The Marine Biodiversity Observation Network (MBON) and the AIR Centre will host a small, hands-on, interactive workshop focused on mobilizing marine biological observation datasets to the Ocean Biodiversity Information System (OBIS). The objective is to help data holders understand the value of following good practices for standardizing biological data, using widely accepted biodiversity standards like Darwin Core. This would include records of different biological attributes and ecosystem observations from different types of sampling methodologies. A complementary activity of the workshop will contemplate a field work day in which participants will receive training on the collection and processing of benthic photo-quadrat imagery and their analysis following MBON Pole to Pole monitoring protocols, aiming to enhance capacity for long-term monitoring of rocky intertidal communities.
By the end of the workshop, attendees will have a clear understanding of the process of mobilizing biological data to OBIS and will have brought one of their datasets to a final maturity state that aligns with best practices for data sharing and biodiversity documentation. The workshop will also enhance awareness of improving the quality of marine biodiversity data and will increase the availability of marine biological data for scientific research, species conservation, and ecosystem-based management by promoting data publication through OBIS. Additionally, the workshop will foster collaborative research efforts among participants and contribute to the MBON community of practice by increasing capacity in the implementation of coordinated and standardized biodiversity observing and publishing efforts.
Software Carpentry
aims to help researchers get their work done
in less time and with less pain
by teaching them basic research computing skills.
This hands-on workshop will cover basic concepts and tools,
including program design, version control, data management,
and task automation.
Participants will be encouraged to help one another
and to apply what they have learned to their own research problems.
Who:
The course is aimed at graduate students and other researchers.
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.
Where:
Hotel Terceira Mar, Portões de São Pedro, nº1, 9700-097, Angra do Heroísmo.
Get directions with
OpenStreetMap
or
Google Maps.
Requirements:
Participants must bring a laptop with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.
Participants are expected to have familiarity with:
Working with taxonomic occurrence data
Using spreadsheet tools (e.g., Excel, LibreOffice, Google Sheets).
File handling & different file formats (Working with CSV, TXT, and Excel formats).
Basic Python or R programming.
Study of sandy beach or rocky shore environments (not mandatory).
Basic data wrangling skills for marine biodiversity data management (e.g., data structuring).
Familiarity with a few specific software packages are recommended (listed below).
Accessibility:
We are committed to making this workshop
accessible to everybody.
The workshop organizers have checked that:
The room is wheelchair / scooter accessible.
Accessible restrooms are available.
We are dedicated to providing a positive and accessible learning environment for all.
We do not require participants to provide documentation of disabilities or disclose any unnecessary personal information.
However, we do want to help create an inclusive, accessible experience for all participants.
We encourage you to share any information that would be helpful to make your Carpentries experience accessible.
To request an accommodation for this workshop, please fill out the
accommodation request form.
If you have questions or need assistance with the accommodation form please email us.
Glosario is a multilingual glossary
for computing and data science terms. The glossary helps
learners attend workshops and use our lessons to make sense of computational and programming jargon written in English by offering it
in their native language. Translating data science terms also provides a teaching tool for Carpentries Instructors to reduce barriers
for their learners.
Workshop Recordings:
This workshop is designed to be interactive rather than lecture-based, with lessons that build upon one another.
The workshop is in-person only; there will not be a virtual option.
As a result, workshop recordings not be available to learners.
Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.
Schedule
Reference materials for each section are linked in the schedule below.
To participate in a
Software Carpentry
workshop,
you will need access to software as described below.
In addition, you will need an up-to-date web browser.
To install WSL 2, you will need Administrator (“admin”) privileges on your laptop/PC.
If you have a device provided by an institution that does not give you admin rights, please either request that they:
Give you admin rights (temporarily or otherwise) to install WSL 2 yourself OR
Install WSL 2 for you
If you experience any issues, please install Git for Windows using the instructions below.
Click on the Windows Start Menu button in the bottom left corner of your screen, or tap the Windows button on your keyboard, and type “System” in the search bar.
Click the “System (Control Panel)” option.
In the window that opens, there will be information about your current Windows system, including the version. Here is an example from Windows 11:
Depending on your version, please go to the relevant instructions below.
Windows XP/Vista/7/8
These versions of Windows are considered End Of Life, and are not recommended for use in modern data science.
