Automated Capture of Experiment Context for Easier Reproducibility in Computational Research

被引：62

作者：

Davison, Andrew P. ^{[1
]}

机构：

[1] Ctr Natl Rech Sci, Unite Neurosci Informat & Complexite, Neuroinformat Grp, Orsay, France

来源：

COMPUTING IN SCIENCE & ENGINEERING | 2012年 / 14卷 / 04期

关键词：

reliability; reusable libraries; reusable software; scientific computing; software/program verification;

D O I：

10.1109/MCSE.2012.41

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

Published scientific research that relies on numerical computations is too often not reproducible. For computational research to become consistently and reliably reproducible, the process must become easier to achieve, as part of day-to-day research. A combination of best practices and automated tools can make it easier to create reproducible research.

引用

页码：48 / 56

页数：9

共 10 条

[1]

[Anonymous], 2009, P EV METH MACH LEARN

[2] Paper Mache: Creating Dynamic Reproducible Science [J].

Brammer, Grant R. ;

Crosby, Ralph W. ;

Matthews, Suzanne J. ;

Williams, Tiffani L. .

PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE (ICCS), 2011, 4 :658-667

[3] Simulation of networks of spiking neurons:: A review of tools and strategies [J].

Brette, Romain ;

Rudolph, Michelle ;

Carnevale, Ted ;

Hines, Michael ;

Beeman, David ;

Bower, James M. ;

Diesmann, Markus ;

Morrison, Abigail ;

Goodman, Philip H. ;

Harris, Frederick C., Jr. ;

Zirpe, Milind ;

Natschlaeger, Thomas ;

Pecevski, Dejan ;

Ermentrout, Bard ;

Djurfeldt, Mikael ;

Lansner, Anders ;

Rochel, Olivier ;

Vieville, Thierry ;

Muller, Eilif ;

Davison, Andrew P. ;

El Boustani, Sami ;

Destexhe, Alain .

JOURNAL OF COMPUTATIONAL NEUROSCIENCE, 2007, 23 (03) :349-398

[4]

Crook S., 20 YEARS CO IN PRESS

[5]

Guo P.J., 2011, P 2011 US ANN TECHN

[6] The systems biology markup language (SBML):: a medium for representation and exchange of biochemical network models [J].

Hucka, M ;

Finney, A ;

Sauro, HM ;

Bolouri, H ;

Doyle, JC ;

Kitano, H ;

Arkin, AP ;

Bornstein, BJ ;

Bray, D ;

Cornish-Bowden, A ;

Cuellar, AA ;

Dronov, S ;

Gilles, ED ;

Ginkel, M ;

Gor, V ;

Goryanin, II ;

Hedley, WJ ;

Hodgman, TC ;

Hofmeyr, JH ;

Hunter, PJ ;

Juty, NS ;

Kasberger, JL ;

Kremling, A ;

Kummer, U ;

Le Novère, N ;

Loew, LM ;

Lucio, D ;

Mendes, P ;

Minch, E ;

Mjolsness, ED ;

Nakayama, Y ;

Nelson, MR ;

Nielsen, PF ;

Sakurada, T ;

Schaff, JC ;

Shapiro, BE ;

Shimizu, TS ;

Spence, HD ;

Stelling, J ;

Takahashi, K ;

Tomita, M ;

Wagner, J ;

Wang, J .

BIOINFORMATICS, 2003, 19 (04) :524-531

[7]

Koop D, 2010, LECT NOTES COMPUT SC, V6187, P397, DOI 10.1007/978-3-642-13818-8_28

[8]

McConnell S., 2004, Code complete, V2nd

[9] The Collage Authoring Environment [J].

Nowakowski, Piotr ;

Ciepiela, Eryk ;

Harezlak, Daniel ;

Kocot, Joanna ;

Kasztelnik, Marek ;

Bartynski, Tomasz ;

Meizner, Jan ;

Dyk, Grzegorz ;

Malawski, Maciej .

PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE (ICCS), 2011, 4 :608-617

[10] SHARE: a web portal for creating and sharing executable research papers [J].

Van Gorp, Pieter ;

Mazanek, Steffen .

PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE (ICCS), 2011, 4 :589-597

← 1 →