Making neurophysiological data analysis reproducible: Why and how?

Abstract

Reproducible data analysis is an approach aiming at complementing classical printed scientific articles with everything required to independently reproduce the results they present. "Everything" covers here: the data, the computer codes and a precise description of how the code was applied to the data. A brief history of this approach is presented first, starting with what economists have been calling replication since the early eighties to end with what is now called reproducible research in computational data analysis oriented fields like statistics and signal processing. Since efficient tools are instrumental for a routine implementation of these approaches, a description of some of the available ones is presented next. A toy example demonstrates then the use of two open source software programs for reproducible data analysis: the "Sweave family" and the org-mode of emacs. The former is bound to R while the latter can be used with R, Matlab, Python and many more "generalist" data processing software. Both solutions can be used with Unix-like, Windows and Mac families of operating systems. It is argued that neuroscientists could communicate much more efficiently their results by adopting the reproducible research paradigm from their lab books all the way to their articles, thesis and books.

Jug: Software for Parallel Reproducible Computation in Python

“…For example, a first Jugfile might perform all heavy-duty computation and be run on a computing cluster. A second script could be embedded inside an executable paper to generate tables and plots [16]. This faster script could be run as part of building the paper.…”

Computational reproducibility in archaeological research: Basic principles and a case study of their implementation

“…This practice of having documentation and code in a single interwoven source document is known as literate programming (Knuth, 1984). This is a focus of many efforts to improve the reproducibility of research, for example, by computer scientists and neuroscientists (Abari, 2012;Delescluse, Franconville, Joucla, Lieury, & Pouzat, 2012;Schulte, Davison, Dye, & Dominik, 2012;Stanisic, Legrand, & Danjean, 2015), but is not a mainstream practice in any field.…”

Modelo LaTeX para teses e dissertações em Programa de Pós-Graduação: construção e avaliação de artefato

“…O LaTeX adota o paradigma Typesetting System, que não é intuitivo e atrativo, pois é representado através de linhas de comando com sintaxe própria que deve ser conhecida do usuário (Delescluse, Franconville, Joucla, Lieury, & Pouzat, 2012;Kottwitz, 2011). Para efeito de comparação, uma linguagem parecida à do LaTeX é a HyperText Markup Language (HTML), que é uma linguagem de marcação que se tornou mundialmente utilizada a partir da década de 1990, com o advento da rede mundial de computadores.…”

“…Essa postura, favorece a concentração do autor em sua pesquisa. Assim sendo, a apresentação visual do documento Modelo LaTeX para teses e dissertações em Programa de Pós-Graduação 86 reflete a estrutura lógica, ou seja, o raciocínio empregado e não o contrário (Delescluse et al, 2012;Kottwitz, 2011 Para se trabalhar com o programa, existem diversas plataformas conhecidas por Integrated Development Environment (IDE). Entre as mais usadas está a IDE TexStudio 4 , que se destaca pela gratuidade e facilidade de operação.…”

“…A ênfase no conteúdo lógico é um dos pontos fortes do LaTeX apontados pela literatura (Delescluse et al, 2012;Kottwitz, 2011;Lamport, 1994). As respostas (Tabela 4) indicam que esse fato vai contra a tendência do uso de ferramentas convencionais com ênfase em conteúdo visual.…”