From 72d647628ea6de7b10f3c3c6cc246c1926e29d8c Mon Sep 17 00:00:00 2001 From: mjosse Date: Mon, 13 Apr 2026 16:04:04 +0200 Subject: [PATCH 01/61] start big update introduction to GESS --- .../tutorials/earth_system/tutorial.md | 260 ++++++++---------- 1 file changed, 114 insertions(+), 146 deletions(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index bb0f24f6eab3d9..4fcd29327481a3 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -1,206 +1,174 @@ ---- -layout: tutorial_hands_on -title: Getting your hands-on earth data -subtopic: introduction +layout: tutorial_hands_on +title: Exploring the Earth System and Its Data on Galaxy questions: -- What is the Earth System? -- What type of data is available? + +- What is the Earth System and why is it important? +- What types of Earth data are available on Galaxy? +- How can I access and analyze Earth data for ocean, atmosphere, solid earth, continental surfaces, and biodiversity? objectives: -- Learn about the Earth System terminology -- Learn about the different source of earth data -- Learn about earth observations, reanalysis, and visualisation -time_estimation: 1H +- Understand the Earth System and its components +- Discover the terminology and data sources for Earth science +- Learn about Earth observations, reanalysis, and visualization tools on Galaxy +- Explore European and French subdomains, and their relevance to climate and ecology +time_estimation: 1H30 key_points: -- Earth System -- Essential variables -- Observations, reanalysis, visualisation +- Earth System as a complex, interconnected system +- Essential variables and data types (observations, reanalysis, models) +- European and French subdomains +- Climate and ecology as interconnected themes tags: - earth-system - ocean - - land - atmosphere + - solid-earth + - continental-surfaces - biodiversity -contributions: - authorship: - - Marie59 - funding: - - gallantries - - fairease - - eurosciencegateway ---- - - -This tutotrial aims at familiarzing you with Earth Science and discovering the earth data available on Galaxy. The target audience is not a scientist but -anyone interested in learning about Earth system. + - climate + - ecology + contributions: + authorship: + - Marie59 + funding: + - gaia-data + - gallantries + - fairease + - eurosciencegateway -> -> -> In this tutorial, we will cover: -> -> 1. TOC -> {:toc} -> -{: .agenda} +--- -🌍🌏🌎 +# 🌍 Introduction to the Earth System -The Earth System is a complex and dynamic system that encompasses the interactions between the atmosphere, hydrosphere, geoshpere, and biosphere. Understanding and analyzing data from the Earth System Model is essential, for example to predict and mitigate the impacts of climate change. Currently, [Galaxy Earth System](https://earth-system.usegalaxy.eu/) uses 4 usecases to have an overview of an earth System: ocean, land, atmosphere, and biodiversity. -Of course, these components cross over each other thus, we have data that can fit two or more compartiments. +The **Earth System** is a dynamic and interconnected network of components—**atmosphere, hydrosphere (ocean), geosphere (solid earth), biosphere (biodiversity), and continental surfaces (land)**—that interact to shape our planet’s climate, weather, and life. Understanding these interactions is critical for addressing global challenges like climate change, biodiversity loss, and natural disasters. ![Graphic visualization of an Earth System](../../images/earth_system/earth_system_galaxy.png) -Next we will see for each compartiment which kind of data (and how to get them) are availabe on Galaxy Earth System - - -# 🌊 Ocean 🌊 - -The ocean is a key component of the Earth’s climate system. Thus, it needs continuous real-time monitoring to help scientists better understand its dynamics and predict its evolution. - -## The Argo program -All around the world, oceanographers have managed to join their efforts and set up a Global Ocean Observing System among which Argo is a key component. Argo is an international program that collects information from inside the ocean using a fleet of robotic instruments that drift with the ocean currents and move up and down between the surface and a mid-water level. - -The data available here are from the Argo gliders network. They contain the folowing variables: -- latitude, longitude, and time -- physcical parameters: water temperature, pressure, and salinity -- biogeochemical parameters: chlorophyll, oxygen, and nitrate - -To access those data you can use the ({% tool [Argo