OpenAccessBelV2, Main, Curation, bibRecord, 000268

A framework for streamlining research workflow in neuroscience and psychology

Identifieur interne : 000268 ( Main/Curation ); précédent : 000267; suivant : 000269

A framework for streamlining research workflow in neuroscience and psychology

Source :

Frontiers in Neuroinformatics [ 1662-5196 ] ; 2014.

RBID : PMC:3894454

Abstract

Successful accumulation of knowledge is critically dependent on the ability to verify and replicate every part of scientific conduct. However, such principles are difficult to enact when researchers continue to resort on ad-hoc workflows and with poorly maintained code base. In this paper I examine the needs of neuroscience and psychology community, and introduce psychopy_ext, a unifying framework that seamlessly integrates popular experiment building, analysis and manuscript preparation tools by choosing reasonable defaults and implementing relatively rigid patterns of workflow. This structure allows for automation of multiple tasks, such as generated user interfaces, unit testing, control analyses of stimuli, single-command access to descriptive statistics, and publication quality plotting. Taken together, psychopy_ext opens an exciting possibility for a faster, more robust code development and collaboration for researchers.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894454

DOI: 10.3389/fninf.2013.00052
PubMed: 24478691
PubMed Central: 3894454

Links toward previous steps (curation, corpus...)

to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000465
to stream Pmc, to step Curation: Pour aller vers cette notice dans l'étape Curation :000465
to stream Pmc, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000230
to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :000220
to stream Ncbi, to step Curation: Pour aller vers cette notice dans l'étape Curation :000220
to stream Ncbi, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000220
to stream Main, to step Merge: Pour aller vers cette notice dans l'étape Curation :000268

