scholarly journals Facilitating reproducible research through direct connection of data analysis with manuscript preparation: StatTag for connecting statistical software to Microsoft Word

JAMIA Open ◽  
2020 ◽  
Vol 3 (3) ◽  
pp. 342-358
Author(s):  
Leah J Welty ◽  
Luke V Rasmussen ◽  
Abigail S Baldridge ◽  
Eric W Whitley
Keyword(s):  
Open Source Software ◽  
Software Tool ◽  
Reproducible Research ◽  
Manuscript Preparation ◽  
Multidisciplinary Research ◽  
Research Teams ◽  
Free Open Source Software ◽  
Microsoft Word ◽  
Statistical Program ◽  
Free Open Source

Abstract Objectives To enhance reproducible research by creating a broadly accessible, free, open-source software tool for connecting Microsoft Word to statistical programs (R/R Markdown, Python, SAS, Stata) so that results may be automatically updated in a manuscript. Materials and Methods We developed StatTag for Windows as a Microsoft Word plug-in using C# and for macOS as a native application using Objective-C. Source code is available under the MIT license at https://github.com/stattag. Results StatTag links analysis file(s) (R/R Markdown, SAS, Stata, or Python) and a Word document, invokes the statistical program(s) to obtain results, and embeds selected output in the document. StatTag can accommodate multiple statistical programs with a single document and features an interface to view, edit, and rerun statistical code directly from Word. Discussion and Conclusion StatTag may facilitate reproducibility within increasingly multidisciplinary research teams, improve research transparency through review and publication, and complement data-sharing initiatives.

scholarly journals Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks

2016 ◽  
Vol 116 (2) ◽  
pp. 252-262 ◽  
Author(s):  
David M. Rosenberg ◽  
Charles C. Horn
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Present Report ◽  
Reproducible Research ◽  
Statistical Validation ◽  
Team Members ◽  
Free Open Source Software ◽  
Electrophysiological Recordings ◽  
Compound Action Potentials ◽  
Free Open Source

Neurophysiology requires an extensive workflow of information analysis routines, which often includes incompatible proprietary software, introducing limitations based on financial costs, transfer of data between platforms, and the ability to share. An ecosystem of free open-source software exists to fill these gaps, including thousands of analysis and plotting packages written in Python and R, which can be implemented in a sharable and reproducible format, such as the Jupyter electronic notebook. This tool chain can largely replace current routines by importing data, producing analyses, and generating publication-quality graphics. An electronic notebook like Jupyter allows these analyses, along with documentation of procedures, to display locally or remotely in an internet browser, which can be saved as an HTML, PDF, or other file format for sharing with team members and the scientific community. The present report illustrates these methods using data from electrophysiological recordings of the musk shrew vagus—a model system to investigate gut-brain communication, for example, in cancer chemotherapy-induced emesis. We show methods for spike sorting (including statistical validation), spike train analysis, and analysis of compound action potentials in notebooks. Raw data and code are available from notebooks in data supplements or from an executable online version, which replicates all analyses without installing software—an implementation of reproducible research. This demonstrates the promise of combining disparate analyses into one platform, along with the ease of sharing this work. In an age of diverse, high-throughput computational workflows, this methodology can increase efficiency, transparency, and the collaborative potential of neurophysiological research.

scholarly journals Boiler: Lossy compression of RNA-seq alignments using coverage vectors

2016 ◽  
Author(s):  
Jacob Pritt ◽  
Ben Langmead
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Negative Impact ◽  
Software Tool ◽  
Lossy Compression ◽  
Rna Seq ◽  
Empirical Distributions ◽  
Free Open Source Software ◽  
Link Type ◽  
Free Open Source

AbstractWe describe Boiler, a new software tool for compressing and querying large collections of RNA-seq alignments. Boiler discards most per-read data, keeping only a genomic coverage vector plus a few empirical distributions summarizing the alignments. Since most per-read data is discarded, storage footprint is often much smaller than that achieved by other compression tools. Despite this, the most relevant per-read data can be recovered; we show that Boiler compression has only a slight negative impact on results given by downstream tools for isoform assembly and quantification. Boiler also allows the user to pose fast and useful queries without decompressing the entire file. Boiler is free open source software available from github.com/jpritt/boiler.

scholarly journals SENTIMENT ANALYSIS OF FREE/OPEN SOURCE DEVELOPERS: PRELIMINARY FINDINGS FROM A CASE STUDY

2014 ◽  
Vol 13 (2) ◽  
Author(s):  
Athanasios-Ilias Rousinopoulos ◽  
Gregorio Robles ◽  
Jesús M. González-Barahona
Keyword(s):  
Sentiment Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Free Open Source Software ◽  
Free Open Source

O desenvolvimento de software é uma atividade intensive em esforço humano. Assim, a forma como os desenvolvedores encaram suas tarefas é de suam importância. Em um ambiente como o usual em projetos de FOSS (free/open source software) em que profissionais (desenvolvedores pagos) compartilham os esforços de desenvolvimento com voluntários, a moral da comunidade de desenvolvedores e usuários é fundamental. Neste artigo, apresentamos uma análise preliminary utilizando técnicas de análise de sentimentos realizada em um projeto de FOSS. Para isso, executamos a mineração da lista de endereços eletrônicos de um projeto e aplicamos as técnicas propostas aos participantes mais relevantes. Embora a aplicação seja limitada, no momento atual, experamos que essa experiência possa ser benéfica no future para determiner situações que possam afetar os desenvolvedores ou o projeto, tais como baixa produtividade, abandono do projeto ou bifurcação do projeto, entre outras.

scholarly journals CACTI: Free, Open-Source Software for the Sequential Coding of Behavioral Interactions

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e39740 ◽  
Author(s):  
Lisa H. Glynn ◽  
Kevin A. Hallgren ◽  
Jon M. Houck ◽  
Theresa B. Moyers
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Behavioral Interactions ◽  
Free Open Source Software ◽  
Free Open Source
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