Contact Information

Computer Science Department
Colgate University
McGregory Hall, 3rd Floor
13 Oak Drive
Hamilton, NY 13346
(tel) 315.228.7719
(fax) 315.228.7009
department@cs.colgate.edu

Upcoming events

  • 21

    Oct

    2014

    The speaker for our next department tea will be Farah Fouladi '15, who will talk about the internship she did this past summer. Lunch will be available after her talk.

    Abstract:
    By mathematically modeling biological systems we can predict the effect of small changes in the system that are difficult to measure experimentally. This analysis requires multiple simulations of the model for every parameter variation. While this type of analysis is feasible for isolated cells, running many simulations of large systems of cells is extremely time consuming. To decrease the execution time of these model simulations, I have developed a parallelized environment, which utilizes the architecture of a graphics processing unit.

    The GPU has many processor cores and the ability for thousands of threads to run concurrently on those cores. For my research, a mathematical model of the human ventricular myocyte (ten Tusscher & Panfilov, Am J Physiol 291: H1088–H1100, 2006) was programmed in CUDA. Taking advantage of the parallel hardware, cell computations along with different simulations of the model are completed on the GPU by many threads running simultaneously. To validate this computational design, cell membrane voltage values were compared with an already existing model implementation in MATLAB. Results showed that the added parallelization has no effect on the computational aspect of the model and that the execution time of the CUDA program decreases by orders of magnitude compared to the previously used MATLAB program.

    Using this new computational environment, I analyzed one cause of reentry in cardiac myocytes. Reentry occurs when an electric propagation loops back on itself, abnormally re-exciting cells. There is a short window of time during which a stimulus can excite cardiac tissue and cause a reentry effect due to refractory tissue blocking action potential propagation in only one direction. My program is able to efficiently identify the stimulus-timing interval when reentry occurs in a loop of 1,000 cells.

    This parallelized simulation environment minimizes computational execution time and provides a framework for further analysis of more complex and physiologically relevant systems of cells


Past events

  • 7

    Oct

    2014

    The Raspberry Pi is a small, low-cost, Linux-based computer introduced in 2012 (see http://http://www.raspberrypi.org), which contains interesting capabilities for software development and prototyping. In the CS department, we are planning to use these computers to drive the (currently dark) screens around the department in order to display announcements, information specific to different rooms, and other content. In this department tea, we'll discuss general capabilities and features of the Pi's, as well as examine a prototype display system. The prototype system is written in Python, and the department is interested in having students involved in further development of the system. All students are encouraged to attend, and lunch will be available after the talk and discussion.

  • 30

    Sep

    2014

    For our department tea on 9/30, our speaker will be from Ernst & Young financial services, NYC and will talk about career opportunities in technology consulting. Lunch will be available after their presentation.

Events history