Software may experience issues, and security updates are also not available which puts your machine at risk.
Please consider upgrading your Windows version if you are able to do this yourself, or speak with your local IT administrator to discuss options available to you to upgrade.
If you are running any of these Windows versions, please install Git for Windows using the installation instructions below.
Windows 10 (earlier than version #1903)
For older versions of Windows 10 (version 1903/OS build 18362 and below), please follow the Git for Windows installation instructions below.
Windows 10 (version #1903 and later) and Windows 11
WSL 2 is recommended for more modern versions of Windows as it provides an accurate and representative experience of Linux, but provided from within your Windows environment.
We will install Ubuntu via the Microsoft Store.
It is possible to install WSL within the Windows Powershell command prompt, and full instructions are on the Microsoft website.
Note: You will need to restart your computer after installing WSL 2, so make sure you have saved any work.
Why Ubuntu?
Linux comes in many flavours, called “distributions”, and each has its own benefits, features and quirks!
WSL 2 is a fully fledged Linux environment that runs completely within your Windows 10 or 11 operating system.
While there are many Linux distributions available to install (e.g. Ubuntu, Debian, Fedora, Mint, Arch, Gentoo, and hundreds more!), WSL 2 only supports a handful of distributions listed above due to the way it needs to be integrated with Windows itself.
So, we will use the default that WSL 2 recommends, Ubuntu.
Via the Microsoft Store:
Open the Windows Start Menu button in the bottom left corner of your screen (four blue squares), or tap the Win Windows button on your keyboard (between the bottom left CTRL and ALT keys) and search “store”. Open the Microsoft Store.
In the Microsoft Store search bar, type “wsl ubuntu”, and select the Ubuntu 22.04 or 24.04 option (at the time of writing, Ubuntu 22.04.06 LTS, or Ubuntu 24.04.01 LTS):
If a pop-up window appears asking if you want to make changes to your device, select “Yes”
The install should proceed, and this can take a few minutes depending on your PC performance and internet download speed.
Once installed, restart the computer.
Once restarted, reopen the Windows Start Menu button in the bottom left corner of your screen, or tap the Windows button on your keyboard. In the search bar, type either:
Ubuntu: selecting Ubuntu 22.04.06 LTS or Ubuntu 24.04.01 LTS from the Start Menu will open the bash prompt directly, or
Terminal: this will open a new Windows Terminal window, which will look like a blank black window with a blinking cursor waiting for input. Note: This terminal might default to Powershell, and not Ubuntu. If this is the case, click the down arrow in the Terminal window menu bar at the top, and then click Ubuntu 22.04 or 24.04, depending on the version you installed. It will also show keyboard shortcuts (e.g. Ctrl+Shift+1) to open the various prompts available within the Terminal application.
Once you have installed WSL 2, you will need to install some software within the Ubuntu operating system in order to use it effectively. Make sure you are using Ubuntu by checking you see the bash prompt:
The first thing to do is to update the list of available Ubuntu software packages, using a tool called apt.
Type the following command into the bash prompt:
sudo apt update
Note: You will be prompted to enter your password. This is the password you set when installing Ubuntu, and will not show up on the screen as you type it in.
This is a security feature of the terminal, and is normal behaviour.
Install updated versions of the base packages required across all our lessons, by typing:
Click on "Next" four times (two times if you've previously
installed Git). You don't need to change anything
in the Information, location, components, and start menu screens.
From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
On the page that says "Adjusting the name of the initial branch in new repositories", ensure that
"Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
Ensure that "Git from the command line and also from 3rd-party software" is selected and
click on "Next". (If you don't do this Git Bash will not work properly, requiring you to
remove the Git Bash installation, re-run the installer and to select the "Git from the
command line and also from 3rd-party software" option.)
Select "Use bundled OpenSSH".
Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
Ensure that "Use Windows' default console window" is selected and click on "Next".
Ensure that "Default (fast-forward or merge) is selected and click "Next"
Ensure that "Git Credential Manager" is selected and click on "Next".
Ensure that "Enable file system caching" is selected and click on "Next".
Click on "Install".
Click on "Finish" or "Next".
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press Enter)
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press Enter, you should see SUCCESS: Specified value was saved.
