Discovering co-operative Transcription Factors (TF's) within the genome is a computationally challenging problem, tackled through Monte Carlo-like analysis by the Co-Bind code, developed at the Department of Genetics of the St. Louis Washington University, Due to its statistical nature, Co-Bind is characterized by very long execution times, order of days on current high-end workstations, and could benefit from parallelization and a wise optimization, performed at both the algorithmic and coding levels. This work presents the results achieved by parallelizing Co-Bind and optimising the parallel code and shows that, on a 16-processor architecture, a speed-up greater than two orders of magnitude is achieved with respect to the serial version released by the code's authors.
|Publication status||Published - 2005|
|Event||19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005 - , United States|
Duration: 1 Jan 2005 → …
|Conference||19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005|
|Period||1/1/05 → …|
All Science Journal Classification (ASJC) codes
Lavorgna, G., Marongiu, A., Melchionna, S., Palazzari, P., Rosato, V., & Verrecchia, P. (2005). Statistical methods for the discovery of co-operative transcription factors: The co-bind code revised. Paper presented at 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005, United States. https://doi.org/10.1109/IPDPS.2005.411