Download Bio-CS 251 syllabus `06 - Gettysburg College Computer Science

BIOLOGY/COMPUTER SCIENCE 251 – Spring 2006
INTRODUCTION to BIOINFORMATICS
COURSE SCHEDULE
Steve James
255 Science Center
337-6170
[email protected]
Date
Carl Leinbach
206 Glatfelter Hall
337-6641
[email protected]
Lecture topic
Science Ctr 274
MWF, 10 – 10:50
W, 1 - 3 lab
Glatfelter 203
Laboratory
Jan
20
What is Bioinformatics? Historical overview
No lab
Jan
23
25
27
Building blocks: DNA and RNA structure and chemistry
Building blocks: Protein structure and chemistry
Central Dogma – information flow in living systems
Film – NOVA:
“Cracking the Code”
Jan
Feb
30
1
3
6
8
10
Genetic code: Translation, degeneracy, and wobble hypothesis
Genetic code: Synonymy, non-synonymy, and evolution
Genome structure and function: Viruses
Working with a single
DNA sequence:
C & N, Chap. 5
Genome structure and function: Bacteria
Eukaryotic genome structure: Trypanosomes and fungi
Eukaryotic genome structure: The Human Genome
Sequence identification
resources and use:
C & N, Chap. 3
13
15
17
EXAM 1
Exploring whole
Genomes:
C & N, Chap. 3
Feb
20
22
24
Dynamic Programming and Global Alignments
Semiglobal Alignments
Local Alignment
Wet lab: PCR
amplification of
human DNA
Feb
Mar
27
1
3
Extension of Local Alignment: FASTX and BLAST
FASTX and BLAST continued
Special applications: Phi- and Psi-BLAST
Independent work on
PCR project:
Wed - Thurs - Fri.
Mar
6
8
10
Multiple Sequence Alignment – Hidden Markov Models
Sequence
comparison:
C & N, Chaps. 7,8
Feb
Feb
March
10-20
Mar 20
22
24
How to design PCR primers to obtain your favorite gene
Simple alignments, gaps, and scoring matrices
Multiple sequence alignment – ClustalW & Pileup
EXAM 2
Spring Recess
Evolution and natural selection
Agents of variation: Meiosis, recombination, mutation
Molecular clocks: Estimating rates of genetic change
Multiple Sequence
Alignments
C & N, Chap. 9
Mar
April
Apr
27
29
31
3
5
7
10
12
Application of clocks to the mitochondrial Eve hypothesis
Adam and the evolution of the Y chromosome
Building Phylogenetic
Trees
Phylogenetics: producing proofs or supporting hypotheses?
C & N, Chap. 13
Construction of phylogenetic trees
Distance-based methods of phylogenetics
Character-based methods of phylogenetics
Locating Genes in a
DNA Sequence
C & N, Chap. 5
Genomics & gene recognition prokaryote genomes
Protein Sequences
C & N, Chap. 6
EXAM 3
April
13-18
Easter Recess
Apr
19
21
The transcriptome: cDNA microarrays and DNA chips
Oligonucleotide microarrays – medical applications
Protein Visualization
C & N, Chap. 13
Apr
24
26
28
Proteins, the final frontier: protein chemistry & structure
The protein folding problem
Protein Folding Algorithms: Visualizing protein structure
Work on final project
Protein Threading – Folding in Reverse
Proteomics, protein chips, & medical applications
Work on final project
May
1
3
5
May 10
EXAM 4
FINAL PROJECT DUE
BIOLOGY/COMPUTER SCIENCE 251 – Spring 2006
INTRODUCTION to BIOINFORMATICS
Introduction to Bioinformatics is a hands-on course that will introduce students in biology and
computer science to the emerging field of bioinformatics, where biology and computer science
intersect to interpret the rapidly expanding body of biological information deriving from genome
sequencing and genomic and proteomic approaches to molecular biology and evolution. Application
of bioinformatic software tools to the analysis of gene sequences and protein structures will be
emphasized. Students will undertake a laboratory project combining in silico and in vitro approaches
to isolate and then analyze a segment of their own DNA. An introduction to computer algorithms used
in bioinformatic software will be provided, though no computer science knowledge is required for this
course.
Three lecture hours and two laboratory hours per week, and a final project.
This course serves as an elective in the Biology major and minor, the Biochemistry and
Molecular Biology (BMB) major, and the Computer Science major. This course may be used to fulfill
major requirements in Biology and Computer Science. As an interdisciplinary course, Bio/CS 251
Introduction to Bioinformatics will complement existing courses in Genetics (Bio 211), Cell Biology
(Bio 212), Molecular Genetics (Bio 351), Biochemistry (Bio 334), Introduction to Computer Science
(CS 103), Computer Science I (CS 111), Theory of Computation CS 301), Principles of Database
Systems (CS 360), and Introduction to Artificial Intelligence (CS 371).
Student learning goals:
Students in this course will develop the following competencies -
1. Become proficient at using a wide array of in silico bioinformatic tools; use these tools to
discover and analyze genes and their protein products; learn how to use bioinformatic tools
to probe genome structure and genome organization; learn how to use bioinformatic tools to study
molecular evolution and molecular phylogenetics, with an emphasis on the human genome.
2. Understand the increasingly important roles and contributions of bioinformatics in the
management, analysis, and exploration of biological information;
3. Understand and apply basic principles of computer programming employed in the design of
bioinformatic software;
4. Independently design topical hypotheses relating to gene discovery, proteomics, genome
structure, and molecular evolution, and test them using bioinformatic tools and principles.
Prerequisites:
A 100-level biology course or permission of the instructors
Recommended: CS 103 or CS 111
Instructors:
Steve James, Biology
Carl Leinbach, Computer Science
Lecture:
MWF10-10:50 am
Science Center 260
255 Science Center, x6170, sjames
206 Glatfelter Hall, x6640, leinbach
Laboratory:
W 1-3 pm
Science Center 260
Lecture text:
Krane, D.E. and M.L. Raymer. 2003. Fundamental Concepts of
Bioinformatics. New York: Benjamin Cummings.
Laboratory text:
Claverie, J-M. and C. Notredame. 2003. Bioinformatics for Dummies.
New York: Wiley Publishing Company.
Course Grade:
Four one hour exams
Bioinformatics final project
Quizzes and homework
Laboratory assignments
15%each
15%
5%
20%
Final project:
Option 1: each student choosing this option will use bioinformatic tools to perform genomic and
proteomic analyses of a novel, recently released genome. The student will employ methods for gene
discovery and analysis, and will study genome structure and genome evolution. The student will
also employ in silico DNA microarray methods for measuring global gene expression, and will use
proteomic tools for in silico analysis of the products encoded by genes that are discovered in the
course of the project.
Option 2: each student choosing this option will write programs in the language of to their choice
to implement the algorithms that have been illustrated in class and keep an electronic portfolio of
these programs with sample data from a publicly available web site. Each program must be able
to read the data and analyse it. The portfolios will be inspected and programs run by the
instructors at periodically announced intervals. At the end of the semester the student will use the
programs in the portfolio to perform an appropriate bioinformatics investigation.
Attendance policy: Attendance in lecture and lab is mandatory. A student with more than three
unexcused absence from lectures, or from one laboratory, will be invited to leave the course.