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.
Accounts
ELIXIR ID
ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers.
Register using an existing account from your university, Google, LinkedIn or ORCID: https://elixir-europe.org/register Links to an external site.
(Optional) Learn more about ELIXIR: https://elixir-europe.org/about-us/what-we-do Links to an external site.
SciLifeLab DSW account
SciLifeLab DSW is an online service for creating data management plans from questionnaires using the Data Stewardship Wizard (DSW) software tool. The software is installed at SciLifeLab and is managed by SciLifeLab and NBIS.
Register by logging in using your ELIXIR account (University Login): https://dsw.scilifelab.se/ Links to an external site.
(Optional) Learn more about SciLifeLab: https://www.scilifelab.se/ Links to an external site.
(Optional) Learn more about DSW: https://ds-wizard.org/ Links to an external site.
Webin submission account
The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data. To submit sequences you need a Webin submission account.
Register for a Webin submission account: https://www.ebi.ac.uk/ena/submit/webin/ Links to an external site.
(Optional) Learn more about ENA: https://www.ebi.ac.uk/training/events/european-nucleotide-archive-introduction/ Links to an external site.
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 Links to an external site.
(Optional) Learn more about GitHub: https://www.nature.com/news/democratic-databases-science-on-github-1.20719 Links to an external site.
(Optional) Explore alternatives to GitHub: https://github.com/ianchanning/awesome-github-alternatives Links to an external site.
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/ Links to an external site.
To install Google Chrome: https://www.google.com/chrome/ Links to an external site.
(macOS only) Find Safari Links to an external site. 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 Links to an external site. (Anteckningar Links to an external site.)
macOS: Text edit (Textredigeraren) Links to an external site.(Optional) Install the text editor Atom by following the instructions at: https://flight-manual.atom.io/getting-started/sections/installing-atom/ Links to an external site.
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 Links to an external site.
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 Links to an external site. (Note: Select the latest version of R for your plattform, e.g. R 4.1.1 for macOS Links to an external site. and Windows Links to an external site. at the time of writing)
- Install the tidyverse R package by following instructions at: https://docs.google.com/presentation/d/1FMrM7mzydNfzy9UrS8U3j7mfa7rIfpXx/ Links to an external site.
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://openrefine.org/download.html Links to an external site. (Note: Either the “Windows kit with embedded Java” and “Mac-kit” downloads includes the necessary Java Runtime Environment)
(Otional) 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 Links to an external site.).
Install a JRE recommended by your IT department
(Optional) Learn more about Zulu OpenJDK: https://www.azul.com/downloads/zulu-community/ Links to an external site.
(Optional) Learn more about AdoptOpenJDK: https://adoptopenjdk.net/ Links to an external site.