Preparing for the workshop

This course includes a series of hands-on computer exercises and you need to prepare by ensuring that you have access to the accounts and software that you will use. If you need help you can join the Pre-course Q&A session (see course schedule).

Accounts

Life Science ID

The Life Science Login enables researchers to use their home organisation credentials or community or other identities (e.g. Google, Linkedin) to sign in and access data and services they need.

Open the link https://signup.aai.lifescience-ri.eu/fed/registrar/?vo=lifescience

Choose your home organization, or if you cannot find it on the list, pick one of the supported commercial/community services, and log in with your credentials.

Fill in the registration form. Review and accept usage policy and click on Submit.

You will receive an email with a verification link. Click the link in the email to verify your email address.

(Optional) Learn more about Life Science login: https://lifescience-ri.eu/ls-login.html

SciLifeLab DSW account

SciLifeLab DSW is an online service for creating data management plans from questionnaires using the Data Stewardship Wizard (DSW) software tool.

Register by logging in using your Life Science IR (university): https://dsw.scilifelab.se/

(Optional) Learn more about SciLifeLab: https://www.scilifelab.se/

(Optional) Learn more about DSW: https://ds-wizard.org/

GitHub account

GitHub is a widely used cloud platform for hosting and sharing Git repositories for collaborative versioning. It offers a web interface and provides functionality and a mixture of both free and paid services for working with such repositories.

Register by creating a new account using your e-mail address: https://github.com/join

(Optional) Learn more about GitHub: https://www.nature.com/news/democratic-databases-science-on-github-1.20719

(Optional) Explore alternatives to GitHub: https://github.com/ianchanning/awesome-github-alternatives

Software

You might need to contact your local IT department, if you don’t have administrative rights on your laptop, and ask them to do the installation.

Firefox, Google Chrome or Safari

A browser that is compatible with the tools and services used in this workshop. We have tested the content using Firefox, Google Chrome and Safari. Please configure your computer to use one of these as your default web browser.

Find or install one of the browsers Firefox, Google Chrome or Safari:
To install Firefox: https://www.mozilla.org/en-US/firefox/new/
To install Google Chrome: https://www.google.com/chrome/
(macOS only) Find Safari on your computer

A text editor of your choice

a text editor can open, edit and save files as plain text (ren text) that only contains characters (e.g., letters, symbols and spaces). You will often find that a text editor is installed on your computer.

Find the text editor that is already installed on your computer:
Windows: Notepad (Anteckningar)
macOS: Text edit (Textredigeraren)

(Optional) Install the text editor Atom by following the instructions at: https://flight-manual.atom.io/getting-started/sections/installing-atom/

GitHub Desktop

a tool that allows you to interact with Git repositories stored on your own computer and on the GitHub cloud platform using an intuitive graphical user interface.

Install by following the instructions at: https://docs.github.com/en/desktop/installing-and-configuring-github-desktop/installing-github-desktop

RStudio Desktop & R

RStudio Desktop is a set of integrated tools designed to help you be more productive with R and Python. R is a piece of software that allows you to run programs written in the R programming language.

Install by following instructions at: https://rstudio.com/products/rstudio/download/#download (Note: Select the latest version of R for your plattform, e.g. R 4.1.1 for macOS and Windows at the time of writing)

Install the tidyverse R package by following instructions at: https://docs.google.com/presentation/d/1FMrM7mzydNfzy9UrS8U3j7mfa7rIfpXx/

Microsoft Excel

a commercial spreadsheet software, please consult your IT department for instructions on how to get access to the software. You may use another spreadsheet software but you will be expected to know how to navigate the menus to access features for data validation, value formatting (numbers/dates/etc) and importing and exporting CSV/TSV files.

OpenRefine

a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.

Install by following the instructions at: https://docs.openrefine.org/manual/installing (Note: Either the “Windows kit with embedded Java” and “Mac-kit” downloads includes the necessary Java Runtime Environment)

(Optional) A Java Runtime Environment (JRE)

A JRE is a piece of software that is designed to run Java-based software. There are many JRE:s to choose from with varying licensing conditions. Please consult your IT department before choosing your runtime. (Note: Oracle changed its licensing agreements in April 2019 and may not be advisable for use at some universities).

Install a JRE recommended by your IT department

(Optional) Learn more about Zulu OpenJDK: https://www.azul.com/downloads/zulu-community/

(Optional) Learn more about AdoptOpenJDK: https://adoptopenjdk.net/