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Reproducible

Reproducibility and Open Science Working Group

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[Overview and index]

Guidelines for Reproducible and Open Science

Moore/Sloan Data Science Environment

More links: http://uwescience.github.io/reproducible/

Under construction: Most of the pages linked below don’t have much content yet.

Our working definition for reproducible research is that a research result can be replicated by another investigator. Our focus is data science and the reproducibility of computational studies and/or analysis of digital data.

This note summarizes best practices to facilitate reproducible research in data science (and computational science more generally). It is expected that all research conducted with funding from the DSE will be performed in accordance with these guidelines to the extent possible.

See Goals for a discussion of the goals and benefits of adopting these guidelines.

Version control

Use version control for all code and documents describing software, workflow, data provenance, etc. Get in the habit of doing this for all projects, whether or not you intend to eventually share it with others.

Git is the recommended version control system. Back up your repositories by maintaining clones on other computers or in the cloud. Using Github is recommended since it greatly facilitates collaboration and eventual sharing. See Git for more details.

Replicable computations

Use scripts rather than GUIs with data analysis or visualization tools in order in insure that you can reproduce the results. Keep the scripts under version control.

When appropriate, use notebook environments as an easy way to capture and replicate the sequence of instructions (interspersed with documentation and commentary) that led to a result. Suggested tools include IPython notebooks, Sage Worksheets, RStudio (all open source), or Mathematica, Maple, Matlab Publish. See Notebooks for more details.

More generally, document your code so that you can decipher it later and others can understand what you have done. Use literate programming tools to facilitate this when possible. Some examples include doxygen, CWEB, Sphinx. See Code for more details.

When suitable, use workflow management systems to track a series of experiments performed, versions of code used, data provenance, etc. Suggested tools include VisTrails, Taverna, Galaxy. See Workflow for more details.

Data and code provenance, sharing and archiving

Data used in publications (and associated metadata) should be available to readers of the publication - subject of course to privacy requirements or related issues, but sharing should be the default. Data should be deposited in archives that are appropriate for the discipline, data size, and the nature of access. Ensure that your code and data can be properly cited. Many repositories issue a DOI, for example. See Repositories for more details.

Metadata and provenance of data (e.g. original source, date acquired, etc.) should be recorded and archived with the data. See Data for more details.

Code developed as part of the research (e.g. to illustrate a new algorithm or to perform data analysis) should be made available to readers.

Perform internal code reviews and replication studies within your research group to insure that you have archived and adequately documented all code and data needed to reproduce published results. See Code for more details.

Make it clear what the rules are for others to use your code or data, e.g. by attaching a suitable license to code. This increases the chances that others will build on it, and that you will get the proper credit. See Data or Code for more details.

Replicable environment

The computation environment should be documented with sufficient detail so that others can create an equivalent environment. It is preferred to use automated tools such as Vagrant for Virtual Machines or make for Unix.

Use virtualization when appropriate to archive the environment in which a code runs, e.g. VirtualBox (which is free) or VMWare, or machine images on cloud computing platforms such as AWS or Windows Azure.

See Virtualization for more details.

Other resources

See Resources for more discussion of these guidelines and links to other resources and tutorials.