Summary and Setup

Academic libraries are relied upon to provide essential skills for quantitative researchers. Librarians are increasingly seeking out conceptual understanding of open and reproducible research best practices. But not all librarian skills necessarily overlap with skills needed by the dedicated researchers they support. Librarians can massively benefit from gaining firsthand experience with certain new skills and best practices that researchers may turn to them to learn about. Firsthand experience can create a paradigm shift for librarians, enabling them to “speak from experience” when supporting researchers, and staging librarians for further acquisition of key researcher skills.

This lesson builds upon the conceptual framework of Reproducible Research Workflows, which provides librarians with an understanding of reproducible research and its critical role in open science. This sequel will engage librarians inspired by an enhanced understanding of reproducibility who are eager to personally experience a reproducible research workflow.

Learning Objectives

After following this lesson, learners will be able to:

  • explain the concept of cloud computing
  • describe three benefits of cloud computing in open and reproducible research
  • list at least three parameters that one may need to choose when creating an instance of a cloud computer
  • identify resources typically needed to utilize cloud computing
  • identify advantages and disadvantages of cloud computing versus local computing when presented with various researcher scenarios
  • log in to a remote computer using ssh
  • execute basic shell navigation commands such as cd, ls, cp, rm.
  • describe a command shell and its uses
  • log in to RStudio server running on a remote computer, via web browser
  • Download open data from a public URL using {R code or wget/curl - TBD}
  • Use scp to transfer a set of files from a local computer to a remote computer
  • clone a public github repository onto a remote computer
  • Run R code to analyze data, within a remote RStudio server session
  • Use scp to transfer files containing program results from a remote computer to a local computer
  • describe essential skills for librarians to help researchers plan reproducible research
  • identify opportunities for librarians to personally gain further experience with and employ skills for open and reproducible research

FIXME: Setup instructions live in this document. Please specify the tools and the data sets the Learner needs to have installed.

Data Sets

Download the data zip file and unzip it to your Desktop

Software Setup

Details

Setup for different systems can be presented in dropdown menus via a spoiler tag. They will join to this discussion block, so you can give a general overview of the software used in this lesson here and fill out the individual operating systems (and potentially add more, e.g. online setup) in the solutions blocks.

Use PuTTY

Use Terminal.app

Use Terminal