data access](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) %})tool. - -For more information follow the tutorial related to it called [Analyse Argo data]({% link topics/climate/tutorials/argo_pangeo/tutorial.md %}) or use the workflow Full Analyse Argo data `https://earth-system.usegalaxy.eu/u/marie.josse/w/full-analyse-argo-data` - - -## Copernicus Data Space Ecosystem - -The Copernicus Data Space Ecosystem provides access to Earth observation data. -The goal of the **Sentinel-3 mission** is to accurately and reliably measure sea surface topography, sea and land surface temperature, and ocean and land surface color. This data will support ocean forecasting systems, environmental monitoring, and climate monitoring. - -To access those data you can use the [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) tool. - -For more information follow the tutorial related to it called [Sentinel 5P data visualisation]({% link topics/climate/tutorials/sentinel5_data/tutorial.md %}). - -Once you get into the Jupyterlab go in the left pannel in `samples > openeo > Sentinel_3.ipynb `. Yhis way you have an example on how to get Sentinel 3 data. - -## EMODnet Chemistry +### Why Study the Earth System? -[EMODnet Chemistry](https://emodnet.ec.europa.eu/en/chemistry) provides easy access to marine chemical data, standardised, harmonised and validated data collections and data products for visualisation. These are relevant for the European marine environmental policies to assess the status and trends of ecosystems. -Numerous substances are considered, most of which are invisible to the naked eye and are monitored using specialised sensors or laboratory analyses. This evidence-based information supports action against environmental changes that pose a threat to marine ecosystems and human health. +- **Climate Change**: Monitor and predict impacts on temperature, sea levels, and extreme weather. +- **Biodiversity**: Track ecosystems and species to protect natural habitats. +- **Natural Resources**: Manage water, soil, and minerals sustainably. +- **Human Health**: Understand air quality, pollution, and disease vectors. -### A focus on ODV (Ocean Data View) collections +### 🔗 Join the Conversation -This [webODV](https://emodnet-chemistry.webodv.awi.de/) service facilitates to explore, subset, visualize, and extract data sets in multiple formats from the harmonized, standardized, validated data collections that EMODnet Chemistry is regularly producing and publishing for all European sea basins for eutrophication and contaminants. -You can also find these collections on the [Sextant catalogue](https://sextant.ifremer.fr/eng/Data/Catalogue#/search?isTemplate=n&from=1&to=30&sortBy=dateStamp&sortOrder=desc&languageStrategy=searchInDetectedLanguage&any=EMODnet%20Chemistry) +Connect with the community and ask questions in our **[Matrix Channel](https://matrix.to/#/#galaxy-earth-system:matrix.org)**. +Explore visualizations and datasets in our **[Earth System Dashboard](https://earth-system.usegalaxy.eu/)**. -You can analize thes kind of data through the [Ocean Data View (ODV)](https://usegalaxy.eu/root?tool_id=interactive_tool_odv) tool. - -For more information follow the related tutorials and workflows: - - [Ocean's variables study]({% link topics/climate/tutorials/ocean-variables/tutorial.md %}) and the corresponding workflow `https://usegalaxy.eu/u/marie.josse/w/oceans-var-v2` - - [Ocean Data View (ODV)]({% link topics/climate/tutorials/ocean-data-view/tutorial.md %}) - - -## Copernicus Marine Data Store - -The [Copernicus Marine Data Store](https://marine.copernicus.eu/access-data) offers a ocean product catalogue, to download or visualize data accross nearly 15variables, including hindcast, current and forecast data. - -A tool is currently being develop to enable easy access to this data. More information to come. - - - -# 🏜️ Land 🏞️ - -This component comprehend all from the solid part of earth land, rock, volcano activities to the deragation of the land surface. This compartiment amis at assessing land and soil degradation, such as erosion, loss of organic matter and soil biodiversity, compaction, salinization, landslides, contamination, sealing, desertification and climate change. - -## Copernicus Data Space Ecosystem - -The Copernicus Data Space Ecosystem provides access to Earth observation data. +--- -The Copernicus Sentinel-2 mission consists of two polar-orbiting satellites that are positioned in the same sun-synchronous orbit, with a phase difference of 