Quit command prompt by typing exit then pressing Enter
This will provide you with both Git and Bash in the Git Bash program.
Video Tutorial
The default shell in Mac OS X Ventura and newer versions is Zsh, but
Bash is available in all versions, so no need to install anything.
You access Bash from the Terminal (found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep Terminal in your dock for this workshop.
To see if your default shell is Bash type echo $SHELL
in Terminal and press the Return key. If the message
printed does not end with '/bash' then your default is something
else, you can change your current shell to Bash by typing
bash and then pressing Return. To check
your current shell type echo $0 and press Return.
To change your default shell to Bash type chsh -s /bin/bash and
press the Return key, then reboot for the change to take effect. To
change your default back to Zsh, type chsh -s /bin/zsh, press the
Return key and reboot. To check available shells, type
cat /etc/shells.
The default shell is usually Bash and there is usually no need to
install anything.
To see if your default shell is Bash type echo $SHELL
in Terminal and press the Return key. If the message
printed does not end with '/bash' then your default is something
else, you can change your current shell to Bash by typing
bash and then pressing Return. To check
your current shell type echo $0 and press Return.
To change your default shell to Bash type chsh -s /bin/bash and
press the Return key, then reboot for the change to take effect. To
change your default back to Zsh, type chsh -s /bin/zsh, press the
Return key and reboot. To check available shells, type
cat /etc/shells.
Note for Windows Users
If you have used Windows Subsystem for Linux ("WSL2") please open your Ubuntu bash terminal and follow the Linux instructions for each of the software packages below.
If not, please follow the Windows instructions.
Git
Git is a version control system that lets you track who made changes
to what when and has options for easily updating a shared or public
version of your code
on github.com. You will need a
supported
web browser.
You will need an account at github.com
for parts of the Git lesson. Basic GitHub accounts are free. We encourage
you to create a GitHub account if you don't have one already.
Please consider what personal information you'd like to reveal. For
example, you may want to review these
instructions
for keeping your email address private provided at GitHub.
Please open the Terminal app, type git --version and press
Enter/Return. If it's not installed already,
follow the instructions to Install the "command line
developer tools". Do not click "Get Xcode", because that will
take too long and is not necessary for our Git lesson.
After installing these tools, there won't be anything in your /Applications
folder, as they and Git are command line programs.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
(Note: this project is no longer maintained.)
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open in the pop-up dialog.
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo dnf install git.
Text Editor
When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on macOS and
Linux is usually set to Vim, which is not famous for being
intuitive. If you accidentally find yourself stuck in it, hit
the Esc key, followed by :+q+!
(colon, lower-case 'q', exclamation mark), then hitting Return to
return to the shell.
nano is a basic editor and the default that instructors use in the workshop.
It is installed along with Git.
nano is a basic editor and the default that instructors use in the workshop.
See the Git installation video tutorial
for an example on how to open nano.
It should be pre-installed.
nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.
R
R is a programming language
that is especially powerful for data exploration, visualization, and
statistical analysis. To interact with R in our lessons, we typically use
RStudio.
Note that if you have separate user and admin accounts, you should run the
installers as administrator (right-click on .exe file and select "Run as
administrator" instead of double-clicking).
Otherwise problems may occur later, for example when installing R packages.
Navigating to CRAN and following the instructions outlined there, using your package manager. We have reproduced the commands below:
Use the terminal command prompt to type/copy-and-paste these commands in, pressing Enter after each line to run the command.
Do not run the lines with # at the start of each line, as this indicates a comment and is not part of the command.
# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# add the signing key for these repos
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# add the repo from CRAN
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
# install R itself
sudo apt install --no-install-recommends r-base
# install dependencies
sudo apt install -y r-base-core r-recommended r-base-dev gdebi-core build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev
sudo apt install --no-install-recommends gdebi-core
# cd ~/Downloads
# download the latest RStudio Server .deb file
wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2025.05.1-513-amd64.deb
# install the .deb file
sudo gdebi rstudio-server-2025.05.1-513-amd64.deb
# start the RStudio Server
sudo systemctl start rstudio-server
# enable RStudio Server to start on boot
sudo systemctl enable rstudio-server
After installation of RStudio Server, check you can access it by:
Opening a web browser and navigating to http://localhost:8787.
