Biol425 2011: Difference between revisions

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*Course Overview
*Course Overview
*'''Tutorial:''' UNIX Account, Tools, & Emacs [Lecture Slides]
*'''Tutorial:''' UNIX Account, Tools, & Emacs [Lecture Slides]
*'''Assignment #1:'''
* '''Homework:'''
**Unix Exercises (Part I on above page)
**Read Chapter 1
 
{| class="collapsible collapsed wikitable"
{| class="collapsible collapsed wikitable"
|-
|- style="background-color:lightsteelblue;"
! This is the header cell, which is always shown
! Assignment #1
|-
|- style="background-color:powderblue;"
| This cell is not shown by default.
| '''Linux Proficiency'''<br />
#Display the absolute path of your home directory
#List files in your home directory in long format & ordered by their time stamps
#List files in the "/data/yoda/b/bio425_2011/" directory from your home directory
#Copy of the file "/data/yoda/b/bio425_2011/data/GBB.seq" into your home directory
#Count the number of lines in the file "GBB.seq"
#Show the first five lines of the file "GBB.seq" & save it to a file with arbitrary name
#Show your last ten commands using "history"
|-style="background-color:powderblue;"
| '''Read''' Chapter 1
|}
|}


===February 5===
===February 5===
*Chapter 1. Central Dogma & Wet Lab Tools [Lecture Slides]
*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
*Homework:
{| class="collapsible collapsed wikitable"
|- style="background-color:lightsteelblue;"
! Assignment #2
|- style="background-color:powderblue;"
| '''Linux and Molecular Sequences'''<br />
#Stay in your home directory (without changing into the "bio425" directory), count the number of ORFs in the sequence file "GBB.seq" using a single "grep" command and one option
#Achieve the same purpose as above, by using "grep" and "wc"
#Again, stay in your home directory, filter the DNA sequences in the file "/data/yoda/b/bio425/data/TenSeq.nuc" into upper cases
#Filter out the "a"s in the above sequence
#Using "sed", filter out the string "plasmid" in the sequence names from the file "/data/yoda/b/bio425/data/GBB.1con"
#Using "cut", extract the third field delimited by "_"
#Compose regular expressions matching the Thr, Ser, and Glu codons, respectively
#Write a BASH loop to count the number of sequences in every *.pep file in the directory "/data/yoda/b/bio425/data/"
|-style="background-color:powderblue;"
| '''Problems'''<br />
(pg.31-32): 1.2, 1.3, 1.5, 1.7, 1.9, 1.10, 1.11
|}


===February 12===
===February 12===
'''NO CLASS'''
'''NO CLASS'''
(Read Chapter 6 for next class)


===February 19===
===February 19===
'''Yozen will not be lecturing'''
'''Yozen will not be lecturing'''
Chapter 6. Gene and Genome Structures [Lecture Slides]
 
Tutorial: ORF Prediction using GLIMMER
*Chapter 6. Gene and Genome Structures [Lecture Slides]
Assignment #3. Gene Identification
*'''Tutorial:''' ORF Prediction using GLIMMER
*Assignment #3.
<!--Gene Identification, read Appendix 1--> '''(To be posted)'''


===February 26===
===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. '''(To be posted)'''
<!--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===
===March 5===
Object-Oriented PERL & BioPerl [Lecture Slides]
*Object-Oriented PERL & BioPerl [Lecture Slides]
Assignment #5. BioPerl
*Assignment #5. '''(To be posted)'''
<!--BioPerl-->


===March 12===
===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 19===
===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 26===
===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 2===
===April 2===
Line 107: Line 136:


===April 9===
===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 16===
===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 23===
===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


===April 30===
===April 30===
Statistics
*Statistics
Tutorial: Statistical Visualization using R
*Tutorial: Statistical Visualization using R
Assignment #12. R Exercises
*Assignment #12. R Exercises


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


===May 21===
===May 21===

Revision as of 20:10, 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]
  • Homework:

February 5

  • Chapter 1. Central Dogma & Wet Lab Tools [Lecture Slides]
  • Homework:

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. 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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