180°. +# 🌎 European and French Subdomains -It aims to monitor changes in land surface conditions. The satellites have a wide swath width (290 km) and a high revisit time. This capability will support monitoring of changes on the Earth's surface. +The **Galaxy Earth System** platform focuses on **European and French** dedicated spaces to provide specific data and tools for analysis. These platforms are: -The Sentinel-2 twin satellites provide image data that largely contribute to existing and ongoing multispectral observations. + - **[Earth System European subdomain](https://earth-system.usegalaxy.eu/)**. The original subdomain, fully operational. + - **[Earth System French lab](https://earth-system.usegalaxy.fr/)**. On this french instance the interactive tools are not working. -These satellites support a variety of services and applications offered by Copernicus, including: -- Land monitoring -- Agriculture -- Emergency management -- Risk mapping -- Security -- Forestry -- Climate change -- Disaster control -- Marine -- Humanitarian relief operations -The Scene Classification algorithm uses the reflective properties of scene features to establish the presence or absence of clouds in a scene. It is based on a series of threshold tests that use as input: TOA reflectance of several Sentinel-2 spectral bands, band ratios and indexes like Normalised Difference Vegetation Index (NDVI) and Normalised Difference Snow and Ice Index (NDSI). For each of these threshold tests, a level of confidence is associated. It produces at the end of the processing chain a probabilistic cloud mask quality indicator and a snow mask quality indicator. The most recent version of the SCL algorithm includes also morphological operations, usage of auxiliary data like Digital Elevation Model and Land Cover information and exploit the parallax characteristics of Sentinel-2 MSI instrument to improve its overall classification accuracy. -The NDVI ratio can be determined from the contribution of visible wavelength and near-infra-red wavelengths. Strong and well-nourished vegetation will absorb most of the visible wavelengths that it receives and will reflect back a large proportion of the near-infra-red light, whereas poor condition vegetation or thin areas, will reflect more visible wavelength light and less near-infra-red light. +### 📚 Learning Pathway: Building the European Subdomain -To access those data you can use the [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) tool. +Discover how we created the **European subdomain** on Galaxy in our dedicated **[Learning Pathway](learning-pathways/dev_tools_training.md)**. This pathway covers: -For more information follow the tutorial related to it called [From NDVI data with OpenEO to time series visualisation with Holoviews]({% link topics/ecology/tutorials/ndvi_openeo/tutorial.md %}). +- Set up your subdomain for your community +- Build a batch tool +- Build an interactive tool +--- -## QGIS (Geographical Information System) +# 🌐 Climate and Ecology: Strongly Linked Themes -Based on a [QGIS official tutorial](https://docs.qgis.org/2.18/en/docs/training_manual/online_resources/wfs.html), you can learn how to access, filter and import GIS data through WFS web service using [QGIS Galaxy interactive tool](https://usegalaxy.eu/root?tool_id=interactive_tool_qgis) +Climate and ecology are **inextricably linked**: -In the Geographical Information System landscape, there is existing standards to help users deal with remote data. The most common web services are Web Map Services (WMS) and Web Feature Services (WFS). If WMS allows users only to access and display maps stored remotely, WFS is giving access to the features of data so you can modify it and create your own data and maps. +- **Climate** drives ecological processes (e.g., temperature affects species distribution). +- **Ecology** influences climate (e.g., forests absorb CO₂, oceans regulate heat). +On Galaxy, you can explore these connections through: +- **Climate Data**: ERA5 reanalysis, Sentinel-5P atmospheric data. +- **Ecological Data**: OBIS biodiversity records, Sentinel-2 land cover. +- **Integrated Workflows**: Combine climate and ecological datasets to study impacts like habitat loss or carbon cycles. -To learn more on how to do that folow [QGIS Web Feature Services]({% link topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md %}) +💬 **Discuss these links in our [Matrix Channel](https://matrix.to/#/#galaxy-earth-system:matrix.org)**! -# ☁️ Atmosphere 🌫️ +--- -This