For 2011, the Bioc 5080 course will be include a section on NextGen sequence data analysis, including mapping, ChIP-seq, and RNA-seq, as well as sections on metagenomics, expression analysis and pathways.
This course will teach use of Unix at the command line level, the
use of a Unix Editor, and basic Perl scripting, as well as the 'R' Statistics language.
Tuesday/Thursday 9:00 - 10:30
Jordan Hall, Room 1-17
Friday/ 12:00 Noon - 1:00 PM
Biochem Library, Jordan 6th floor
Course directors:
William R. Pearson, Jordan Hall Rm 6-057, wrp@virginia.edu and
Stefan Bekiranov, Jordan 6-054, sb3de@virginia.edu
Texts:
BIOINFORMATICS: Sequence and Genome Analysis 2nd ed., D. W. Mount (2004) Cold Spring Harbor Press ISBN 0-879-69712-1
BIOINFORMATICS FOR DUMMIES, J.-M. Claverie, C. Notredame (2003) Wiley ISBN 0-764-51696-5
BIOINFORMATICS 2nd ed., A. D. Baxevanis and B. F. Ouellette (2001) Wiley-Interscience ISBN 0-471-38391-0
| R | 1/20 | Course Overview/Data resources | Mackey |
| T | 1/25 | Intro to Unix -- the Unix shell, directories, file transfer | Mackey |
| R | 1/27 | Unix -- files and editors, shell scripting, text commands | Mackey |
| F | 1/28 | Unix Lab | |
| T | 2/1 | Unix -- Perl 1 | Mackey |
| R | 2/3 | Unix -- Perl 2 | Mackey |
| F | 2/4 | Perl lab | |
| T | 2/8 | Unix -- Perl regular expressions, functions | Mackey |
| R | 2/10 | Unix -- Perl Modules, and debugging | Pearson |
| F | 2/11 | Lab -- Perl programming | |
| T | 2/15 | Unix -- BED tools | Quinlan |
| R | 2/17 | Sequence alignment - Comparison and Statistics | Pearson |
| F | 2/18 | BLAST Lab | |
| T | 2/22 | Sequence alignment - Alignment algorithms/Bioperl | Pearson |
| R | 2/24 | Sequence alignment - Linking to protein resources | Pearson |
| F | 2/25 | BioPerl Lab | |
| T | 3/1 | Homework review, Q&A | |
| R | 3/3 | Student projects | |
| F | 3/4 | Student projects | |
| T | 3/8 | Spring Break | |
| R | 3/10 | Spring Break | |
| T | 3/15 | Stats/Null 1a | Bekiranov |
| R | 3/17 | Stats/Null 2a | Bekiranov |
| F | 3/18 | Review | |
| T | 3/22 | R prog 1a | Bekiranov |
| R | 3/24 | R prog 2a | Bekiranov |
| F | 3/25 | 'R' lab | |
| T | 3/29 | Microarray 1a | Bekiranov |
| R | 3/31 | Microarray 1b | Bekiranov |
| F | 4/1 | Bioconductor | |
| T | 4/5 | NextGen Sequencing technologies | Mackey |
| R | 4/7 | NGS Mapping | Hall |
| F | 4/8 | Lab - BWA, Novoalign, IGV | |
| T | 4/12 | NGS WG assembly | Mackey |
| R | 4/14 | RNA Seq 1a | Mackey |
| F | 4/15 | Lab - TopHat, CuffLinks, IGV | |
| T | 4/19 | Chip Seq 1a | Bekiranov |
| R | 4/21 | Chip Seq 1a | Bekiranov |
| F | 4/22 | Lab - MACS, IGV | |
| T | 4/26 | Genetic Variation 1a | Hall |
| R | 4/28 | Genetic Variation 1b | Hall |
| F | 4/29 | Lab - GATK, SAM Tools | |
| T | 5/3 | Student projects | |
| R | 5/5 | Student projects | |
Links to other Computational Biology Courses
Last modified: Friday, 28-Jan-2011 21:28:02 EST