Parallel calculation of multi-electrode array correlation networks

• Type: Article in International Scientific Journal
• Date: 2009

Authors

Pedro Ribeiro (Author) Other; Jennifer Simonotto (Author) Other; Marcus Kaiser (Author) Other; Fernando Silva (Author) FCUP

Journal

Title: Journal of Neuroscience Methods

Vol. 184

Pages: 357-364

ISSN: 0165-0270

Publisher: Elsevier

Indexing

ISI Web of Knowledge - 2 Citations

Scopus - 2 Citations

Scientific classification

FOS: Medical and Health sciences > Basic medicine

Other information

Authenticus ID: P-003-EBY

DOI: 10.1016/j.jneumeth.2009.08.001

Abstract (EN): When calculating correlation networks from multi-electrode array (MEA) data, one works with extensive computations. Unfortunately, as the MEAs grow bigger, the time needed for the computation grows even more: calculating pair-wise correlations for current 60 channel systems can take hours on normal commodity computers whereas for future 1000 channel systems it would take almost 280 times as long, given that the number of pairs increases with the square of the number of channels. Even taking into account the increase of speed in processors, soon it can be unfeasible to compute correlations in a single computer. Parallel computing is a way to sustain reasonable calculation times in the future. We provide a general tool for rapid computation of correlation networks which was tested for: (a) a single computer cluster with 16 cores, (b) the Newcastle Condor System utilizing idle processors of university computers and (c) the inter-cluster, with 192 cores. Our reusable tool provides a simple interface for neuroscientists, automating data partition and job submission, and also allowing coding in any programming language. It is also sufficiently flexible to be used in other high-performance computing environments.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 8