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.

Note: GitHub requires Multi-Factor Authentication (MFA), which is also useful in other contexts. You can learn about MFA and recommended applictions by consulting your university’s website, e.g. MFA at Uppsala University .

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)

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. (Not available for Linux)

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

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. Such as:

Windows: https://support.microsoft.com/en-us/office/text-import-wizard-c5b02af6-fda1-4440-899f-f78bafe41857#ID0EBBJ=Newer_versions

MacOS: https://support.microsoft.com/en-us/office/import-data-from-a-csv-html-or-text-file-b62efe49-4d5b-4429-b788-e1211b5e90f6

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: The “Windows kit with embedded Java” and “Mac-kit” downloads includes the necessary Java Runtime Environment. For Linux, install java using your package manager before you run OpenRefine.)

Run OpenRefine by following the instructions at: https://openrefine.org/docs/manual/running