CSE 498K/598K
Computational Biology
Fall Semester
8/24/04
CSE 498K/598K:
“Computational Biology” (3-0-3)
This course studies a subset of important problems in computational biology
at the molecular level (proteins and nucleic acids), cellular level (metabolic
and other biological networks), and organism level (development, cellular
interactions). The emphasis is on the contributions that computer science can
bring to the study of biological problems in the post genomic data era. From
the engineering perspective, both mathematical and computational issues are
considered. An introduction to the biological issues is also provided.
Texts:
Tamar Schlick, Molecular
Modeling and Simulation: An Interdisciplinary Guide, Springer-Verlag, 2002. ISBN 0-387-95404-X
J. Setubal and J. Meidanis,
Introduction to Computational Molecular Biology,
PWS Publishing Co., 1997. ISBN
Course packet
Faculty-in-Charge: Jesús A. Izaguirre
Course Goals:
At the end of
the course, one should: (1) understand some of the major computational problems
in molecular and cellular modeling; (2) have familiarity with computational
biology applications such as protein folding, computer assisted drug design,
and the prediction of protein-protein and gene regulatory networks; (3)
understand deterministic approaches to solving some of these problems (e.g.,
molecular dynamics, reaction-diffusion partial differential equations); (4)
understand stochastic approaches for other problems (e.g., Markov Chain Monte
Carlo methods, Potts model, stochastic cellular automata); (5) understand
combinatorial approaches for solving biological network problems (e.g., graph
algorithms applied in biology); (6) have familiarity with object-oriented and
data modeling for computational biology, using the languages XML and C++; (7)
understand basic concepts of high performance and grid computing as they help
to solve challenging problems in computational biology (e.g., MPI, Condor); (8)
be able to undertake some research projects or take more advanced classes in
computational biology and bioinformatics.
Prerequisite: None, although familiarity
with C++ or Java or another modern programming language is desirable.
CSE 498K/598K “Computational Biology”
Page 2
Weekly class schedule:
1.
Introduction
to computational biology:
Molecular, cellular, and organism levels
2.
Problems
in biomolecular modeling I:
Molecular dynamics
3.
Problems
in biomolecular modeling II:
Conformational sampling and protein folding
4.
Problems
in biomolecular modeling III:
Docking and drug design
5.
Problems
in biomolecular modeling IV:
Fast methods for the N-body problem
6.
Computational
issues I:
Parallelism and grid computing
7.
Computational
issues II:
Object-oriented modeling
8.
Problems
in biological networks:
Predicting protein-protein interactions
9.
Problems
in biological networks II:
Sequence comparison and database search
10.
Problems
in cellular modeling I:
Reaction-diffusion and pattern formation
11.
Problems
in cellular modeling II:
Simulating cellular dynamics
12.
Problems
in developmental biology:
Modeling growth
13.
Computational
issues III:
Data modeling using XML
14.
Conclusion
and open research projects
15.
Final
project presentations
Semester: Usually offered fall.
Homework: The homework consists
of 5 assignments. Some of the assignments require programming. Students will be
able to use and extend software developed by the instructors group (open source
frameworks ProtoMol and CompuCell, domain specific
language BioLogo, and software tool MDSimAid).
Laboratory usage: Some students will obtain
accounts in high performance clusters at Notre Dame and elsewhere.
CSE 498K/598K “Computational Biology”
Page 3
Grading:
Homework (5 assignments) 40%
Term paper/final project 45%
In-class presentation/participation 15%
From weeks 2-13
there will be one lecture by the instructor and a presentation by a student.
Students will also do a presentation of their final project at the end of the
semester. Several final projects in the past have become conference or journal
papers.
Students are
allowed 3 unexcused absences from class during the semester. You may receive an
excuse by talking to the instructor in advance.
Course
Content:
Engineering
Science: 1.5
credit (50%)
Engineering Design: 1.5
credit (50%)