Selected Topics in Zoology (Section 33948):
Cyberinfrastructure-enabled Computational Genome Science Laboratory
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
HTML version of this schedule
| DAY | DATE | LECTURE | TOPIC | LECTURER | 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 |