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BIOL L531 (Z620) Spring 2014

Selected Topics in Zoology (Section 33948):
Cyberinfrastructure-enabled Computational Genome Science Laboratory

BIOL L531 (Z620) Spring 2014

Course description


Lecture times and locations

Mon, Wed 9:30a - 10:45a (Credits: 3.0); Lindley Hall (LH) 030

Tentative schedule (class notes can be viewed with Adobe Acrobat Reader)

btn_printerFriendly.gif version of this schedule

Mon Jan 13 1.1 Orientation
Introduction to cyberinfrastructure resources

Some useful tutorials:
Linux Command Shell
Volker Brendel
Wed Jan 15 1.2 Working with cyberinfrastrucure resources:

iPlant Discovery Environment Login

iPlant Atmosphere Login

iPlant Data Store
Mon Jan 20 MLK Jr. Day no class
Wed Jan 22 2.1 Introduction to NGS data
Quality control issues
Mon Jan 27 3.1 Prokaryotic genome assembly Instructors
Wed Jan 29 3.2 Evaluating and comparing assemblies Instructors
Mon Feb 3 3.3 Project work Students
Wed Feb 5 4.1 Eukaryotic genome assemby Instructors
Mon Feb 10 4.2 Evaluating and comparing assemblies Instructors
Wed Feb 12 4.3 Project work Students
Mon Feb 17 5.1 De novo transcriptome assembly Instructors
Wed Feb 19 5.2 Evaluating transcriptome assemblies Instructors
Mon Feb 24 5.3 Project work on transcriptome assembly Students
Wed Feb 26 6.1 Read mapping Instructors
Mon Mar 3 6.2 Differential gene expression analysis Instructors
Wed Mar 5 6.3 Project work on differential gene expression Students
Mon Mar 10 7.1 SNP calling Instructors
Wed Mar 12 8.1 Preliminary project presentations Students
Mon Mar 17 SPRING BREAK - no class n/a
Wed Mar 19 SPRING BREAK - no class n/a
Mon Mar 24 9.1 Re-sequencing
Mapping of short reads to reference genomes
Wed Mar 26 9.2 Project work on read mapping Instructors
Mon Mar 31 10.1 Introduction to genome annotation Instructors
Wed April 2 10.2 Genome annotation Instructors
Mon April 7 10.3 Genome annotation Instructors
Wed April 9 10.4 Project work on genome annotation Instructors
Mon April 14 11.1 Introduction to genome browsers
Editing of annotation tracks
Wed April 16 11.2 Project work on genome visualization Instructors
Mon April 21 12.1 Final project preparation Students
Wed April 23 12.2
Final project preparation
Mon April 28 13.1 Project presentations ** Students
Wed April 30 13.2 Project presentations ** Students
Wed May 7 11:59pm Final Projects due Students