Logging in with the username and password you used when you set up Linux / WSL2.
If you are using Windows and WSL2, the full in-depth instructions for installing R on WSL2 can be found in this
POSIT article.
Python
Python is a popular language for
research computing, and great for general-purpose programming as
well. Installing all of its research packages individually can be
a bit difficult, so we recommend
Conda-forge,
an all-in-one installer.
Regardless of how you choose to install it,
please make sure you install a Python version >= 3.9
(e.g. 3.11 is fine, 3.6 is not).
We will teach Python using the Jupyter Notebook,
a programming environment that runs in a web browser (Jupyter Notebook will be installed by Miniforge). For this to work you will need a reasonably
up-to-date browser. The current versions of the Chrome, Safari and
Firefox browsers are all
supported
(some older browsers, including Internet Explorer version 9
and below, are not).
OneDrive is used by many institutions to sync your user folder (C:\Users\[your-username]\) within an organisation.
It may cause issues with the installation of the Carpentries environment.
If you have OneDrive set up, please ensure that you can access your C:\Users\[your-username]\Downloads folder:
Open File Explorer
Right click on the "Downloads" folder in the left-hand navigation pane
Select "Properties"
In the "Location" tab, ensure that the path is set to C:\Users\[your-username]\Downloads
If you encounter problems, please contact your IT support team and workshop organisers for assistance before the workshop.
Save the file to your C:\Users\[your-username]\Downloads folder.
Make sure that the filename is carpentries_environment.yml and the "Save as type" option is set to YML file (*.yml) The following steps requires using the Miniforge Prompt command line. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.
Open your Start Menu from your taskbar, or use the Win Windows key.
Search for the application "Miniforge Prompt", and click the icon to open it.
Once open, ensure the prompt shows your C:\Users\[your-username] folder. If it does, continue to Step 8 below:
In this case, the prompt shows C:\Users\froggleston. Your username will be different!
If it doesn't:
Find your username by typing whoami and press Enter
Your username will be shown as [machine-name]\[your-username]. You only need the [your-username] part after the slash, i.e. froggleston in this example.
Type cd C:\Users\[your-username] and press Enter
Continue to Step 8 below
If you get stuck, please contact your workshop organisers to get assistance before the workshop starts.
In the Miniforge Prompt window, run the following commands:
Type cd Downloads and press Enter
Type conda env create -f carpentries_environment.yml and press Enter
The installation may take a few minutes depending on your internet connection speed. Once complete, you can close the Miniforge Prompt window.
Download the appropriate Miniforge installer for macOS The following steps require using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.
Open a terminal window and navigate to the directory where the executable is downloaded (e.g., cd ~/Downloads).
Type
bash Miniforge3-
and then press Tab to autocomplete the full file name.
The name of file you just downloaded should appear.
Press Enter (or Return depending on your keyboard).
Follow the text-only prompts in the terminal. To move through the text, press Spacebar.
Type yes and press Enter (or Return) to approve the license.
Press Enter (or Return) to approve the default location for the files.
Type yes and press Enter (or Return) to prepend Miniforge to your PATH (this makes the Miniforge distribution the default Python).
Download the appropriate Miniforge installer for Linux The following steps require using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.
Open a terminal window and navigate to the directory where the executable is downloaded (e.g., cd ~/Downloads).
Type
bash Miniforge3-
and then press Tab to autocomplete the full file name.
The name of file you just downloaded should appear.
Press Enter (or Return depending on your keyboard).
Follow the text-only prompts in the terminal.
To move through the text, press Spacebar.
Type yes and press Enter (or Return) to approve the license.
Press Enter (or Return) to approve the default location for the files.
Type yes and press Enter (or Return) to prepend Miniforge to your PATH (this makes the Miniforge distribution the default Python).
In the terminal, run: conda env create -f ~/Downloads/carpentries_environment.yml
Close the terminal window.
CoralNet
CoralNet is a popular software
for automated tagging of organisms from photoquadrat images.
To prepare for using coralnet you will need to create an account.
Depending on your version, please go to the relevant instructions below.
![Miniforge Prompt [your-username] as froggleston](assets/img/miniforge_prompt.png)
