L519: BIOINFORMATICS: THEORY & APPLICATION
Spring 2003

Lecture: 4pm-6pm M JH248

Lab: 9:30am-10:45am R I109

Instructor: Sun Kim

Office Hours

227 Informatics Building, 901 10th Street
9:30am-11:30am Friday
by appointment

Associate Instructor

Henry Hyun-il Paik

Course Outline

As the size of biological databases grows exponentially and new computational methods becomes available quickly, it is challenging, even for experts in bioinformatics, to combine these databases and tools for research problems in biology. The first half of the course will be devoted to survey computational methods and databases for bioinformatics. The second half will discuss how we can combine these tools and databases to solve real world problems.

Text Books

  • Bioinformatics: sequence, structure, and databank
    Edited by Des Higgins and Willie Taylor, 2000, Oxford University Press ISBN 0 19 963790 3
  • Developing Bioinformatics Computer Skills
    Cynthia Gibas & Per Jambeck April 2001, O'Reilly ISBN 1-56592-664-1

    Prerequisites

    No background in bioinformatics or biology is assumed.
    Some programming experience on Unix or Linux is required as each student will need to develop a small bioinformatics system as a term project.

    Grading

    Grading for Bioinformatics majors and non-majors will be separate. I expect (about 50%) more work from major stduents and more technical term project.
  • Exam (20%)
  • Homeworks and Quiz (30%)
  • Term project (40%)
  • Presentation (10%)

    Computing resources

    The course will use Unix or Linux and the official programming language will be Perl. Students can choose different language such as Java, C, Python, C++, etc. However, all examples and libraries will be provided only for Perl (I cannot provide multiple environments) and it is your responsibility to create a computing environment of your own if you choose a language other than Perl .
  • Linux servers at Inforamtics
  • IBM SP here
    The assignment of groups to aries 0X 
    Microarray 1
BioPerl 2
NCBI 3
Protein Structure 4
Comparative Grammene 5
Sequence Structure 8
  • sunflower.bio.indiana.edu

    Links to Lecture, Lab, Data, and Homework

    Lecture
    lab ( rediected to lecture )
    quiz
    data
    homework
    exams
    group presentation
    manual

    Links to genome web sites

  • human genome
  • flybase
  • Organism-specific database

    Links to bioinformatics web sites

    The International Society for Computational Biology
    NAR journal 2002 database list
    NAR journal 2003 database list
    NCBI
    EBI
    TIGR
    Bioinformatics class list at ISCB

    Links to some useful web sites for computational tools in bioinformatics (very premature; just started to collecting)

    Jason Wang's list for Biological Pattern Discovery Tools
    Steven Salzberg's page
    a page for gene finding
    a page for bioinformatics tools
    ATGC bioinformatics
    NCBI page

    Links to some useful web sites for Biology and Programming

    Science Primer at NCBI
    1992 Primer on Molecular Genetics

    Kimball's Biology Pages
    Gene Expression: Transcription
    Gene Translation: RNA to Protein

    perl debugging
    Please findmore on the web..

    Perl scripts for molecular biology and sequence analysis
    Perl for Biology at UCSF (inactive)
    Lincoln Stein's Pages
    Perl Tutorial site at UIUC
    Perl Totorial site at UGA
    A Beginner's Guide to Perl
    How do I convert between Unix and DOS text files?
    How do I convert between Unix and Mac OS text files?
    What is Perl, and where can I get more information about it?
    BioPerl
    BioJava

    Lecture Schedule 

    Bioinformatics Introduction
	Lecture note

Unix and Perl,
	 Chap 4, 5, 12 (Gibas and Jambeck)

Bioinformatics on the Web and Sequence analysis, 
	Chap 6 and 7 (Gibas and Jambeck)

Multiple Seq. Alignment and Tools for Genomics, 
(sequence assembly and genome comparison tools)
	Chap 8 and 11 (Gibas and Jambeck)

GCG and SRS
	Ch. 10 (Higgins and Taylor)
	Guest lecturers: Don Gilbert and Sue Olson

Database Searching 
	Ch. 8 (Higgins and Taylor)

Family-based Homolgy Detection 
	Ch. 5 (Higgins and Taylor)

Multiple Sequence Aligment
	Ch. 3. (Higgins and Taylor)

Hidden Markov Models
	Ch. 4 (Higgins and Taylor)

Pattern Discovery 
	Ch. 7 (Higgins and Taylor)

Protein Structure Prediction and Visualization 
	Ch.9 and 10 (Gibas and Jambeck)

Predicting protein Secondary Structure
	Ch. 6 (Higgins and Taylor)

Threading Methods for protein Structure Prediction
	Ch. 1 (Higgins and Taylor)

Phylogenetic Analysis

Computational Comparative Genomics

Gene Expression Profiling Data Analysis