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Original Research ARTICLE

Front. Neuroinform., 03 April 2012 | http://dx.doi.org/10.3389/fninf.2012.00007

The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows

Pierre Bellec1,2*, Sébastien Lavoie-Courchesne1,2,3, Phil Dickinson1,3, Jason P. Lerch4,5, Alex P. Zijdenbos6 and Alan C. Evans3
  • 1Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montréal, QC, Canada
  • 2Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, QC, Canada
  • 3McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
  • 4Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
  • 5Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
  • 6Biospective Incorporated, Montréal, QC, Canada

The analysis of neuroimaging databases typically involves a large number of inter-connected steps called a pipeline. The pipeline system for Octave and Matlab (PSOM) is a flexible framework for the implementation of pipelines in the form of Octave or Matlab scripts. PSOM does not introduce new language constructs to specify the steps and structure of the workflow. All steps of analysis are instead described by a regular Matlab data structure, documenting their associated command and options, as well as their input, output, and cleaned-up files. The PSOM execution engine provides a number of automated services: (1) it executes jobs in parallel on a local computing facility as long as the dependencies between jobs allow for it and sufficient resources are available; (2) it generates a comprehensive record of the pipeline stages and the history of execution, which is detailed enough to fully reproduce the analysis; (3) if an analysis is started multiple times, it executes only the parts of the pipeline that need to be reprocessed. PSOM is distributed under an open-source MIT license and can be used without restriction for academic or commercial projects. The package has no external dependencies besides Matlab or Octave, is straightforward to install and supports of variety of operating systems (Linux, Windows, Mac). We ran several benchmark experiments on a public database including 200 subjects, using a pipeline for the preprocessing of functional magnetic resonance images (fMRI). The benchmark results showed that PSOM is a powerful solution for the analysis of large databases using local or distributed computing resources.

Keywords: pipeline, workflow, Octave, Matlab, open-source, parallel computing, high-performance computing, neuroimaging

Citation: Bellec P, Lavoie-Courchesne S, Dickinson P, Lerch JP, Zijdenbos AP and Evans AC (2012) The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows. Front. Neuroinform. 6:7. doi: 10.3389/fninf.2012.00007

Received: 07 November 2011; Accepted: 05 March 2012;
Published online: 03 April 2012.

Edited by:

Andrew P. Davison, Centre National de la Recherche Scientifique, France

Reviewed by:

Ivo Dinov, University of California, USA
Yann Cointepas, CEA - NeuroSpin, France

Copyright: © 2012 Bellec, Lavoie-Courchesne, Dickinson, Lerch, Zijdenbos and Evans. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.

*Correspondence: Pierre Bellec, Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, 4545 chemin Queen-Mary, Montréal, QC H3W 1W5, Canada. e-mail: pierre.bellec@criugm.qc.ca