Biol425 2011
Computational Molecular Biology
BIOL 425/790.49, Spring 2011
Hunter College of the City University of New York
Course information
Instructors: Che Martin and Yozen Hernandez
Class Hours: Room 1000G HN; Saturday 11am-2pm
Office Hours: Room 839 HN; Thursdays 12-2pm or by appointment
Contact information:
- Che: cmartin@gc.cuny.edu, 917-684-0864
- Yozen: yzhernand@gmail.com, 347-829-6936
Course Description
Background
Biomedical research is becoming a high-throughput science. As a result, information technology plays an increasingly important role in biomedical discovery. Bioinformatics is a new interdisciplinary field formed between molecular biology and computer science.
Contents
This course will introduce both bioinformatics theories and practices. Topics include: database searching, sequence alignment, molecular phylogenetics, structure prediction, 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 session of hands-on exercises.
Learning Goals
Students are expected to be able to:
- Approach biological questions evolutionarily ("Tree-thinking")
- Evaluate and interpret computational results statistically ("Statistical-thinking")
- Formulate informatics questions quantitatively and precisely ("Abstraction")
- Design efficient procedures to solve problems ("Algorithm-thinking")
- Manipulate high-volume textual data using UNIX tools, Perl/BioPerl, R, and Relational Database ("Data Visualization")
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 CSCI132 (Practical Unix and Perl Programming) and BIOL300 (Biochemistry) or BIOL302 (Molecular Genetics), or permission by the instructor.
Textbook
Krane & Raymer (2003). Fundamental Concepts of Bioinformatics. Pearson Education, Inc. (ISBN 0-8053-4633-3)
This book should be available in the Hunter Bookstore, as well as through several popular retailers and resellers online.
Grading & Academic Honesty
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.
Student performance will be evaluated by Weekly Assignments and Projects. While these are take-home projects and students are allowed to work in groups and answers to some of the questions are provided in the back of the textbook, students are expected to compose the final short answers, computer commands, and codes independently. There are virtually unlimited number of ways to solve a computational problem, as are ways and personal styles to implement an algorithm. Writings and blocks of codes that are virtually exact copies between individual students will be investigated as possible cases of plagiarism (e.g., copies from the Internet, text book, or each other). In such a case, the instructor will hold closed-door exams for involved individuals. Zero credits will be given to ALL involved individuals if the instructor considers there is enough evidence for plagiarism. To avoid being investigated for plagiarism, Do Not Copy from Others & Do Not Let Others Copy Your Work.
Submit assignments in Printed Hard Copies. Email attachments will NOT be accepted. Each assignment will be graded based on timeliness (10%), completeness (30%), whether executable or having major errors (20%), correctness of the final output (20%), algorithm efficiency (10%), and cleanness and readability in programming styles (10%).
Course Schedule (All Saturdays)
"Lecture slides" links will be available either during or before each lecture, in PDF.
January 29
- Course Overview
- Tutorial: UNIX Account, Tools, & Emacs [Lecture Slides]
- Homework:
| Assignment #1 |
|---|
Linux Proficiency
|
| Read Chapter 1 |
February 5
- Chapter 1. Central Dogma & Wet Lab Tools [Lecture Slides]
- Homework:
| Assignment #2 |
|---|
Linux and Molecular Sequences
|
| Problems (pg.31-32): 1.2, 1.3, 1.5, 1.7, 1.9, 1.10, 1.11 |
February 12
NO CLASS
(Read Chapter 6 for next class)
February 19
Yozen will not be lecturing
- Chapter 6. Gene and Genome Structures [Lecture Slides]
- Tutorial: ORF Prediction using GLIMMER
- Assignment #3. (To be posted)
February 26
- Appendix 1. Basic PERL [Lecture Slides]
- Assignment #4. (To be posted)
March 5
- Object-Oriented PERL & BioPerl [Lecture Slides]
- Assignment #5. (To be posted)
March 12
- Information Theory
- Tutorial: Sequence Logo
- Assignment #6. (To be posted)
March 19
- Chapter 2. Data Search and Alignments
- Tutorial: Pairwise Alignment using BLAST & NUCMER
- Tutorial: Multiple Alignment using CLUSTALW
- Assignment #7. (To be posted)
March 26
- Chapter 3. Molecular Evolution
- Assignment #8. (To be posted)
April 2
NO CLASSES
April 9
- Chapter 4. Phylogenetics I. Distance Methods
- Tutorial: PROTDIST and NEIGHBOR using T-Rex Server
- Assignment #9. (To be posted)
April 16
- Chapter 5. Phylogenetics II. Character-Based Methods
- Tutorial: DNAML and bootstrap analysis using T-Rex Server
- Assignment #10. (To be posted)
April 23
- Relational Database and SQL
- Tutorial: the Borrelia Genome Database
- Assignment #11. (To be posted)
April 30
- Statistics
- Tutorial: Statistical Visualization using R
- Assignment #12. (To be posted)
May 7
- Chapter 6 (Gene Expression) & Chapter 8 (Proteomics)
- Tutorial: Array Data Visualization and Analysis
- Assignment #13. (To be posted)
May 14
- Chapter 7. Protein Structure Prediction
- Assignment #14 (Final Comprehensive Project). (To be posted)
May 21
- Final Project Due (TBA)
© Weigang Qiu, Hunter College, Last Update Jan 2011