Syllabus prepared by Dr. Laurence Boxer, January '06
Catalog Description
Theory and practice in problems of scientific computing. We will study the development of solutions to important scientific problems requiring powerful computing resources. Students will write programs for a parallel supercomputer.
D. Gusfield, Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge University Press, New York, 1997
R. Miller and L. Boxer, Algorithms Sequential and Parallel: a Unified Approach, 2nd ed., Charles River Media, Inc., Hingham, MA, 2005
Based on examinations, homework problems, programming projects, attendance and contributions to discussion
A student's grade is determined by the student's percentage of possible points.
For example, if there are, say, 225 possible points on programming projects, and 2 exams each with 100 possible points, and if there are 200 possible points of quizzes and non-programming homework, and if there are 30 possible points for attendance and participation, there would be a total of 655 possible points; a student with 550 points would have a semester average of 550 / 655, which is about 84%.
Approximate grading standards (the instructor reserves the right to adjust these as required by the interests of justice):
88% - 100%: B+ to A
72% - 88%: C+ to B+
55% - 72%: D+ to C+
45% - 55%: D
0% - 45%: F
See my Web page Remarks on Grading of Programs for information on how programming assignments are graded.
Exams/quizzes may be open- or closed-book. You may be asked to analyze the execution of, or write a piece of code; offer a short essay; sketch an algorithm in pseudo-code; etc.
The list given below is approximate. Deadlines may be changed according to the needs of the course. Details of assignment specifications will be posted in Blackboard.
See
http://www.niagara.edu/cis/announcement/policy.htm#att
Since we continually build on previously studied material, the wise student makes every effort
to maintain perfect attendance. If you must miss class, get a classmate's
notes. However, this isn't nearly as good a learning experience as being
in class to take your own notes.
The university will make reasonable accommodations for students with documented disabilities. Students should notify the Coordinator of Specialized Support Services (located in Seton Hall) and their instructors of any special needs. Instructors should be notified within the first two weeks of classes.
Students having trouble coping with the stresses of University life or related problems are encouraged to use the Niagara University Counseling Services.
S.G. Akl, Parallel Computation: Models and Methods, Prentice Hall, Upper Saddle River, NJ, 1997
M.A. Arbib and J.A. Robinson, eds., Natural and
Artificial Parallel Computation, MIT Press, Cambridge, MA, 1990,
QA76.58 .N37 1990A.
A.D. Baxevanis and B.F.F. Ouellette, eds., Bioinformatics; A Practical Guide to the Analysis of Genes and Proteins, 2nd ed., Wiley-Liss, New York, 2001
B. Bergeron, Bioinformatics Computing, Prentice Hall, Upper Saddle River, NJ, 2003
K.A. Berman and J.L. Paul, Fundamentals of Sequential and Parallel Algorithms, PWS Publishing, Boston, 1997
J-M Claverie and C. Notredame, Bioinformatics for
Dummies, Wiley, New York, 2003,
QH324.2 .C44 2003
T.H. Cormen, C.E. Leiserson, R.L. Rivest, and C. Stein,
Introduction to Algorithms, MIT Press, Cambridge, MA,, 2001,
QA76.6 .I5858 2002
F.T. Leighton, Introduction to Parallel Algorithms
and Architectures: Arrays, Trees, Hypercubes, M. Kaufmann Publishers, San
Mateo, CA, 1992,
QA76.58 .L45 1992
R. Miller and Q.F. Stout, Parallel Algorithms for Regular Architectures: Meshes and Pyramids, MIT Press, Cambridge, MA, 1996.
D.W. Mount, Bioinformatics: Sequence and Genome
Analysis, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY,
2001,
QH441.2 .M68 2001
E.F. Van de Velde, Concurrent Scientific Computing,
Springer-Verlag, New York, 1994,
QA76.58 .V35 1994
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