From WakeDEAC

One of the most important responsibilities the DEAC/Osiris cluster undertakes is the education of the students at Wake Forest University. Clusters provide enormous computational power to tackle more advanced scientific problems, opening up the possibility for our students to gain a unique perspective on topics in the forefront of research today. Any faculty member can (and is encouraged to!!!) request the use of the cluster for a course they are teaching. Several courses have already used the DEAC/Osiris cluster to enhance the student's exposure to the advanced computing environment provided by the University. Below, we've broken down (by academic year) the courses that have utilized the cluster as an instructional tool.

Academic Year 2006-2007

Fall 2006

Computational Biophysics Laboratory (PHY 323/623) Students in this course will be performing dynamics simulations (NAMD), trajectory analysis (CHARMM) and molecular visualization (VMD)of Eglin C mutants. The Computational Biophysics Lab uses a research-based learning format, in which students are taught methods and theory, but then apply the methods and theory to a problem for which the answer is not known. Student observations, analyses of the results, and critical comparison of to the results produced by other students thus become a critical part of the learning process. Each student will submit a research paper on their work at the end of the semester.

Academic Year 2005-2006

Spring 2006

Computational Physics Lab (PHY 346) 

Required for all Physics BS majors, PHY 346 introduces students to several types of research areas. The purpose of the computational physics segment was to introduce some of the basic concepts of computation and to provide several examples of computation on the DEAC cluster. One exercise involved calculating the electronic structure of an atom another exercise involved a simple molecular dynamics simulation. In both cases, the results could be visualized with graphics software. For the first exercise the students could construct radial plots of the electron densities and wavefunctions using a gnuplot script. For the second exercise, students could visualize a movie of their simulation using a public domain software package -- xcrysden.

http://www.wfu.edu/~natalie/s06phy346/

Fall 2005

Bioinformatics (CSC 385/685; PHY 327/627; BICM 715) 

Students in this course used the cluster in the project assignment to distribute their independent computations across several processors.

http://www.cs.wfu.edu/~djj/CSC685/

Academic Year 2004-2005

Fall 2004

Parallel Algorithms (CSC726) 

Students in this course learn how to develop parallel versions of their favorite serial algorithms that are scalable and efficient. To enhance their design efforts, they are required to implement their algorithms on the cluster in half of the assignments.

http://www.cs.wfu.edu/~djj/CSC726

http://www.wfu.edu/~millerte/courses/CSC726

Bioinformatics (CSC 385/685; PHY 327/627; BICM 715) 

Students in this course used the cluster in the project assignment to distribute their independent computations across several processors.

http://www.wfu.edu/~fetrowjs/Courses/BioinformaticsFal04

Computational Biophysics Laboratory (PHY 323/623) 

Students in this course will be performing dynamics simulations (NAMD) and electrostatic calculations (MEAD) of peroxiredoxin monomer units, trajectory analysis (CHARMM), and molecular visualizations (VMD).

http://www.wfu.edu/~fetrowjs/Courses/CompMolBiophysFal04

Additional information about the course 

The Computational Biophysics Lab uses a research-based learning format, in which students are taught methods and theory, but then apply the methods and theory to a problem for which the answer is not known. Student observations, analyses of the results, and critical comparison of to the results produced by other students thus become a critical part of the learning process. In the Fall 2004, semester, each student will be assigned one peroxiredoxin protein structure to analyze during the course. They will apply each method to their own peroxiredoxin structure and submit a research paper on their work at the end of the semester.

Academic Year 2003-2004

Fall 2004

Parallel Computation (CSC346/646) 

Students in this course learned how to create distributed and multiprocessor programs. Their efforts in the distributed programming material helped produce the software components used in "Fibonacci and Phi".

http://www.cs.wfu.edu/~burg/Courses/Fall03/CSC346-646/

http://www.wfu.edu/~millerte/courses/CSC346/

Spring 2004

Bioinformatics (CSC 385/685; PHY 327/627; BICM 715) 

Students in this course used the cluster in the project assignment to distribute their independent computations across several processors.