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'''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%).
'''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)===
==Course Schedule (All Saturdays)==
'''"Lecture slides" links will be available either during or before each lecture, in PDF.'''


*January 29.
===January 29===
Course Overview
*Course Overview
Tutorial: UNIX Account, Tools, & Emacs [Lecture Slides]
*'''Tutorial:''' UNIX Account, Tools, & Emacs [Lecture Slides]
Assignment #1. Unix Exercises
*'''Assignment #1:'''
February 6.
<div class="NavFrame">
Chapter 1. Central Dogma & Wet Lab Tools [Lecture Slides]
  <div class="NavHead">[... This is the title of your collapsible content ...]</div>
Assignment #2. Assignment 1 (above, Part II. 5-8); Problems (pg.31-32): 1.2, 1.3, 1.5, 1.7, 1.9, 1.10, 1.11
  <div class="NavContent">
February 20.
    [... The content you want to hide goes here ...]
  </div>
</div>
**Unix Exercises (Part I on above page)
**Read Chapter 1
 
===February 5===
*Chapter 1. Central Dogma & Wet Lab Tools [Lecture Slides]
*Assignment #2. Part II Assignment 1 (above, Part II. 5-8); Problems (pg.31-32): 1.2, 1.3, 1.5, 1.7, 1.9, 1.10, 1.11
 
===February 12===
'''NO CLASS'''
 
===February 19===
'''Yozen will not be lecturing'''
Chapter 6. Gene and Genome Structures [Lecture Slides]
Chapter 6. Gene and Genome Structures [Lecture Slides]
Tutorial: ORF Prediction using GLIMMER
Tutorial: ORF Prediction using GLIMMER
Assignment #3. Gene Identification
Assignment #3. Gene Identification
February 27.
 
===February 26===
Appendix 1. Basic PERL [Lecture Slides]
Appendix 1. Basic PERL [Lecture Slides]
Assignment #4. Write a PERL script to print the reverse complementary strand of a DNA sequence (print the original, complement, and reverse complement strings; 5 pts).  Questions & Problems (pg.234): A1.2 (5 pts)
Assignment #4. Write a PERL script to print the reverse complementary strand of a DNA sequence (print the original, complement, and reverse complement strings; 5 pts).  Questions & Problems (pg.234): A1.2 (5 pts)
March 6.
 
===March 5===
Object-Oriented PERL & BioPerl [Lecture Slides]
Object-Oriented PERL & BioPerl [Lecture Slides]
Assignment #5. BioPerl
Assignment #5. BioPerl
March 13.
 
===March 12===
Information Theory
Information Theory
Tutorial: Sequence Logo
Tutorial: Sequence Logo
Assignment #6. Information Contents at Intron-Exon junctions
Assignment #6. Information Contents at Intron-Exon junctions
March 20.
 
===March 19===
Chapter 2. Data Search and Alignments
Chapter 2. Data Search and Alignments
Tutorial: Pairwise Alignment using BLAST & NUCMER
Tutorial: Pairwise Alignment using BLAST & NUCMER
Tutorial: Multiple Alignment using CLUSTALW
Tutorial: Multiple Alignment using CLUSTALW
Assignment #7. Questions & Problems (pg.54-55): 2.1, 2.2, 2.3, 2.4
Assignment #7. Questions & Problems (pg.54-55): 2.1, 2.2, 2.3, 2.4
March 27.
 
===March 26===
Chapter 3. Molecular Evolution
Chapter 3. Molecular Evolution
Assignment #8. Questions & Problems (pg.75-76): 3.1, 3.2, 3.3 (use first ten codons), 3.4, 3.5, 3.7
Assignment #8. Questions & Problems (pg.75-76): 3.1, 3.2, 3.3 (use first ten codons), 3.4, 3.5, 3.7
April 10.
 
===April 2===
'''NO CLASSES'''
 
===April 9===
Chapter 4. Phylogenetics I. Distance Methods
Chapter 4. Phylogenetics I. Distance Methods
Tutorial: PROTDIST and NEIGHBOR using T-Rex Server
Tutorial: PROTDIST and NEIGHBOR using T-Rex Server
Assignment #9. Questions & Problems (pg.95-96): 4.1, 4.3, 4.4, 4.7, 4.8
Assignment #9. Questions & Problems (pg.95-96): 4.1, 4.3, 4.4, 4.7, 4.8
April 17.
 
