Applications in Bioinformatics
ENG BF 527 / Fall 2009
Course Description:
The field of Bioinformatics is concerned with the management and analysis of large biological datasets (such as the human genome) for the purpose of improving our understanding of complex living systems. This course introduces graduate students and upper-level undergraduate students to the core problems in bioinformatics, along with the databases and tools that have been developed to study them. Computer labs emphasize the acquisition of practical bioinformatics skills for use in students’ research. Familiarity with basic molecular biology is a prerequisite; no prior programming knowledge is assumed. Specific topics will include the analysis of biological sequences, structures, and networks.
Course Times and Location:
Lecture: Tue & Thu 3:00 – 4:00 PM in LSEB 105
Lab: Tue & Thu 4:00 – 5:00 PM in LSEB B03
Labs and Programming:
Labs will involve applying concepts learned during the lecture to practical bioinformatics problems. Students will learn to use the major bioinformatics databases as well as on- and off-line tools. Python programming will be taught during lab, leading to the creation of small but useful bioinformatics-oriented programs. Homework assignments will be focused on practicing skills introduced during labs.
Textbook:
There is no required text book. All reading materials will be provided in class or through open access websites.
Instructor Information:
Eric Franzosa () & Jignesh Parikh ()
Office location: LSEB 101
Office hours: Tue & Thu 1:30 – 2:30 PM
*NOTE* When sending general email, please put “BF527” in the subject line
Grading Policy:
Homework: 60% (written and computational)
Midterm: 15% (1 hour, Thursday, Oct 15th)
Participation: 10% (lecture and lab)
Final Exam: 15% (1 hour, Thursday, Dec 10th)
Incompletes will not be given
Collaboration / Academic Honesty:
Students may discuss homework with each other, but must not share answers or code. All course participants must adhere to the CAS Academic Conduct Code. All instances of academic dishonesty will be reported to the academic conduct committee.
Homework Policy:
There will be a total of 6 homework assignments, distributed roughly once every two weeks (four lectures). Assignments 1-5 are due one week after they are assigned unless otherwise noted. Each assignment must be submitted electronically before 3 PM on the due date. Late assignments will be docked ten percentage points per day late (1% of the final grade). The last homework (HW 6) will be a mini-project and *must* be turned in the day of the final.
Course Schedule: # / Date / Lecture1 / Thursday, September 03 / Class Introduction
2 / Tuesday, September 08 / Biological Sequences and Sequencing Technology
3 / Thursday, September 10 / Sequence Similarity and Dot Plots
4 / Tuesday, September 15 / Global Alignment and Dynamic Programming
5 / Thursday, September 17 / Local and Semiglobal Alignment, Scoring Schemes
6 / Tuesday, September 22 / Statistics and Probability Primer
7 / Thursday, September 24 / Practical BLAST
8 / Tuesday, September 29 / BLAST Theory
9 / Thursday, October 01 / Multiple Sequence Alignment
10 / Tuesday, October 06 / Phylogenetic Trees
11 / Thursday, October 08 / Machine Learning Overview/ Midterm Review
12 / Tuesday, October 13 / NO CLASS: Monday Schedule
13 / Thursday, October 15 / MIDTERM EXAM
14 / Tuesday, October 20 / Gene Ontology
15 / Thursday, October 22 / Gene Finding
16 / Tuesday, October 27 / TBA / Protein Domains
17 / Thursday, October 29 / Transcription Factor Binding Analysis
18 / Tuesday, November 03 / Microarray Technology and Data
19 / Thursday, November 05 / Protein Expression Technology and Data
20 / Tuesday, November 10 / RNA Folding
21 / Thursday, November 12 / Protein Structure Technology and Data
22 / Tuesday, November 17 / Biological Network Technology and Data
23 / Thursday, November 19 / Network Statistics and Motifs
24 / Tuesday, November 24 / Directed Networks I, Signaling
25 / Thursday, November 26 / NO CLASS: Fall Break
26 / Tuesday, December 01 / Directed Networks II, Metabolic
27 / Thursday, December 03 / TBA / Mini Project (Homework 6)
28 / Tuesday, December 08 / TBA / Final Review
29 / Thursday, December 10 / FINAL EXAM