Links to Exploration step

PMC:3894454

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A framework for streamlining research workflow in neuroscience and psychology</title>
<author><name sortKey="Kubilius, Jonas" sort="Kubilius, Jonas" uniqKey="Kubilius J" first="Jonas" last="Kubilius">Jonas Kubilius</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">24478691</idno>
<idno type="pmc">3894454</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894454</idno>
<idno type="RBID">PMC:3894454</idno>
<idno type="doi">10.3389/fninf.2013.00052</idno>
<date when="2014">2014</date>
<idno type="wicri:Area/Pmc/Corpus">000465</idno>
<idno type="wicri:Area/Pmc/Curation">000465</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000230</idno>
<idno type="wicri:Area/Ncbi/Merge">000220</idno>
<idno type="wicri:Area/Ncbi/Curation">000220</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000220</idno>
<idno type="wicri:Area/Main/Merge">000268</idno>
<idno type="wicri:Area/Main/Curation">000268</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A framework for streamlining research workflow in neuroscience and psychology</title>
<author><name sortKey="Kubilius, Jonas" sort="Kubilius, Jonas" uniqKey="Kubilius J" first="Jonas" last="Kubilius">Jonas Kubilius</name>
</author>
</analytic>
<series><title level="j">Frontiers in Neuroinformatics</title>
<idno type="eISSN">1662-5196</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Successful accumulation of knowledge is critically dependent on the ability to verify and replicate every part of scientific conduct. However, such principles are difficult to enact when researchers continue to resort on <italic>ad-hoc</italic>
 workflows and with poorly maintained code base. In this paper I examine the needs of neuroscience and psychology community, and introduce <italic>psychopy_ext</italic>
, a unifying framework that seamlessly integrates popular experiment building, analysis and manuscript preparation tools by choosing reasonable defaults and implementing relatively rigid patterns of workflow. This structure allows for automation of multiple tasks, such as generated user interfaces, unit testing, control analyses of stimuli, single-command access to descriptive statistics, and publication quality plotting. Taken together, <italic>psychopy_ext</italic>
 opens an exciting possibility for a faster, more robust code development and collaboration for researchers.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ashburner, J" uniqKey="Ashburner J">J. Ashburner</name>
</author>
<author><name sortKey="Friston, K J" uniqKey="Friston K">K. J. Friston</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Barnes, N" uniqKey="Barnes N">N. Barnes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cox, R W" uniqKey="Cox R">R. W. Cox</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Davison, A" uniqKey="Davison A">A. Davison</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gorgolewski, K" uniqKey="Gorgolewski K">K. Gorgolewski</name>
</author>
<author><name sortKey="Madison, C" uniqKey="Madison C">C. Madison</name>
</author>
<author><name sortKey="Clark, D" uniqKey="Clark D">D. Clark</name>
</author>
<author><name sortKey="Halchenko, Y O" uniqKey="Halchenko Y">Y. O. Halchenko</name>
</author>
<author><name sortKey="Waskom, M L" uniqKey="Waskom M">M. L. Waskom</name>
</author>
<author><name sortKey="Ghosh, S S" uniqKey="Ghosh S">S. S. Ghosh</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Halchenko, Y O" uniqKey="Halchenko Y">Y. O. Halchenko</name>
</author>
<author><name sortKey="Hanke, M" uniqKey="Hanke M">M. Hanke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hanke, M" uniqKey="Hanke M">M. Hanke</name>
</author>
<author><name sortKey="Halchenko, Y" uniqKey="Halchenko Y">Y. Halchenko</name>
</author>
<author><name sortKey="Sederberg, P" uniqKey="Sederberg P">P. Sederberg</name>
</author>
<author><name sortKey="Hanson, S" uniqKey="Hanson S">S. Hanson</name>
</author>
<author><name sortKey="Haxby, J" uniqKey="Haxby J">J. Haxby</name>
</author>
<author><name sortKey="Pollmann, S" uniqKey="Pollmann S">S. Pollmann</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ince, D C" uniqKey="Ince D">D. C. Ince</name>
</author>
<author><name sortKey="Hatton, L" uniqKey="Hatton L">L. Hatton</name>
</author>
<author><name sortKey="Graham Cumming, J" uniqKey="Graham Cumming J">J. Graham-Cumming</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Joppa, L N" uniqKey="Joppa L">L. N. Joppa</name>
</author>
<author><name sortKey="Mcinerny, G" uniqKey="Mcinerny G">G. McInerny</name>
</author>
<author><name sortKey="Harper, R" uniqKey="Harper R">R. Harper</name>
</author>
<author><name sortKey="Salido, L" uniqKey="Salido L">L. Salido</name>
</author>
<author><name sortKey="Takeda, K" uniqKey="Takeda K">K. Takeda</name>
</author>
<author><name sortKey="O Hara, K" uniqKey="O Hara K">K. O'Hara</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kampstra, P" uniqKey="Kampstra P">P. Kampstra</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kubilius, J" uniqKey="Kubilius J">J. Kubilius</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kubilius, J" uniqKey="Kubilius J">J. Kubilius</name>
</author>
<author><name sortKey="Wagemans, J" uniqKey="Wagemans J">J. Wagemans</name>
</author>
