Hunter
College of the City University of New York
Instructor: Weigang Qiu, Ph.D., Assist. Prof., Department of Biological
Sciences
Lecture & Lab: Room 1000G HN; Wed. 8:10-11 am
Office
Hour: Room 839 HN; Tuesdays 3-5pm
Phone: 212-772-5296;
E-mail:
weigang@genectr.hunter.cuny.edu
Course
website:
http//darwin.hunter.cuny.edu/BIO425.html
Background.
Computation
has permeated into
virtually
every field of biomedical research since the completion of the Human
Genome Project in 2003. Biomedical research is becoming a
high-throughput science and, as a result, information technology
plays an increasingly important role in biomedical discovery.
Contents.
This
course will introduce both bioinformatics theories and practices. Topics
include database
searching, sequence alignment, molecular phylogenetics, structure
predication, and microarray
analysis. The course is held in a UNIX-based
instructional lab specifically configured for bioinformatics
applications. Each session consists of a first-half instruction on
bioinformatics theories and a second-half hands-on exercises.
Student performance is evaluated by six programming
assignments and a
final exam.
Learning Goals. Students are expected to be able to
Pre-requisites. This 3-credit course is designed for upper-level undergraduates and graduate students. Prior experiences in the UNIX Operating System and at least one programming language are required. Hunter pre-requisites are CSCL132 (Practical Unix and Perl Programming) and BIOL 300 (Biochemistry), or permission by the instructor.
Hunter College regards acts of academic dishonesty (e.g., plagiarism, cheating on examinations, obtaining unfair advantage, and falsification of records and official documents) as serious offenses against the values of intellectual honesty. The College is committed to enforcing the CUNY Policy on Academic Integrity and will pursue cases of academic dishonesty according to the Hunter College Academic Integrity Procedures.
| Readings | Lecture | In-Class Exercises | Assignment (Points) | |
| Jan 30 | Course Overview | UNIX
Account Setup; UNIX Tutorial |
Pre-Test
(10); Install SSH (5) |
|
| Feb 6 | Ch
1 (pg.1-27); Ch 6 (pg. 117-137) |
Genome and Gene Structure | Q&P. Emacs Tutorial [PDF] |
|
| Feb 13 | Appendix 1. | Perl Programming | Q&P.A1.1,
A1.2, A1.3 |
Assign #1 (20). Basic Perl: (pg.234) A1.4, A1.5, [3rd Script to write] |
| Feb 20 | Handout: Object-Oriented Perl | BioPerl | ORF identification using Glimmer; BioPerl Tutorial; Bio::SeqIO | Install R (5) |
| Feb 27 | Statistics Handouts | Statistics | Q&P; |
Assign
#2 (20). A BioPerl Exercise |
| March 5 | Ch 2 | Data Search & Alignment | Q&P;
BLAST |
|
| March 12 | Handouts | Information
Theory |
CLUSTALW; R Tutorial: A Sample Session |
Assign #3 (20). An investigation of sequence conservation at intron-exon junctions |
| March 19 | Ch 3 | Molecular Evolution | Q&P |
|
| April 2 | Ch 4 | Phylogenetics I. Distance Methods | Tree-thinking
Challenge; Q&P |
|
| April 9 | Ch 5 | Phylogenetics II. Parsimony Methods | SeqLogo; PHYLIP Q&P; |
Assign #4 (20). Identification of orthologs |
| April 16 | Ch 7 | Protein Structure Prediction | Q&P |
|
| April 30 | Ch
8; SQL Handouts |
Relational Database | MySQL
Tutorial; Perl DBI |
Assig
#5 (20). Perl script with Embedded SQL |
| May 7 | Handouts | Gene Expression | Dictyosteilium chemotaxis mutants | |
| May 14 | Handouts | Gene Expression | E.coli SOS response | Assign #6 (50). Final Project |
| May
23, 2008, 5pm: Final Project Due |
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