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Chapter 7 Glossary

7.1 Acronym

An acronym is a word or name formed as an abbreviation from the initial components of a phrase or a word. (Wikipedia)

7.2 Small research institute

Research institute with less than about 100 employees.

A detailed glossary covering the following topics is provided by
Rokem and Chirigati (2018) is used throughout the glossary.

7.3 Reproducibility

"… is a cornerstone of science. Definitions vary greatly across scientific disciplines, but the meaning that we find most prevalent is the ‘calculation of quantitative scientific results by independent scientists using the original datasets and methods’ (Stodden, Leisch, & Peng, 2014). The goals of reproducibility go beyond duplicating someone else’s investigation: it also entails having reproducibility for yourself, defeating self-deception in scientific results (Ioannidis, 2005; Nuzzo, 2015), and extending another researcher’s methods to build your own work. Reproducibility is a matter of degree, not of kind. We say that research is reproducible if reproducibility applies to the results to some extent. That is, some of the corresponding experiments and scientific methods are deemed to be reproducible.

— (Rokem and Chirigati 2018)

For more details see: Rokem and Chirigati (2018)

7.4 Provenance

“As the volume of digital data increases and the complexity of computational processes that manipulate these data grows, it is becoming increasingly important to manage their provenance. The Oxford English Dictionary defines provenance as the source or origin of an object; its history and pedigree; a record of the ultimate derivation and passage of an item through its various owners. Provenance helps determine the value, accuracy, and authorship of an object.”

— (Rokem and Chirigati 2018)

For more details see: Rokem and Chirigati (2018)

7.5 Techniques

• Version control

• Literate Programming

• Data Publication

• Data cleaning/munging

• Software Testing

• Continuous Integration

• Workflow Management

• File Format Standards

• Licensing

• Virtualization and Environment Isolation

For details see: Rokem and Chirigati (2018)

7.6 Tools

• Programming Language and Related Tools

• Documentation Generators

• Version Control

• Data Munging and Analysis

• Data Visualization

• Software Testing and Continuous Integration

• Virtualization and Environment Isolation

• Data Sharing and Repositories

• Document Authoring

• File Formats

For details see: Rokem and Chirigati (2018)

References

Rokem, Ariel, and Fernando Chirigati. 2018. “Glossary.” In The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences, edited by Justin Kitzes, Daniel Turek, and Fatma Deniz. Oakland, CA: University of California Press. https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html.