National Centre for Biosecurity and Infectious Disease

Oct 4th & 8th, 2019

9:00 am - 4:30 pm

Instructors: Ben Waite, Joep de Ligt, David Eccles

Helpers: Alessandra Santana

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 66 Ward St, Wallaceville, Upper Hutt 5018. Get directions with OpenStreetMap or Google Maps.

When: Oct 4th & 8th, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. During the ESR workshops, participants will be provided with laptops to use that contain software pre-installed. They should have a few specific software packages installed (listed below).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email ben.waite@esr.cri.nz or Joep.DeLigt@esr.cri.nz for more information.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Syllabus


Setup

To participate in a Data Carpentry workshop, you will need access to the software described below. During the ESR workshops, participants will be provided with laptops to use that contain this software pre-installed. Setup for personal/home use of the software is described below.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.

Visit SqliteBrowser and download and install it. Version 3.11.0 or greater.

Visit SqliteBrowser and download and install it. Version 3.11.0 or greater.

Visit SqliteBrowser and download and install it. Version 3.11.0 or greater.