a national resource for computational science education

HOME BWPEP Shodor Blue Waters

View Position
Project TitleUndergraduate Petascale Drug Discovery Intern 1
SummaryThe undergraduate student intern will work with the mentor to learn how to conduct virtual screening of molecules on the Blue Waters supercomputer to try to identify molecules that will help treat or cure diseases, including histoplasmosis. The student will then develop software to process the results from virtual screens that will enable us to compile a list of molecules identified by multiple docking programs (GLIDE and AutoDock Vina) as potentially useful for treating or curing the diseases. The student’s software will enable us to communicate which molecules were "hits" in multiple docking programs so they can then be screened by the biology and chemistry professors and their students to further refine the list.
Job DescriptionThe intern will work with the mentor to learn to use the Blue Waters supercomputer to conduct virtual screening of molecules using the AutoDock Vina and Dock6 docking programs. The intern will learn to use shell scripting to conduct the virtual screens and techniques to analyze the data produced by the virtual screens. The student will create electronic documentation as well as videos for people to be able to learn to conduct this research in the future with minimal training.

The intern will have to solve problems encountered with the volume of data produced due to the high speed processing capabilities of the Blue Waters system. These problems did not exist when screens were conducted on the Ranger supercomputer at TACC, but began appearing when virtual screening began being conducted on the Stampede supercomputer at TACC after Ranger was decommissioned. The problem is that the file system of the supercomputers gets swamped when reading and writing too many files in a short period, which is caused by the faster processors of the newest supercomputers. The intern and I will work on reducing the data that AutoDock Vina writes and then the intern will conduct performance comparisons of the new version of AutoDock Vina we create with the old version to see what the impact is on the amount of time required to conduct a virtual screen.

The intern will also compare the effectiveness of and the modified version of AutoDock Vina on other architectures with the effectiveness of it on the Blue Waters system.
Conditions/QualificationsThe intern must have completed the first two courses in computer science (CPSC 220 and CPSC 230) by the beginning of the internship. The intern must be an undergraduate computer science major at the University of Mary Washington and able to spend the summer working closely with the mentor on the University of Mary Washington campus. Some basic background in chemistry is required. Must be able to work with a remote biology professor and chemistry professor at Merrimack College, as part of an interdisciplinary research team.
Start Date05/15/2014
End Date05/14/2015
LocationComputer Science Department
University of Mary Washington
Fredericksburg, VA
Sharon Itzkoff