===April 16===
Chapter 5. Phylogenetics II. Character-Based Methods
Chapter 5. Phylogenetics II. Character-Based Methods
Tutorial: DNAML and bootstrap analysis using T-Rex Server
Tutorial: DNAML and bootstrap analysis using T-Rex Server
Assignment #10. Questions & Problems (pg.115-116): 5.1, 5.2, 5.3, 5.4
Assignment #10. Questions & Problems (pg.115-116): 5.1, 5.2, 5.3, 5.4
April 24.
 
===April 23===
Relational Database and SQL
Relational Database and SQL
Tutorial: the Borrelia Genome Database
Tutorial: the Borrelia Genome Database
Assignment #11. SQL-embedded PERL
Assignment #11. SQL-embedded PERL
May 1.
 
===April 30===
Statistics
Statistics
Tutorial: Statistical Visualization using R
Tutorial: Statistical Visualization using R
Assignment #12. R Exercises
Assignment #12. R Exercises
May 8.
 
===May 7===
Chapter 6 (Gene Expression) & Chapter 8 (Proteomics)
Chapter 6 (Gene Expression) & Chapter 8 (Proteomics)
Tutorial: Array Data Visualization and Analysis
Tutorial: Array Data Visualization and Analysis
Assignment #13. Gene Expression Data Analysis using R
Assignment #13. Gene Expression Data Analysis using R
May 15.
 
===May 14===
Chapter 7. Protein Structure Prediction
Chapter 7. Protein Structure Prediction
Assignment #14 (Final Comprehensive Project).
Assignment #14 (Final Comprehensive Project).
May 22. Final Project Due
 
© Weigang Qiu, Hunter College, Last Update Jan 2010
===May 21===
*Final Project Due (TBA)
 
© Weigang Qiu, Hunter College, Last Update Jan 2011

Revision as of 19:07, 25 January 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]
  • Assignment #1:
[... This is the title of your collapsible content ...]
   [... The content you want to hide goes here ...]
    • Unix Exercises (Part I on above page)
    • Read Chapter 1

February 5

  • Chapter 1. Central Dogma & Wet Lab Tools [Lecture Slides]
  • Assignment #2. Part II Assignment 1 (above, Part II. 5-8); Problems (pg.31-32): 1.2, 1.3, 1.5, 1.7, 1.9, 1.10, 1.11

February 12

NO CLASS

February 19

Yozen will not be lecturing Chapter 6. Gene and Genome Structures [Lecture Slides] Tutorial: ORF Prediction using GLIMMER Assignment #3. Gene Identification

February 26

Appendix 1. Basic PERL [Lecture Slides] Assignment #4. Write a PERL script to print the reverse complementary strand of a DNA sequence (print the original, complement, and reverse complement strings; 5 pts). Questions & Problems (pg.234): A1.2 (5 pts)

March 5

Object-Oriented PERL & BioPerl [Lecture Slides] Assignment #5. BioPerl

March 12

Information Theory Tutorial: Sequence Logo Assignment #6. Information Contents at Intron-Exon junctions

March 19

Chapter 2. Data Search and Alignments Tutorial: Pairwise Alignment using BLAST & NUCMER Tutorial: Multiple Alignment using CLUSTALW Assignment #7. Questions & Problems (pg.54-55): 2.1, 2.2, 2.3, 2.4

March 26

Chapter 3. Molecular Evolution Assignment #8. Questions & Problems (pg.75-76): 3.1, 3.2, 3.3 (use first ten codons), 3.4, 3.5, 3.7

April 2

NO CLASSES

April 9

Chapter 4. Phylogenetics I. Distance Methods Tutorial: PROTDIST and NEIGHBOR using T-Rex Server Assignment #9. Questions & Problems (pg.95-96): 4.1, 4.3, 4.4, 4.7, 4.8

April 16

Chapter 5. Phylogenetics II. Character-Based Methods Tutorial: DNAML and bootstrap analysis using T-Rex Server Assignment #10. Questions & Problems (pg.115-116): 5.1, 5.2, 5.3, 5.4

April 23

Relational Database and SQL Tutorial: the Borrelia Genome Database Assignment #11. SQL-embedded PERL

April 30

Statistics Tutorial: Statistical Visualization using R Assignment #12. R Exercises

May 7

Chapter 6 (Gene Expression) & Chapter 8 (Proteomics) Tutorial: Array Data Visualization and Analysis Assignment #13. Gene Expression Data Analysis using R

May 14

Chapter 7. Protein Structure Prediction Assignment #14 (Final Comprehensive Project).

May 21

  • Final Project Due (TBA)

© Weigang Qiu, Hunter College, Last Update Jan 2011

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