SciLifeLab Research Data Management Guidelines

This is the repository for SciLifelab Research Data Management (RDM) guidelines, a central resource to provide information about data management.

Background and motivation

There is an information and competence gap regarding data management in the Swedish life science community
SciLifeLab and NBIS had many sources of information regarding research data management
There is a need to make a unified set of guidelines that can then be used as a resource and reference for the life science community in Sweden.
Information can be unified and kept up do date by the team and the community if there is only one set of guidelines, and not multiple sources, as well as clear and easy ways of contributing.

Project goals

Create the authoritative set of Research data management (RDM) best practice guidelines for life science research in Sweden, hosted at data.scilifelab.se (to ensure that unified information is conveyed to all recipients), including information about human data
A single point of entry web portal/resource for national use and to connect to other efforts, eg. Training, RDMkit

How to contribute

For internal / editorial contribution process, please see internal contribution page.

Step 1: Access the code

The code is hosted on GitHub, so you'll need an account.

Next, visit the code repository: https://github.com/ScilifelabDataCentre/RDM-guidelines

In the top right, you'll see a button that says "Fork". Click this, then select your username. This makes a copy of the repository under your personal account that you can edit.

Step 2a: Edit the files (online)

This is best if you only want to make one or two minor tweaks. If you want to make more substantial edits over a longer time frame, we recommend editing locally (Step 2b).

The easiest way to edit the website files is on the GitHub website.

On the web page of your forked copy of the repository, look in the content/ directory. Go to the markdown file that you want to edit, then click the Pencil icon ✏️ in the top right.

This opens a web-based editor where you can add and edit content. When you're finished, scroll to the bottom and fill in / submit the "Commit changes" form.

You're nearly done - you can now skip to Step 3.

Step 2b: Edit the files (locally)

Git setup

If you prefer, you can edit the website files on your computer in your favourite text editor. Just fork the repository to your machine:

git clone git@github.com:[YOUR-USERNAME]/RDM-guidelines
cd RDM-guidelines

To make it easier to pull in changes made by others, you can add the main repository as a remote:

git remote add upstream https://github.com/ScilifelabDataCentre/RDM-guidelines.git

Then you can fetch changes at any time from this remote:

git pull upstream main

When you have finished editing, commit and push to your fork:

git add .
git commit -m "My changes"
git push

Testing locally

To view your changes as they will appear in the final website, you need to install Hugo. You can find instructions on the Hugo website: getting-started/installing/

If you're using Mac OSX, it's recommended to use Homebrew - if homebrew is already set up, installing Hugo is just a case of:

brew install hugo

For Windows users (additional instructions can be found here):

Open Windows Explorer.
Create a new folder: C:\Hugo, assuming you want Hugo on your C drive, although this can go anywhere
Create a subfolder in the Hugo folder: C:\Hugo\bin
Go to the Hugo Releases page. The latest release is announced on top. Scroll to the bottom of the release announcement to see the downloads. They’re all ZIP files. Find the Windows files near the bottom (they’re in alphabetical order, so Windows is last) – download either the 32-bit or 64-bit file depending on whether you have 32-bit or 64-bit Windows. (If you don’t know, see here.)
Move the ZIP file into your C:\Hugo\bin folder.
Double-click on the ZIP file and extract its contents. Be sure to extract the contents into the same C:\Hugo\bin folder – Windows will do this by default unless you tell it to extract somewhere else.
In PowerShell or your preferred CLI, add the hugo.exe executable to your PATH by navigating to C:\Hugo\bin (or the location of your hugo.exe file) and use the command set PATH=%PATH%;C:\Hugo\bin. If the hugo command does not work after a reboot, you may have to run the command prompt as administrator.

Once Hugo is installed, simply run the following command in the repository root (RDM-guidelines) directory:

$ hugo serve

Use the URL printed at the bottom of the message (http://localhost:1313/) to view the site. Every time you save a file, the page will automatically refresh in the browser.

Step 3: Make a pull request

Once you're finished with your edits and they are committed and pushed to your forked repository, it's time to open a pull request.

You can find full documentation on the GitHub help website, however in short:

Visit the main repository: https://github.com/ScilifelabDataCentre/RDM-guidelines
Click the button that reads "New Pull Request"
Click the text link near the top that says "compare across forks"
In the right-hand "head repository" drop down, select your username / fork.
If you're happy with the list of commits shown, and the diff in the "Files Changed" tab, fill in a title and description and click "Create pull request"

Once created, a member of the website team will review your changes. Once approved, they will be merged and deployed.

How to get help

If in doubt, you can ask for help by emailing data-management@scilifelab.se.

License

The content documents are dedicated to the public domain under a CC-0 license. Software are made available under an MIT license. More information about our license can be found on our license page.

Credits

The website was built by SciLifeLab Data Centre and NBIS.

wna-se / RDM-guidelines