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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

    BIOL L531 CGSL

    Lecture times and locations

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

    Tentative schedule (click the icon for a PrinterFriendly.gif version)

    DAYDATELECTURETOPICLECTURER
    Mon Jan 13 1.1 Orientation
    Introduction to cyberinfrastructure resources

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

    iPlant Discovery Environment Login

    iPlant Atmosphere Login

    iPlant Data Store     		Instructors
    Mon Jan 20 MLK Jr. Day no class
    Wed Jan 22 2.1 Introduction to NGS data
    Quality control issues     		Instructors
    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     		Instructors
    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     		Instructors
    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     		Students
    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