Statistical methods for the discovery of co-operative transcription factors: The co-bind code revised

Giovanni Lavorgna, Alessandro Marongiu, Simone Melchionna, Paolo Palazzari, Vittorio Rosato, Paolo Verrecchia

Research output: Contribution to conferencePaper

Abstract

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.
Original languageEnglish
DOIs
Publication statusPublished - 2005
Externally publishedYes
Event19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005 - , United States
Duration: 1 Jan 2005 → …

Conference

Conference19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005
CountryUnited States
Period1/1/05 → …

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All Science Journal Classification (ASJC) codes

  • Engineering(all)

Cite this

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