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University of
the Sciences in Philadelphia
Misher
College of Arts and Sciences
Department of
Mathematics, Physics and Computer Science
Special Topics in Bioinformatics
Simulation Methods for Bioinformatics
BI 860
Summer 2005
Instructor:
Dr. Anatoly Kurkovsky
Semester
Credit Hours:
3
Limit number
of students in class:
up
to 10
Lecture and
Seminars:
Telephone:
(215) 596 – 7615
E-mail:
a.kurkov@usip.edu
Course
Description:
Prerequisites: permission of instructor.
The problems
facing the industry, commerce, government, society, and science in general
continue to grow in size and complexity. The need for procedures and techniques
for resolving such problems is apparent. Modeling and, in particular, simulation
modeling is an effective and a universal method for solving complex problems in
different areas.
The goal of this course is to provide graduate bioinformatics students with a
good background in Computer Simulation and to introduce the design of Simulation
Models with Visual SLAM, AweSim, and Dynetica. Subjects covered include:
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Introduction to
modeling and simulation; |
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Methodological basics
of simulation modeling; |
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Introduction to SLAM
simulation language; |
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AweSim and Dynetica
simulation environments; |
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Examples of simulation
modeling in bioinformatics. |
Materials
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Required Textbook:
"Simulation with Visual SLAM and AweSim" by A. Alan B. Pritsker and Jean
J. O'Reilly, 2nd Edition. 1999, John Wiley & Sons. ISBN: 0-471-35293-4 |
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Optional Textbook:
"Handbook of Simulation" edited by Jerry Banks. 1998, John Wiley & Sons.
ISBN 0-471-13403-1. |
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The User’s guide to
Dynetica. |
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Software: Pritsker
AweSim, version 3.1 and Dynetica, version 2.0 |
Methods of Instruction:
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Lectures, seminars and
discussions |
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Take-home assignments |
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Final exam |
Evaluation:
Student
performance in this class will be measured by assignments (15%), tests (20%),
class participation (25%), and final exam, course material’s synopsis, or
project (40%).
The types of
assignments may include:
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small in-class project
discussions, |
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take-home (reading)
assignments, |
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take-home (questions)
assignments. |
Evaluation of
student participation will include:
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attendance, |
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understanding of the
course material, |
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responsibility to
answer professor’s questions. |
Final grade
will be derived from student performance on the assignments, class
participation, and final exam (project) as follows:
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A: 90 – 100 |
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B: 80 – 89 |
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C: 70 – 79 |
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D: 60 – 69 |
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F: below 60 |
Tentative
Schedule:
(These dates
may change depending upon the pace of the course.)
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Week |
Ch. |
Topic |
Assignment/
Test/Project |
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1. |
1,2 |
Introduction to modeling and simulation. Systems,
models, model building, definition of simulation, data collection
and analysis. Simulation modeling perspectives. Modeling word view,
discrete simulation modeling, continuous simulation modeling,
combined discrete-continuous models. |
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2. |
3, 4, 9 |
Modeling and simulation process. Problem formulation,
specification and building. Discrete simulation environment.
Simulate model, support decision making, and AweSim with Visual
SLAM. Applications of simulation. AweSim simulation support system.
AweSim overview, building networks in AweSim, Visual SLAM output
reports. |
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3 |
4, 5 |
Examples of simulation models. Basic network
modeling. Visual SLAM network modeling.
Illustrations: two parallel servers (I5-1), two types of
entities (I5-2). Introduction to basic network elements. CREATE,
QUEUE, nodes. Example: work stations in series (E5-1). |
Assignment 1 |
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4 |
5 |
Introduction to basic network elements. TERMINATE,
ASSIGN, GOON, and COLCT nodes. Activities. Illustration: conditional
and probabilistic branching (I5-4). Example: inspection and
adjustment stations on a production line (E5-2). Resources and
Gates. GROUP, GATE, PREEMPT, OPEN and CLOSE block and nodes.
Illustration: machine breakdowns (I6-4). Example: single-line
traffic analysis (E6-5). |
Test |
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5. |
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Continuous simulation within Dynetica environment.
Structure of Dynetica environment. Simulation examples from
bioinformatics subject domain. |
Assignment 2 |
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6. |
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Discussion of student final course material’s
synopsis or student project. |
Final exam or Student project |
Attendance
policy:
It is
required that students attend every seminar. Students are allowed to miss up to
two seminars without a written excuse. If a student misses more than two
seminars his/her grade will be reduced according to the number of missed
seminars.
Plagiarism
and cheating:
Students may
work together and share ideas on any take-home assignment or seek help from
anyone. However, submitting identical final essay will be considered cheating.
No cheating in any form will be tolerated.
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