8/20/07
BCB 444/544 Introduction to Bioinformatics
Syllabus – Fall 2007
BCB 444/544 Introduction to Bioinformatics. (3-2) Cr. 4.
Broad overview of bioinformatics with a significant problem-solving component, including hands-on practice using
computational tools to solve a variety of biological problems. Topics include: database searching, sequence
alignment, gene prediction, RNA and protein structure prediction, construction of phylogenetic trees, comparative
and functional genomics.
Prereqs:
Math 165 or Stat 401 or equiv. or permission of instructor.
Co-listings:
BCB/Biol/ComS/CprE/Gen 444 / BCB/ComS/CprE/GDCB 544
Course Goals:
to convey the importance of bioinformatics and computational biology for solving problems in
modern biomedical research and to provide hands-on experience using software, critically
evaluating results, and interpreting their biological significance.
Students will understand:
• fundamental biomedical questions and how to apply appropriate computational
tools to address them
• basic principles underlying computational approaches, limitations of available
tools and how to critically interpret results
Intended audience:
Undergraduate & graduate students interested in a broad introduction to the fundamental biomedical problems &
computational approaches in Bioinformatics and Computational Biology research. Note: this course does not fulfill
core course requirements for BCB PhD students, but can be used to fulfill Bioinformatics course requirements for certain other
graduate majors or fellowships (e.g., IGERT, MGET). BCB graduate students are welcome to audit the lectures or register for
the course (lectures & lab) as an elective.
Course Website:
http://www.public.iastate.edu/~f2007.com_s.544/
Instructor:
Drena Dobbs
ddobbs@iastate.edu
Mon/Fri 11-12, or by appointment - in 106 Molecular Biology Building (MBB) 4-4991
Office Hrs:
Co-Instructors:
Office Hrs:
Teaching Assistants:
Office Hrs:
Michael Terribilini
terrible@iastate.edu
Mon 1-2 PM, or by appt
Jae-Hyung Lee
jhlee777@iastate.edu
Fri 1-2 PM, or by appt
Pete Zaback
petez@iastate.edu
Fri 12-1 PM, or by appt
Jeff Sander
jdsander@iastate.edu
Fri 2-3 PM, or by appt
All Office Hrs in 106 Molecular Biology Building (MBB) 4-4991
Class Meetings:
Lectures:
Computer Lab:
Textbook:
Essential Bioinformatics
MWF 10:00 – 10:50 AM
Thurs 1:10 – 3:00 PM
Jin Xiong, Cambridge University Press, 2006
ISBN-13: 9780521600828
in MBB 1420
in MBB 1340
Revised 8/20/07 p 2
Required Reading, Homework & Projects:
BCB 444:
BCB 544:
• Reading: Assigned chapters in the textbook & supplemental materials provided in class or on
the course website should be read prior to lecture (see Schedule).
• Take-home & Lab Assignments: Weekly assignments to assess comprehension of readings,
lecture and laboratory will be required.
• Reading & Take-home & Lab Assignments: same as BCB 444
In addition, BCB 544 students will be required to complete:
• Additional Reading & Discussion Questions - BCB 544 students will be required to read
assigned journal articles & answer discussion questions that emphasize critical evaluation of
experiments & results presented, including fundamental concepts, experimental design, and
interpretation of results.
• Team Semester Research Projects - BCB 544 students will form 3-4 person teams & complete
a 4-week research project. A written summary and a group oral presentation on the term
project will be required.
Exams:
Grading:
There will be 2 Midterm Exams and a Final Exam. The Final will be cumulative with emphasis on the most
recent material and general concepts from earlier material. In addition, there will be Take-home
assignments based on material covered in the lectures and laboratory. Details are provided in Grading
Policy online.
BCB 444:
200 pts
200
100
500 pts
Midterm Exams = 100 points each
Take-home & Laboratory assignments = 200 points
Final Exam
Total for BCB 444
BCB 544:
200 pts
200
100
200
700 pts
Midterm Exams = 100 points each
Take-home & Laboratory assignments
Final Exam
Discussion Questions & Team Research Projects
Total for BCB 544
Intended Learning Outcomes:
Students are expected to gain an understanding of the importance of bioinformatic approaches in modern biological
research. For each of the topics covered, they will understand the fundamental biological questions and be able to
apply appropriate computational tools. They will understand basic principles underlying computational approaches,
realize the limitations of available tools, and be able to critically interpret results.
Students with Disabilities:
If you have a disability and require accommodations, please contact one of the instructors early in the semester so
that your learning needs may be appropriately met. You will need to provide documentation of your disability to the
Disability Resources (DR) office, located on the main floor of the Student Services Building, Room 1076, 515-2946624.
