Keyword search (3,448 papers available)


File-based localization of numerical perturbations in data analysis pipelines.

Author(s): Salari A, Kiar G, Lewis L, Evans AC, Glatard T

BACKGROUND: Data analysis pipelines are known to be affected by computational conditions, presumably owing to the creation and propagation of numerical errors. While this process could play a major role in the current reproducibility crisis, the precise cau...

Article GUID: 33269388
Comparing perturbation models for evaluating stability of neuroimaging pipelines.

Author(s): Kiar G, de Oliveira Castro P, Rioux P, Petit E, Brown ST, Evans AC, Glatard T

With an increase in awareness regarding a troubling lack of reproducibility in analytical software tools, the degree of validity in scientific derivatives and their downstream results has become unclear. The nature of reproducibility issues may vary across ...

Article GUID: 32831546
Cyberinfrastructure for Open Science at the Montreal Neurological Institute.

Author(s): Das S, Glatard T, Rogers C, Saigle J, Paiva S, MacIntyre L, Safi-Harab M, Rousseau ME, Stirling J, Khalili-Mahani N, MacFarlane D, Kostopoul...

Front Neuroinform. 2016;10:53 Authors: Das S, Glatard T, Rogers C, Saigle J, Paiva S, MacIntyre L, Safi-Harab M, Rousseau ME, Stirling J, Khalili-Mahani N, MacFarlane D, Kostopoulos P, Rioux P, Ma...

Article GUID: 28111547
Best practices in data analysis and sharing in neuroimaging using MRI.

Author(s): Nichols TE, Das S, Eickhoff SB, Evans AC, Glatard T, Hanke M, Kriegeskorte N, Milham MP, Poldrack RA, Poline JB, Proal E, Thirion B, Van Ess...

Nat Neurosci. 2017 Feb 23;20(3):299-303 Authors: Nichols TE, Das S, Eickhoff SB, Evans AC, Glatard T, Hanke M, Kriegeskorte N, Milham MP, Poldrack RA, Poline JB, Proal E, Thirion B, Van Essen DC, ...

Article GUID: 28230846
Boutiques: a flexible framework to integrate command-line applications in computing platforms.

Author(s): Glatard T, Kiar G, Aumentado-Armstrong T, Beck N, Bellec P, Bernard R, Bonnet A, Brown ST, Camarasu-Pop S, Cervenansky F, Das S, Ferreira da...

Gigascience. 2018 05 01;7(5): Authors: Glatard T, Kiar G, Aumentado-Armstrong T, Beck N, Bellec P, Bernard R, Bonnet A, Brown ST, Camarasu-Pop S, Cervenansky F, Das S, Ferreira da Silva R, Flandin...

Article GUID: 29718199
A Serverless Tool for Platform Agnostic Computational Experiment Management.

Author(s): Kiar G, Brown ST, Glatard T, Evans AC

Front Neuroinform. 2019;13:12 Authors: Kiar G, Brown ST, Glatard T, Evans AC

Article GUID: 30890927
Biomarkers, designs, and interpretations of resting-state fMRI in translational pharmacological research: A review of state-of-the-Art, challenges, and opportunities for studying brain chemistry.

Author(s): Khalili-Mahani N, Rombouts SA, van Osch MJ, Duff EP, Carbonell F, Nickerson LD, Becerra L, Dahan A, Evans AC, Soucy JP, Wise R, Zijdenbos AP...

Hum Brain Mapp. 2017 04;38(4):2276-2325 Authors: Khalili-Mahani N, Rombouts SA, van Osch MJ, Duff EP, Carbonell F, Nickerson LD, Becerra L, Dahan A, Evans AC, Soucy JP, Wise R, Zijdenbos AP, van G...

Article GUID: 28145075
Title:Boutiques: a flexible framework to integrate command-line applications in computing platforms.
Authors:Glatard T,  Kiar G,  Aumentado-Armstrong T,  Beck N,  Bellec P,  Bernard R,  Bonnet A,  Brown ST,  Camarasu-Pop S,  Cervenansky F,  Das S,  Ferreira da Silva R,  Flandin G,  Girard P,  Gorgolewski KJ,  Guttmann CRG,  Hayot-Sasson V,  Quirion PO,  Rioux P,  Rousseau MÉ,  Evans AC
Link:https://www.ncbi.nlm.nih.gov/pubmed/29718199?dopt=Abstract
Category:Gigascience
PMID:29718199
Dept Affiliation: ENCS
1 Department of Computer Science and Software Engineering, Concordia University, Montreal, Canada.
2 McGill University, Montreal, Canada.
3 Montreal Neurological Institute, Montreal, Canada.
4 Centre de Recherche de l'Institut de Gériatrie de Montréal CRIUGM, Montréal, QC, Canada.
5 University of Lyon, CNRS, INSERM, CREATIS, Villeurbanne, France.
6 University of Southern California, Information Sciences Institute, Marina del Rey, CA, USA.
7 Wellcome Trust Centre for Neuroimaging, London, UK.
8 Department of Psychology, Stanford University, Stanford, California, USA.
9 Center for Neurological Imaging, Department of Radiology, Brigham and Women's Hospital,, Boston, Massachusetts, USA.
10 Compute Canada, 155 University Ave, Suite 302, Toronto, ON M5H 3B7, Canada.

Description:

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

Gigascience. 2018 05 01;7(5):

Authors: Glatard T, Kiar G, Aumentado-Armstrong T, Beck N, Bellec P, Bernard R, Bonnet A, Brown ST, Camarasu-Pop S, Cervenansky F, Das S, Ferreira da Silva R, Flandin G, Girard P, Gorgolewski KJ, Guttmann CRG, Hayot-Sasson V, Quirion PO, Rioux P, Rousseau MÉ, Evans AC

Abstract

We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.

PMID: 29718199 [PubMed - indexed for MEDLINE]