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The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows
2012
Frontiers in Neuroinformatics
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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
2017
Frontiers in Neuroinformatics
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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
2018
GigaScience
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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
2019
Frontiers in Neuroinformatics
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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
2014
F1000Research
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.: 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
2015
F1000Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
.: 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
2017
Nature Neuroscience
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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