Revised 8/20/07 p 3
BCB 444/544
Tentative Lecture Schedule - Fall 2007
#
Date
Topic
1
2
3
4
5
6
7
8
9
10
11
12
13
Aug 20
Aug 22
Aug 24
Aug 27
Aug 29
Aug 31
Sept 3
Sept 5
Sept 7
Sept 10
Sept 12
Sept 14
Sept 17
Sept 19
14
15
16
17
18
19
20
21
22
23
24
25
Oct 17
W Protein Structure Visualization
Ch 13
26
27
28
Oct 19
Oct 22
Oct 24
F Protein Secondary Structure Prediction
M Protein Tertiary Structure Prediction
W Protein Tertiary Structure Prediction
Ch 14
Ch 15
Ch 15
29
Oct 26
F
30
31
32
33
34
35
36
37
38
39
40
41
Oct 29
M
Oct 31
W
Nov 2
F
Nov 5
M
Nov 7
W
Nov 9
F
Nov 12
M
Nov 14
W
Nov 16
F
Nov 19-23
Nov 26
M
Nov 28
W
Nov 30
F
-
Dec 3-7
-
M
W
F
M
W
F
M
W
F
M
W
F
M
W
What is Bioinformatics?
Biological Databases
Brief Biology Review
Pairwise Sequence Alignment
Pairwise Sequence Alignment
Scoring Matrices and Alignment Statistics
NO CLASS – Veteran’s Day Holiday
Database Searching with BLAST
Multiple Sequence Alignment
Multiple Sequence Alignment
Position Specific Scoring Matrices and Profiles
Position Specific Scoring Matrices and Profiles
Hidden Markov Models
Hidden Markov Models
Sept 21
F
Midterm Exam #1
Sept
Sept
Sept
Oct
Oct
Oct
Oct
Oct
Oct
Oct
M
W
F
M
W
F
M
W
F
M
Protein Families, Domains, and Motifs
Protein Families, Domains, and Motifs
Protein Families, Domains, and Motifs
Gene Structure and Prediction
Gene Structure and Prediction
Gene Structure and Prediction
Phylogenetics
Phylogenetics
Phylogenetics
Introduction to Protein Structure
Reading & URLs
(before lecture)
24
26
28
1
3
5
8
10
12
15
Dec 10
Ch 4
Ch 5
Ch 5
Ch 6
Ch 6
Ch 6
Ch 6
Ch 7
Ch 7
Ch 7
Ch 8,9
Ch 8,9
Ch 8,9
Ch 10,11
Ch 10,11
Ch 10,11
Ch 12
Midterm Exam #2
RNA Structure Prediction
Genomics
Genomics
Genomics
Genomics
Proteomics
Proteomics
Proteomics
Protein Interactions
NO CLASS - Thanksgiving Break
Systems Biology
Systems Biology
Systems Biology
BCB 544 Team Project Presentations
M
Xiong, Ch 1
Ch 2
Genomics & HGP Primer
Ch 3
Ch 3
Ch 3
FINAL EXAM
Ch 16
Ch 17, 18
Ch 17,18
Ch 17,18
Ch 17,18
Ch 19
Ch 19
Ch 19
Ch 19
Revised 8/20/07 p 4
BCB 444/544
Tentative Lab Schedule - Fall 2007
#
Date
(Thurs)
Topics
Reading
& Exercises
1
Aug 23
Literature Resources for Bioinformatics
Note: This lab only will meet in Rm 32 Library
Lab 1
2
Aug 30
NCBI - Sequence Databases & Tools
Pairwise Sequence Alignment & Analysis
Lab 2
3
Sept 6
Database Searching (BLAST)
Lab 3
4
-
Sept 13
Sept 20
Multiple Sequence Alignment
Lab 4
5
Sept 27
Protein Function Prediction
(Sequence-based, Structure-based)
Lab 5
6
Oct 4
Gene Prediction
Lab 6
7
Oct 11
Phylogenetic Analysis
(CLUSTAL, PHYLIP)
Lab 7
8
Oct 18
Structure Databases & Visualization
(PDB, PyMol, JMol, Cn3D, STING)
Lab 8
Review & Independent Projects
-
Oct 25
Review & Independent Projects
9
Nov 1
10
Nov 8
Protein Structure Prediction
Comparative Genomics
Genome Viewers, SNP Analysis
11
Nov 15
Programming in R; Network & Pathway Analysis
-
Nov 22
NO LAB – Thanksgiving Break
12
Nov 29
-
Dec 6
BCB 444 Review & Independent Projects
BCB 544 Team Meetings
BCB 544 Team Project Presentations
-
Dec 13
NO LAB – Finals Week
Lab 9
Lab 10
Lab 11