For 2009, Bioch508 course will be substantially reorganized, with
greatly increased emphasis on Expresssion analysis, pathways, and
comparative genomics.
This course will require use of Unix at the command line level, the
use of a Unix Editor (emacs preferred), and basic Perl scripting.
Tuesday and Thursday 2:00 - 3:30
Biochemistry Library, Jordan Hall, Room 6-6
Perl Tutorial -- Wednesday 10:30 - 11:30
ITC-ACHS Conference Room
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 | 1/15 | Course Organization/Molecular Biology Overview Lecture PDF | Bekiranov |
| T | 1/20 | Sequence Resources / Protein Evolution Lecture PDF | Pearson |
| Tutorial on Protein Evolution and Sequence Comparison | |||
| R | 1/22 | NOTE CHANGE Protein Evolution II / BLAST Searching | Pearson |
| T | 1/27 | Protein Evolution LAB (ITC-ACHS) | Pearson |
| Unix login test | |||
| W | 1/28 | Perl -- Introduction to Unix/Editors/Perl, Perldoc Lecture PDF | Pearson |
| fasta35/lalign35 documentation | |||
| R | 1/29 | Similarity scoring matrices - Profiles/PSSMs Lecture PDF | Pearson |
| T | 2/3 | Multiple sequence alignment Lecture PDF | Pearson |
| W | 3/4 | Perl -- Perl Variables: Scalars, Arrays, Hashes, Control Structures Lecture PDF | Pearson |
| R | 2/5 | Advanced comparison - Hidden Markov Models Lecture PDF | Pearson |
| T | 2/10 | Phylogenetics I | Pearson |
| W | 2/11 | Perl -- Perl I/O, Regular Expressions, string manipulation Biochem Library Lecture PDF | Pearson |
| R | 2/12 | Phylogenetics II | Pearson |
| F | 2/13 | Exam I (Due Friday, Feb 13!!) 2004 exam | |
| T | 2/17 | PHYLIP Lecture PDF | Pearson |
| Phylip Exercises | |||
| W | 2/18 | Perl -- Modules/Object Oriented Progamming: LWP Get/LWP UserAgent/Bioperl Lecture PDF | Pearson |
| R | 2/19 | Evaluating Trees Lecture PDF | Pearson |
| T | 2/24 | Phylogeny Projects I | |
| W | 2/25 | Perl -- Bioperl Lecture PDF | Pearson |
| R | 2/26 | Phylogeny Projects II | |
| T | 3/3 | Spring Break | |
| R | 3/5 | Spring Break | |
| T | 3/10 | High Throughput Technologies Lecture PDF | Bekiranov |
| R | 3/12 | Statistics Overview Lecture PDF | Bekiranov |
| T | 3/17 | Introduction to R Lecture PDF | Bekiranov |
| R introduction from 'R' home page | |||
| R | 3/19 | R Lab (ACHS) Lecture PDF | Bekiranov |
| T | 3/24 | Microarray I Lecture PDF | Bekiranov |
| R | 3/26 | Bioconductor Lab I (ACHS) Lecture PDF | Bekiranov |
| T | 3/31 | Microarray II Lecture PDF | Bekiranov |
| R | 4/2 | Bioconductor Lab II (ACHS) Lecture PDF | Bekiranov |
| T | 4/7 | Exam II (due April 16) Lecture PDF | |
| R | 4/9 | Genomic Tiling Arrays I Lecture PDF | Bekiranov |
| T | 4/14 | Genomic Tiling Arrays II | Bekiranov |
| R | 4/16 | Genomic Tiling Array Lab (ACHS) Lecture PDF | Bekiranov |
| T | 4/21 | High Throughput Sequencing I Lecture PDF | Bekiranov |
| R | 4/23 | High Throughput Sequencing II | Bekiranov |
| T | 4/28 | Projects I Lecture PDF | Bekiranov |
| R | 4/30 | Projects II | Bekiranov |
| T | 5/5 | Possible add'nl day | |
Links to other Computational Biology Courses
Last modified: Thursday, 16-Apr-2009 10:26:41 EDT