component represents the layer of gas around the Earth. +# 🗂️ Explore Earth System Components -## Copernicus Data Space Ecosystem +Click on the boxes below to dive into dedicated trainings for each component of the Earth System. +Each box includes **data sources, tools, and tutorials** to help you get started. -The Copernicus Data Space Ecosystem provides access to Earth observation data. -The Copernicus **Sentinel-5 Precursor** mission is the first Copernicus mission that focuses on monitoring our atmosphere. It is the result of a close partnership between ESA, the European Commission, the Netherlands Space Office, industry, data users and scientists. +--- -To access those data you can use the [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) tool. +## 🌊 [Ocean: Monitoring the Blue Planet](topics/climate/tutorials/argo_pangeo/tutorial.md) -### Volcano 🌋 +**Key Data**: -You can get atmospheric data on volcanic activity by taking a subset of Sentinel 5P L2 data for instance, from the 1st of April to the 30th of may 2021 of the Antilles. Especially of the La Soufriere Saint Vincent (Antilles) where a volcaninc erruption occured 9th of April. This dataset is focused on the dioxide sulfur (SO2) and Aerosol index (AI) spread out. Indeed, the knowledge of volcanic activity at a high temporal resolution is crucial for robustly determining large-scale impacts of volcanoes on atmosphere (air quality, air traffic) and climate. As such, this platform will be also of interest for scientists involved in the field of volcanic impacts at large, including institutions in charge of the monitoring of air quality and aviation safety. - -For more information follow the tutorial related to it called [Sentinel 5P data visualisation]({% link topics/climate/tutorials/sentinel5_data/tutorial.md %}). +- **Argo Program**: Temperature, salinity, and biogeochemical parameters (chlorophyll, oxygen, nitrate) from floating sensors. +- **Copernicus Sentinel-3**: Sea surface temperature, topography, and color for ocean forecasting. +**Tools**: +- [Argo Data Access](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) +- [Copernicus Data Space Ecosystem (JupyterLab)](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) +**Workflow**: [Full Analyse Argo Data](https://earth-system.usegalaxy.eu/u/marie.josse/w/full-analyse-argo-data) +--- -## Climate Data Store +## ☁️ [Atmosphere: The Invisible Shield](topics/climate/tutorials/sentinel5_data/tutorial.md) -Dive into this wealth of information about the Earth's past, present and future climate with the ({% tool [Climate Data Store](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0) %}). With this tool you can have acces to atmospheric data such as ERA5 data. ERA5 provides a snapshot of the atmosphere, land surface and ocean waves for each hour from 1959 onwards (for 1950 to 1958 a preliminary version is available). It includes an uncertainty estimate which highlights the considerable evolution of the observing system, on which reanalysis products rely. +**Key Data**: +- **Sentinel-5P**: Atmospheric composition (SO₂, NO₂, O₃, aerosol index) for air quality and climate studies. +- **ERA5 (Climate Data Store)**: Hourly atmospheric, land, and ocean wave data from 1959–present. +**Tools**: +- [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) +- [Climate Data Store](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0) +**Use Case**: [Volcanic Activity Monitoring (La Soufrière, 2021)](topics/climate/tutorials/sentinel5_data/tutorial.md) -# 🐙 Biodiversity 🐿️ +--- -This englobes the part of the land, ocean, and athmosphere in which organisms are able to live. +## 🏔️ [Solid Earth: The Planet’s Foundation] -## Marine biodiversity 🐳 +**Key Data**: -European marine microbial biodiversity is a poorly understood and under-exploited component of continental biodiversity. This component aims to provide a set of tools for the analysis -of spatial- and time-comparable marine microbial metagenomics data sets for the exploration of biodiversity and its correlations with environmental quality. +- **Seismic and Volcanic Data**: Monitor earthquakes, volcanic eruptions, and tectonic activity. +- **Geodetic Data**: Measure Earth’s shape, gravity, and crustal movements. +**Tools**: +- [QGIS Galaxy Interactive Tool](https://usegalaxy.eu/root?tool_id=interactive_tool_qgis) (for geological maps and WFS services). +**Tutorial**: [Coming Soon!] -### OBIS Ocean Biodiversity Information System +--- -OBIS is a global open-access data and information