Course Title and Number: Analysis and Modeling of Bio. Structures BINF 5341
Instructor: Dr. Michela Taufer
Time: Tuesday and Thursday 9:00PM-11:50PM
Room:
Office Hours: Per appointment.
Email Address: taufer AT acm DOT org
Campus Office Number: 6957

IMPORTANT: This course has three key modules that are tought by three instructors during the semester. Please note that this document is the syllabous of the first part of this course.

Course Desciption
This first part of the course, presented in the syllabous, provides students with advanced knowledge in modeling techniques that are commonly used to study molecular behaviors in high performance computer simulations. Molecular dynamics simulation algorithms for particles will be implemented for desktop machines and massively parallel, distributed computing platforms. Scientific visualization using OpenGL programming and grid computing for large-scale molecular simulations will be introduced.

Goals
This course is intended to provide student in Bioinformatics with an understanding of molecular simulations, their principals, and their sequential and parallel algorithms. The student will learn the fundamental aspects of coding, compilation and execution. Emphasis is placed on the algorithmic and code components of the simulation and visualization algorithms. The student is encouraged to analyze performance of these algorithms.

Course Information and Web Site
The material related to this course (e.g., syllabus, news, reading material, slides, etc.) are available through WebCT. In WebCT, a mailbox, a public forum for discussions, and the course calendar are also available. Every week, the instructor will update the information on the course in WebCT. Therefore you are encouraged to consult the information available on WebCT on a weekly base.

Prerequisites
Students must have prior programming experience using either C or Perl on Unix/Linux computing systems, plus mathematics coursework through calculus. Experience using and developing scientific codes and mathematics coursework through differential equations is helpful but not required.

Tentative Class Schedule:

Week 1: Introduction in C programming (3 hours)
Week 2: Molecular Dynamics (MD) simulations (3 hours)
Week 3: Advanced Molecular Dynamics (3 hours)
Week 4: Introduction in Parallel Computing (3 hours)
Week 5: Parallel Molecular Dynamics simulations (3 hours)
Week 6: Visualizing Molecular Dynamics (3 hours)
Week 7: Grid Scientific Computing (3 hours)