Simulation Bio
Up Orientation Data Structures Architecture Simulation Simulation Env Simulation Bio Special Topics Student Projects



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


 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:

bullet Introduction to modeling and simulation;
bullet Methodological basics of simulation modeling;
bullet Introduction to SLAM simulation language;
bullet AweSim and Dynetica simulation environments;
bullet Examples of simulation modeling in bioinformatics.


bullet 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
bullet Optional Textbook: "Handbook of Simulation" edited by Jerry Banks. 1998, John Wiley & Sons.  ISBN 0-471-13403-1.
bullet The User’s guide to Dynetica.
bullet Software: Pritsker AweSim, version 3.1 and Dynetica,  version 2.0

 Methods of Instruction:

bullet Lectures, seminars and discussions
bullet Take-home assignments
bullet Final exam


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:

bullet small in-class project discussions,
bullet take-home (reading) assignments,
bullet take-home (questions) assignments.

Evaluation of student participation will include:

bullet attendance,
bullet understanding of the course material,
bullet 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:

bullet A: 90 – 100
bullet B: 80 – 89
bullet C: 70 – 79
bullet D: 60 – 69
bullet F: below 60

 Tentative Schedule:

(These dates may change depending upon the pace of the course.)








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.



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.



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



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).




Continuous simulation within Dynetica environment. Structure of Dynetica environment. Simulation examples from bioinformatics subject domain.

Assignment 2



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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This Web site is © 2003 - 2012 by Anatoly Kurkovsky

Last updated: May 30, 2012