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

Pierre Bellec, Sébastien Lavoie-Courchesne, Phil Dickinson, Jason P. Lerch, Alex P. Zijdenbos, Alan C. Evans
2012 Frontiers in Neuroinformatics  
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.  ...  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  ...  Salma Mesmoudi, and M. Pierre Rioux for insightful discussions. Several authors of existing pipeline solutions have reviewed the introduction section and provided very valuable feedback: Dr.  ... 
doi:10.3389/fninf.2012.00007 pmid:22493575 pmcid:PMC3318188 fatcat:gwucpbklrrhcbdz4iola7zpaum

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System

Jonathan Passerat-Palmbach, Romain Reuillon, Mathieu Leclaire, Antonios Makropoulos, Emma C. Robinson, Sarah Parisot, Daniel Rueckert
2017 Frontiers in Neuroinformatics  
OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala.  ...  The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines.  ...  The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007(FP/ -2013/ERC Grant Agreement no. 319456.  ... 
doi:10.3389/fninf.2017.00021 pmid:28381997 pmcid:PMC5361107 fatcat:sqi7f56s5bg5jjwcstwuimsjqu

Boutiques: a flexible framework to integrate command-line applications in computing platforms

Tristan Glatard, Gregory Kiar, Tristan Aumentado-Armstrong, Natacha Beck, Pierre Bellec, Rémi Bernard, Axel Bonnet, Shawn T Brown, Sorina Camarasu-Pop, Frédéric Cervenansky, Samir Das, Rafael Ferreira da Silva (+9 others)
2018 GigaScience  
We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms.  ...  A set of core tools facilitates the construction, validation, import, execution, and publishing of applications.  ...  We also thank Compute Canada and Calcul Québec for providing a computing infrastructure supporting Docker and Singularity containers.  ... 
doi:10.1093/gigascience/giy016 pmid:29718199 pmcid:PMC6007562 fatcat:2acmyhkvmjdevgcyuxtt6kgyci

A Serverless Tool for Platform Agnostic Computational Experiment Management

Gregory Kiar, Shawn T. Brown, Tristan Glatard, Alan C. Evans
2019 Frontiers in Neuroinformatics  
We present Clowdr, a lightweight tool to launch experiments on HPC systems and clouds, record rich execution records, and enable the accessible sharing and re-launch of experimental summaries and results  ...  While these standards lower the barrier to adoption of HPC and cloud systems for neuroscience applications, they still require the consolidation of disparate domain-specific knowledge.  ...  ACKNOWLEDGMENTS The authors would like to thank Pierre Rioux and Valerie Hayot-Sasson for their insight and many helpful discussions.  ... 
doi:10.3389/fninf.2019.00012 pmid:30890927 pmcid:PMC6411646 fatcat:7uwik54sbjddxd3w553xilt2ha

PRN: a preprint service for catalyzing R-fMRI and neuroscience related studies

Chao-gan Yan, Qingyang Li, Lei Gao
2014 F1000Research  
.: The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows. Front Neuroinform. 2012; 6: 7.  ...  PubMed Abstract | Publisher Full Text Chao-Gan Y, Yu-Feng Z: DPARSF: A MATLAB Toolbox for "Pipeline" Data Analysis of Resting-State fMRI. Front Syst Neurosci. 2010; 4: 13.  ...  Xavier Castellanos and Yu-Feng Zang for their assistance and support for the PRN effort. This work is supported by the community contributors (http://rfmri. org/Contributors).  ... 
doi:10.12688/f1000research.5951.1 pmid:25844159 pmcid:PMC4367516 fatcat:yfxzpgi7ovd6fnxc2q6okvoxxa

PRN: a preprint service for catalyzing R-fMRI and neuroscience related studies

Chao-gan Yan, Qingyang Li, Lei Gao
2015 F1000Research  
.: The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows. Front Neuroinform. 2012; 6: 7.  ...  PubMed Abstract | Publisher Full Text Chao-Gan Y, Yu-Feng Z: DPARSF: A MATLAB Toolbox for "Pipeline" Data Analysis of Resting-State fMRI. Front Syst Neurosci. 2010; 4: 13.  ...  Xavier Castellanos and Yu-Feng Zang for their assistance and support for the PRN effort. This work is supported by the community contributors (http://rfmri. org/Contributors).  ... 
doi:10.12688/f1000research.5951.2 pmid:25844159 pmcid:PMC4367516 fatcat:oqyi3t3tvjbqhftnn3f2mdtomy

Best practices in data analysis and sharing in neuroimaging using MRI

Thomas E Nichols, Samir Das, Simon B Eickhoff, Alan C Evans, Tristan Glatard, Michael Hanke, Nikolaus Kriegeskorte, Michael P Milham, Russell A Poldrack, Jean-Baptiste Poline, Erika Proal, Bertrand Thirion (+3 others)
2017 Nature Neuroscience  
For each of seven areas of a study we provide tabular listing of over 100 items to help plan, execute, report and share research in the most transparent fashion.  ...  The open science movement is reshaping scientific culture and addressing the challenges of transparency and reproducibility of research.  ...  The full list of members is as follows (in alphabetical order).  ... 
doi:10.1038/nn.4500 pmid:28230846 pmcid:PMC5685169 fatcat:76jlqlntrvfg7iz74anmuxreja