Dunedin

5 -7 July, 2021

Scroll down for details and registration.

Install instructions for each of the workshop sessions can be found HERE

Venue

This is an in-person event. The workshops will be held in either rm1.17 or rm1.19 of the Otago Business School (aka Commerce Building), University of Otago.

Timetable

The timetable is shown below

Workshop sessions are designed to be tasters for the topics rather than comprehensive lessons. A laptop will be required to fully participate in most workshop sessions.

Skill level description:
In order to convey the skill level of a particular workshop the following terms are used to describe the assumed levels of prior knowledge or experience.

Beginner: Someone new to the topic with minimal prior knowledge of the workshop topic beyond the stated pre-requisites

Post-beginner: Greater expectation of prior knowledge or experience beyond the direct topic being covered in the workshop

In general, the "Entry" stream is recommended for beginners, and the "Other" stream recommended for previous ResBaz or Carpentries workshop attendees.

Monday 5th July

Birds of a Feather (BoF): R users - meet over lunch with other people using R

Click on workshop names to expand the description

Entry Stream:

This workshop will provide an overview of how to get started working with R. This will be done by providing a explaination of the RStudio environment and and introduction to the R programming language syntax.

Targeted skill level: beginner

Software required: R and RStudio

This workshop will introduce how to get started with data in R using the dplyr and tidyr packages for R which are useful for data manipulation and tidying.

Targeted skill level: beginner

Software required: R and RStudio

This workshop will introduce how to make plots using the ggplot2 package in R for visualising data.

Targeted skill level: beginner

Software required: R and RStudio

Other Stream:

This workshop will extend your understanding of R and cover how to interact with non-data.frame structured data such as vectors, matrices and lists. We'll also look at creating your own functions and loops.

Targeted skill level: post-beginner

Software required: R and RStudio

Take the time to explore the lesser known functions and packages of the Tidyverse. Learn about how to access googlesheets, use times/dates, manipulate text, use functional programming to replace loops, and more.

Targeted skill level: post-beginner

Software required: R and RStudio

This workshop will introduce you to the power of regular expressions - a way of searching using patterns. We'll cover how to use patterns to find files, and things in files.

Targeted skill level: beginner

Software required: Web browser or UNIX shell

Tuesday 6th July

Birds of a Feather (BoF): Subject Areas - meet over lunch with other people in a similar research subject area

Click on workshop names to expand the description

Entry level:

This session will cover using OpenRefine for cleaning and tidying data. By the end of the session attendees should expect to:
  • Load data into OpenRefine
  • perform basic data cleaning operations
  • Export data from OpenRefine
This session would be useful for people who:
  • clean and organise data
  • want to apply the same data cleaning operation to multiple datasets

Targeted skill level: beginner

Software required: OpenRefine

This workshop will provide a 'good-enough' practices overview for how to go about setting up and working on a project using reproducible research principles.

Targeted skill level: beginner

Software required: Text editor e.g. notepad or textedit

This session will provide you with advice and skills on how to start tackling error messages and where to look for help.

Targeted skill level: beginner

Software required: none - but R and RStudio would be uesful

Other Stream:

This workshop will introduce you to the world of using creating simple websites using the markdown language. A it will involve a pratical application of version control principles which can be applied to other code as well.

  • Creating up a github account
  • Creating a repository
  • Introduction to markdown syntax for formatting
  • Creating a simple webpage with markdown
  • Modifying pages and tracking changes
  • How to use Github for collaboration

Targeted skill level: all

Software required: web-browser

This workshop will introduce you to workflow language systems that are used for creating reproducible research workflows. This workshop will use Snakemake as the example

Targeted skill level: post-beginner

Software required: to be announced

 This presentation will cover general best-practice principles of management, storage and sharing of research data. It will include practical tips for improving data management practices that can be implemented immediately regardless of the type of data. By attending students will feel better prepared to respond to university, employer, funder and/or publisher data requirements.

Targeted skill level: all

Software required: none

Wednesday 7th July

Click on workshop names to expand the description

Entry level:

The power of the unix shell comes from it's reproducibility and ability to automate and scale tasks. This is an introductory session to the unix commandline. By the end of this session participants can expect to:
  • open the commandline
  • understand how to navigate and create files and directories
  • run commandline programs
Useful for:
  • task automation

Targeted skill level: beginner

Software required: MacOS/Linux - Terminal (comes pre-installed). Windows - GitBash

This session will cover useful code snippets that are designed to improve your overall experience doing computational research. This will include how to customise your BASH and R environments, useful keyboard short cuts, and short pieces of code to do common tasks e.g. read a directory of files into R.

Targeted skill level: beginner

Software required: none - useful:R and RStudio, and UNIX shell

Other Stream:

This introductory session will cover creating a reproducible workflow environment using docker images.
  • obtain a pre-built docker image
  • create a dockerfile to create a custom contatiner
  • access the docker container and run a command
  • share data between the host and the container
pre-requisites: Introduction to unix shell or equivalent

Targeted skill level: post-beginner

Software required: Docker

Link to the lesson materials

This workshop will introduce text analysis in R. This will touch on sentiment analysis, word frequencies, and more.

Targeted skill level: post-beginner

Software required: R and RStudio

Install instructions for each of the workshop sessions can be found HERE

Speakers

Dr. Nick Mortimer (GNS). Seeing the big picture: the discovery of Te Riu-a-Māui / Zealandia, Earth’s 8th continent.

Dr. Eddy Dowle (Department of Anatomy). Genome-wide variation and transcriptional changes in diverse developmental processes underly the rapid evolution of seasonality in a temperate fly.

Claire Grant (Genomics Aotearoa). Science Communication

Assoc. Prof David Orlovich (Department of Botany)

Registration Instructions

Open to University of Otago students and staff. This is an in-person event.

Select the appropriate ticket(s)

  • general admission if you want to attend the talks and have food provided*
  • workshop - if you wish to attend one or more workshops

If you have selected a workshop ticket:

  • Select no more than one workshop per session
  • If you are a beginner/novice it is recommended to choose from the Entry stream.

Registration has closed.

Any questions please email carpentries@otago.ac.nz

*Note that during the registration process you will be asked about your food preferences. We are hoping to be able to provide lunch for attendees, but this request is still going through the University's approval process, so we are not yet sure about our ability to cater this event. This will be confirmed with attendees before the event.

Contact