clearing-house on marine biodiversity for science, conservation and sustainable development. In order to get occurences of marine biodiversity from OBIS you can use the ({% tool [OBIS occurences](toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) %}) tool. +## 🌿 [Continental Surfaces: Land in Focus](topics/ecology/tutorials/ndvi_openeo/tutorial.md) -For more information follow the tutorial related to it called [OBIS marine indicators]({% link topics/ecology/tutorials/obisindicators/tutorial.md %}) or use the workflow Marine omics visualisation `https://usegalaxy.eu/u/marie.josse/w/marine-omics-visualisation` +**Key Data**: -## Land biodiversity 🦤 +- **Sentinel-2**: Multispectral imagery for land cover, vegetation (NDVI), and soil degradation. +- **Scene Classification**: Cloud/snow masks, land cover indices (NDVI, NDSI). +**Tools**: +- [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) +- [QGIS Web Feature Services](topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md) +**Workflow**: [From NDVI to Time Series Visualization](topics/ecology/tutorials/ndvi_openeo/tutorial.md) -GBIF (Global Biodiversity Information Facility, www.gbif.org) is for sure THE most remarkable biodiversity data aggregator worldwide giving access to more than 1 billion records across all taxonomic groups. The data provided via these sources are highly valuable for research. However, some issues exist concerning data heterogeneity, as they are obtained from various collection methods and sources (OBIS is part of GBIF). +--- +## 🐾 [Biodiversity: Life on Earth](topics/ecology/tutorials/obisindicators/tutorial.md) +**Key Data**: -To access those data you can use the ({% tool [Get species occurrences data](toolshed.g2.bx.psu.edu/repos/ecology/spocc_occ/spocc_occ/0.9.0) %}) tool. +- **OBIS (Ocean Biodiversity Information System)**: Global marine species occurrence records. +- **Marine Metagenomics**: Microbial biodiversity and environmental correlations. +**Tools**: +- [OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) +**Workflow**: [Marine Omics Visualization](https://usegalaxy.eu/u/marie.josse/w/marine-omics-visualisation) -For more information follow the tutorial related to it called [Cleaning GBIF data for the use in Ecology]({% link topics/ecology/tutorials/gbif_cleaning/tutorial.md %}). +--- +# 🎯 Conclusion and Next Steps +This tutorial introduced the **Earth System** and its five key components, with a focus on **European/French subdomains** and the **links between climate and ecology**. Each component has dedicated trainings, tools, and workflows on Galaxy to help you explore further. -# Conclusion -Here you have an overview of what's is currently available in terms of data accessibility in Galaxy Earth System. This an on going work more is to come ! +### 🔜 What’s Next? -# Extra information +- **More Tutorials**: Stay tuned for new trainings on Earth System data and analysis! +- **Community**: Join our **[Matrix Channel](https://matrix.to/#/#galaxy-earth-system:matrix.org)** to share ideas and get support. +- **Feedback**: Help us improve by contributing to the **[Galaxy Training Network](https://training.galaxyproject.org/)**. -Coming up soon even more tutorials on and other Earth-System related trainings. Keep an {% icon galaxy-eye %} open if you are interested! +🌟 **Keep an eye on Galaxy for updates—happy exploring!** 🌟 + Date: Wed, 15 Apr 2026 09:28:07 +0200 Subject: [PATCH 02/61] major update of the where to start in earth science --- GRANTS.yaml | 11 + assets/images/gaia_data.png | Bin 0 -> 49562 bytes .../tutorials/atmosphere_101/tutorial.md | 92 ++++++ .../tutorials/earth_system/tutorial.md | 268 ++++++++++++------ topics/climate/tutorials/land_101/tutorial.md | 108 +++++++ .../climate/tutorials/ocean_101/tutorial.md | 77 +++++ 6 files changed, 463 insertions(+), 93 deletions(-) create mode 100644 assets/images/gaia_data.png create mode 100644 topics/climate/tutorials/atmosphere_101/tutorial.md create mode 100644 topics/climate/tutorials/land_101/tutorial.md create mode 100644 topics/climate/tutorials/ocean_101/tutorial.md diff --git a/GRANTS.yaml b/GRANTS.yaml index 15e969ce0741a6..a8ce4e7c1d729c 100644 --- a/GRANTS.yaml +++ b/GRANTS.yaml @@ -315,6 +315,17 @@ fondfrance: 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+ - How can I access and analyze atmospheric datasets for climate and air quality? + - What tools are available for monitoring atmospheric composition ? + - How are atmospheric data and climate connected? +objectives: + - Understand