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NEFSC Passive Acoustic Branch Lab Manual
The Passive Acoustic Branch (PAB) is part of the Protected Species Division of the NOAA Fisheries Northeast Fisheries Science Center. Our group uses passive acoustic monitoring (PAM) to study marine animals and ecosystems in the Northeast and Mid-Atlantic waters of the United States.
Required Pages
In order to keep consistency between science centers, the following sections/pages will be required in all lab manuals. These will be directly linked to the National PAM Repository. The links will direct you to the associated template page with more directions on what to include.
- Home Page (this page): Edit this page to include an introduction to your lab, projects you are working on, etc.
- Lab Management
- Data Management
- Hardware
- Software
- Analysis
- Reporting
Optional Pages
Here are some more ideas for pages to include in your lab manual. These are optional and will not be linked to the main National PAM Repo, but they may be helpful for your team
How To Use This Template
This template will create a Quarto website that each lab can copy and edit with their own lab information. Follow the steps below to copy this template to your lab’s GitHub
Click on the ‘Use this template’ button in the top right, select ‘Create new repository’
Edit repository settings
Select the ‘Include all branches’ option
Select your lab organization or yourself as the owner and set the repository name to ‘Lab name Lab Manual’
Make description “Lab manual for ‘insert lab name and FMC’”
Make the repo public
Click create repository
Turn on GitHub pages under Settings->Pages. You will set pages to be made from the gh-pages branch and root directory
Update ‘Actions’ settings
Under Settings -> Actions -> General -> Actions permissions select ‘Allow all actions and reusable workflows’. Select save
Under Settings -> Actions -> General -> Workflow permissions select ‘Read and write permissions’
Note: Both of these settings may already be selected but you have to click save for both
Return to the main page of the repo to edit your website
Click on ‘Code’ in the top left
Click on the settings button next to the ‘About’ section on the right side of the repository
Select ‘Use your GitHub Pages website’. This should autopopulate the website
Select ‘Save Changes’
Example Manuals
Here are two lab manuals to pull inspiration from