40 AM

Other Applications for MPS – RNASeq, Transcriptome, Methylome, etc. (1 hour)
*Recording contains first last Friday morning lectures

Tom Bair

IIHG_Bioinformatics_other_tech-1.pdf

EMRB Atrium

12:00 PM to 1:00 PM

Lunch


 

EMRB Atrium 

1:00 PM to 2:00 PM

Breakout Sessions with Course Instructors -- Q & A

 

 

Hardin Information Commons

2:00 PM to 5:00 PM

Lab Session 3: Annotating and Filtering Data Sets, Identifying Causal Variants, Exome Variant Data

Lab Instructors

LabSession3-overview.pdf
annotation-explanation.pdf
IIHG_Bioinformatics_Course-lab session3.pptx.pdf


5:00 PM

Course Adjourns