<author><name sortKey="Op De Beeck, H P" uniqKey="Op De Beeck H">H. P. Op de Beeck</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lades, M" uniqKey="Lades M">M. Lades</name>
</author>
<author><name sortKey="Vorbruggen, J C" uniqKey="Vorbruggen J">J. C. Vorbruggen</name>
</author>
<author><name sortKey="Buhmann, J" uniqKey="Buhmann J">J. Buhmann</name>
</author>
<author><name sortKey="Lange, J" uniqKey="Lange J">J. Lange</name>
</author>
<author><name sortKey="Von Der Malsburg, C" uniqKey="Von Der Malsburg C">C. von der Malsburg</name>
</author>
<author><name sortKey="Wurtz, R P" uniqKey="Wurtz R">R. P. Wurtz</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Op De Beeck, H" uniqKey="Op De Beeck H">H. Op de Beeck</name>
</author>
<author><name sortKey="Wagemans, J" uniqKey="Wagemans J">J. Wagemans</name>
</author>
<author><name sortKey="Vogels, R" uniqKey="Vogels R">R. Vogels</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pedregosa, F" uniqKey="Pedregosa F">F. Pedregosa</name>
</author>
<author><name sortKey="Varoquaux, G" uniqKey="Varoquaux G">G. Varoquaux</name>
</author>
<author><name sortKey="Gramfort, A" uniqKey="Gramfort A">A. Gramfort</name>
</author>
<author><name sortKey="Michel, V" uniqKey="Michel V">V. Michel</name>
</author>
<author><name sortKey="Thirion, B" uniqKey="Thirion B">B. Thirion</name>
</author>
<author><name sortKey="Grisel, O" uniqKey="Grisel O">O. Grisel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Peirce, J W" uniqKey="Peirce J">J. W. Peirce</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Peirce, J W" uniqKey="Peirce J">J. W. Peirce</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Perez, F" uniqKey="Perez F">F. Perez</name>
</author>
<author><name sortKey="Granger, B E" uniqKey="Granger B">B. E. Granger</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Riesenhuber, M" uniqKey="Riesenhuber M">M. Riesenhuber</name>
</author>
<author><name sortKey="Poggio, T" uniqKey="Poggio T">T. Poggio</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stevens, J R" uniqKey="Stevens J">J. R. Stevens</name>
</author>
<author><name sortKey="Elver, M" uniqKey="Elver M">M. Elver</name>
</author>
<author><name sortKey="Bednar, J A" uniqKey="Bednar J">J. A. Bednar</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wallis, T S" uniqKey="Wallis T">T. S. Wallis</name>
</author>
<author><name sortKey="Taylor, C P" uniqKey="Taylor C">C. P. Taylor</name>
</author>
<author><name sortKey="Wallis, J" uniqKey="Wallis J">J. Wallis</name>
</author>
<author><name sortKey="Jackson, M L" uniqKey="Jackson M">M. L. Jackson</name>
</author>
<author><name sortKey="Bex, P J" uniqKey="Bex P">P. J. Bex</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="White, E P" uniqKey="White E">E. P. White</name>
</author>
<author><name sortKey="Baldridge, E" uniqKey="Baldridge E">E. Baldridge</name>
</author>
<author><name sortKey="Brym, Z T" uniqKey="Brym Z">Z. T. Brym</name>
</author>
<author><name sortKey="Locey, K J" uniqKey="Locey K">K. J. Locey</name>
</author>
<author><name sortKey="Mcglinn, D J" uniqKey="Mcglinn D">D. J. McGlinn</name>
</author>
<author><name sortKey="Supp, S R" uniqKey="Supp S">S. R. Supp</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wilson, G" uniqKey="Wilson G">G. Wilson</name>
</author>
<author><name sortKey="Aruliah, D A" uniqKey="Aruliah D">D. A. Aruliah</name>
</author>
<author><name sortKey="Brown, C T" uniqKey="Brown C">C. T. Brown</name>
</author>
<author><name sortKey="Hong, N P C" uniqKey="Hong N">N. P. C. Hong</name>
</author>
<author><name sortKey="Davis, M" uniqKey="Davis M">M. Davis</name>
</author>
<author><name sortKey="Guy, R T" uniqKey="Guy R">R. T. Guy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Xu, X" uniqKey="Xu X">X. Xu</name>
</author>
<author><name sortKey="Yue, X" uniqKey="Yue X">X. Yue</name>
</author>
<author><name sortKey="Lescroart, M D" uniqKey="Lescroart M">M. D. Lescroart</name>
</author>
<author><name sortKey="Biederman, I" uniqKey="Biederman I">I. Biederman</name>
</author>
<author><name sortKey="Kim, J G" uniqKey="Kim J">J. G. Kim</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Wicri/Belgique/explor/OpenAccessBelV2/Data/Main/Curation

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000268 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Curation/biblio.hfd -nk 000268 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Wicri/Belgique
   |area=    OpenAccessBelV2
   |flux=    Main
   |étape=   Curation
   |type=    RBID
   |clé=     PMC:3894454
   |texte=   A framework for streamlining research workflow in neuroscience and psychology
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Curation/RBID.i   -Sk "pubmed:24478691" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Curation/biblio.hfd   \
       | NlmPubMed2Wicri -a OpenAccessBelV2

This area was generated with Dilib version V0.6.25.
Data generation: Thu Dec 1 00:43:49 2016. Site generation: Wed Mar 6 14:51:30 2024

	Serveur d'exploration autour du libre accès en Belgique
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration autour du libre accès en Belgique

A framework for streamlining research workflow in neuroscience and psychology

A framework for streamlining research workflow in neuroscience and psychology

Source :

Abstract

Links toward previous steps (curation, corpus...)

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki