Research Projects

Applications with Biology, Environmental Science

 * Looking for patterns in Tetrahymena (Spencer Debenport; Professors Freedberg, Brown, Cole); Script to analyze probability in Tetrahymena genetic arangement (Stephen Freedberg and John Giannini)
 * Nitrogen flow in riparian vegetation zones
 * Simulating Nitrogen Flow in Riparian Systems (Tony Waldschmidt; Professors Schade, Brown)
 * Spencer Debenport '10 helped Tony to make his runs, then used Tony's simulation to explore questions about nitrogen flow through sequences of riparian plants (supervised by Brown and Schade), Summer 2007
 * HiPerCiC, High-Performance Computing in the Classroom, is an initiative for combining user interfaces, intermediate software, and computational models to create an application for science students in courses to access those computational models, perhaps running on a Beowulf cluster. A prototype under development in Fall 2007 Capstone, by Jeremy Gustafson, Todd Frederick, and Tony Waldschmidt, supervised by Prof. Brown, will make Tony's riparian model available for students of Prof. Schade's Biogeochemistry lab and other environmental science courses.
 * CCT software (Rutherford, Landsteiner, Olson)
 * Charcoal dispersion modeling
 * Landis II (Installed and running via Mono: John Giannini)
 * Neuroscience research on the leech, Prof. Kevin Crisp
 * In Summer 2006, Prof. Crisp asked for Beowulf assistance in analyzing wave forms that represent readings of neurons in the leech. His team treats leech's with certain agents, then observes their neurons, looking for wave patterns that can be classified as swimming behavior.  These patterns are currently identified by hand.  The team did not have sufficient time/expertise to pursue this problem during Summer 2006.  Interest has since shifted to recognizing crawling behavior in place of swimming behavior.
 * In Fall 2007, Bjorn Paulson '10 began learning about FFT and Fourier transforms in general, exploring these computations using the R programming language, as a step towards identifying behaviors in the leech based on waveform readings. As a first stage, the goal is computational noise reduction (signal noise emanates from fluroescent tubes, cell phones, etc., when observing neuron signals).
 * Prof. Crisp has proposed a collaborative effort to catalog computational models of cardiac myocites (heart muscle cells) according to their action potentials. An ability to query such models would be valuable in neuroscience.  Spencer Debenport '10 began researching such a computational model in Summer 2007.

Applications in Physics

 * Bryan Anderson, a senior Physics major, implemented the first locally developed application on the development cluster, a simulation of part of the solar system. This involved an iterative computational solution to the n-body problem for the four innermost planets and Earth's moon, each body computed in parallel on a dedicated node. Needing 100-digit precision, Bryan introduced a high-precision computation package and a strategy for network communication of those values. Two first-year students taking the introductory course CS 121, Nathaniel Meyerpolys and Charles McEachern, implemented an animation of the results which enabled Bryan to correct and improve his results. Presentation: Science Symposium poster
 * Todd Frederick, a junior Math and Computer Science major, worked with the Center for Geophysical Studies of Ice and Climate to parallelize part of the Seismic Unix software packages used in the analysis of RADAR data from Antarctica. By distributing rows of a matrix among the cluster nodes, computation time decreased from 4 hours to 4 minutes on a particular data set.

Applications in Chemistry

 * Molecular dynamics simulation. Prof. Jeff Schwinefus (Chemistry) met with the Beowulf team to plan for molecular dynamics simulations on the production cluster.  Decided on AMBER package;  software ordered, and the team installed it, ran demos for Prof. Schwinefus, who is now working his way through a tutorial.  (11/07)

Applications in Statistics

 * STATA is a statistics package used by Prof. Legler. During Summer 2007, the Beowulf team helped research and order a copy of STATA for a cluster node, intended to help with exploratory computations for a CIR project.

Applications in Computer Science

 * Design and construction of the clusters, Jan 2006-present
 * Cluster Security
 * Plantir
 * CS1 SVG 2 Youtube video

Applications in Mathematics

 * In Fall 2007, Prof. Garrett, a combinatorist in Mathematics, proposed a questions about congruences of partitions to Prof. Hall-Holt's CS 253 class. The first question involved calculating the number of partitions of a given integer;  her software could produce the first 1000 such values.  Todd Frederick '09 applied Beowulf computing to produce approximately 250,000 values. The second question was to attempt to discover new congruence conjectures for that data.  Thomas McConville '09 and Daniel Edwins '08 were able to discover such conjectures that were consistent with Todd's data set.  The entire process took less than two weeks.