the role of the atmosphere in the Earth's climate system + - Discover key atmospheric datasets (Sentinel-5P, ERA5, etc.) + - Learn how to use Galaxy tools for atmospheric data analysis + - Explore the strong connections between atmospheric data and climate studies + - Access tutorials for visualizing and analyzing atmospheric data +time_estimation: 1H30 +key_points: + - Atmosphere as a layer of gas around the Earth, strongly connected to climate + - Monitoring atmospheric composition with Sentinel-5P + - Accessing ERA5 reanalysis data for climate studies + - Volcanic activity monitoring (SO₂, Aerosol Index) and its climate impacts + - Using Pangeo for advanced atmospheric data analysis +tags: + - earth-system + - atmosphere + - climate +contributors: + - Marie59 +funders: + - gaiadata + - gallantries + - fairease + - eurosciencegateway +--- + +# ☁️ Where to Start with Atmosphere Data in Galaxy + +> Climate 101 Introduction +> Before diving into atmospheric data, it's important to understand the basics of climate science. +> Check out our **[Climate 101 Tutorial](topics/climate/tutorials/climate-101/tutorial.md)** to learn about: +> - The difference between weather and climate +> - Essential Climate Variables (ECVs) +> - Observations, reanalysis, predictions, and projections +{: .comment} + +The **atmosphere** is the layer of gas around the Earth, playing a **critical role in regulating climate, weather, and air quality**. Atmospheric data is **strongly connected to climate studies**, as it helps us understand: +- How greenhouse gases affect global temperatures +- The impact of aerosols on climate patterns +- The relationship between atmospheric composition and extreme weather events + +Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help you explore these connections. + + +## 📌 Key Data Sources and Tools + +### Copernicus Data Space Ecosystem +- **Data**: Atmospheric composition data from the **Sentinel-5 Precursor (Sentinel-5P)** mission, the first Copernicus mission focused on monitoring the atmosphere. + - **Partnership**: Developed by ESA, the European Commission, the Netherlands Space Office, industry, data users, and scientists. + - **Strong Climate Connection**: Sentinel-5P data is essential for studying atmospheric components that drive climate change. +- **Tool**: [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) +- **Tutorials**: + - [Sentinel-5P Data Visualisation](topics/climate/tutorials/sentinel5_data/tutorial.md) + - [Pangeo Tutorial](topics/climate/tutorials/pangeo/tutorial.md) + - [Pangeo Notebook Tutorial](topics/climate/tutorials/pangeo-notebook/tutorial.md) + +#### Volcano 🌋 Use Case +- **Data**: Subset of Sentinel-5P L2 data (e.g., April 1 to May 30, 2021) for the **Antilles region**, focusing on **La Soufrière Saint Vincent** (eruption on April 9, 2021). + - **Variables**: Sulfur dioxide (SO₂) and Aerosol Index (AI). + - **Purpose**: High-temporal-resolution data for studying volcanic impacts on **air quality, air traffic, and climate**. + - **Climate Connection**: Volcanic eruptions can significantly affect climate by injecting aerosols into the stratosphere, which can reflect sunlight and cool the planet. + - **Relevance**: Useful for scientists and institutions monitoring **air quality, aviation safety, and climate impacts**. + + +### Climate Data Store +- **Data**: **ERA5 reanalysis data** providing hourly snapshots of the atmosphere, land surface, and ocean waves from **1959 onwards** (preliminary data available for 1950–1958). + - **Features**: Includes uncertainty estimates to highlight the evolution of observing systems. + - **Strong Climate Connection**: ERA5 is one of the most comprehensive datasets for studying past and present climate. +- **Tool**: [Climate Data Store (Galaxy version 0.2.0)](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0) +- **Tutorial**: [Panoply Tutorial](topics/climate/tutorials/panoply/tutorial.md) (for visualizing atmospheric and climate data). + +## 🔗 Cross-Domain Connections + +The following atmospheric tools and resources **support climate studies** that may overlap with other domains: + +### **Climate Tools (Relevant to All Domains)** +- **[Climate Data Store (ERA5)](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0)** + *Relevant for: Ocean, Land, Biodiversity* + - Hourly atmospheric, land, and ocean wave data for climate studies. + +- **[Sentinel-5P Data](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook)** + *Relevant for: Ocean (marine atmosphere), Land (air quality over land)* + - Atmospheric composition data (SO₂, NO₂, O₃, aerosol index). \ No newline at end of file diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index 4fcd29327481a3..d529d6a0662b30 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -1,174 +1,256 @@ +--- layout: tutorial_hands_on -title: Exploring the Earth System and Its Data on Galaxy -questions: - -- What is the Earth System and why is it important? -- What types of Earth data are available on Galaxy? -- How can I access and analyze Earth data for ocean, atmosphere, solid earth, continental surfaces, and biodiversity? -objectives: -- Understand the Earth System and its components -- Discover the terminology and data sources for Earth science -- Learn about Earth observations, reanalysis, and visualization tools on Galaxy -- Explore European and French subdomains, and their relevance to climate and ecology +title: Where to start with earth system science in Galaxy +zenodo_link: '' # Add Zenodo DOI if available +questions: + - What is the Earth System and why is it important? + - What types of Earth data are available on Galaxy? + - How can I access and analyze Earth data for ocean, atmosphere, solid earth, continental surfaces, and biodiversity? +objectives: + - Understand the Earth System and its components + - Discover the terminology and data sources for Earth science + - Learn about Earth observations, reanalysis, and visualization tools on Galaxy + - Explore European and French subdomains, and their relevance to climate and ecology time_estimation: 1H30 -key_points: -- Earth System as a complex, interconnected system -- Essential variables and data types (observations, reanalysis, models) -- European and French subdomains -- Climate and ecology as interconnected themes -tags: - - earth-system - - ocean - - atmosphere - - solid-earth - - continental-surfaces - - biodiversity - - climate +key_points: + - Earth System as a complex, interconnected system + - Essential variables and data types (observations, reanalysis, models) + - European and French subdomains + - Climate and ecology as interconnected themes +tags: + - earth-system + - ocean + - atmosphere + - solid-earth + - land + - biodiversity + - climate - ecology - contributions: - authorship: +contributors: - Marie59 - funding: - - gaia-data +funders: + - gaiadata - gallantries - fairease - eurosciencegateway --- +> +> +> In this tutorial, we will cover: +> +> 1. TOC +> {:toc} +> +{: .agenda} + # 🌍 Introduction to the Earth System The **Earth System** is a dynamic and interconnected network of components—**atmosphere, hydrosphere (ocean), geosphere (solid earth), biosphere (biodiversity), and continental surfaces (land)**—that interact to shape our planet’s climate, weather, and life. Understanding these interactions is critical for addressing global challenges like climate change, biodiversity loss, and natural disasters. ![Graphic visualization of an Earth System](../../images/earth_system/earth_system_galaxy.png) -### Why Study the Earth System? +## Why Study the Earth System? - **Climate Change**: Monitor and predict impacts on temperature, sea levels, and extreme weather. - **Biodiversity**: Track ecosystems and species to protect natural habitats. - **Natural Resources**: Manage water, soil, and minerals sustainably. - **Human Health**: Understand air quality, pollution, and disease vectors. -### 🔗 Join the Conversation +## 🔗 Join the Conversation Connect with the community and ask questions in our **[Matrix Channel](https://matrix.to/#/#galaxy-earth-system:matrix.org)**. Explore visualizations and datasets in our **[Earth System Dashboard](https://earth-system.usegalaxy.eu/)**. ---- - -# 🌎 European and French Subdomains -The **Galaxy Earth System** platform focuses on **European and French** dedicated spaces to provide specific data and tools for analysis. These platforms are: +## 🌎 European and French Subdomains - - **[Earth System European subdomain](https://earth-system.usegalaxy.eu/)**. The original subdomain, fully operational. - - **[Earth System French lab](https://earth-system.usegalaxy.fr/)**. On this french instance the interactive tools are not working. +The **Galaxy Earth System** platform includes two dedicated spaces for regional analysis: +- **🇪🇺 [Earth System European Subdomain](https://earth-system.usegalaxy.eu/)** +The **original subdomain**, fully operational and designed to: + - Enable **cross-border collaboration** on Earth System research. + - Provide **high-resolution datasets** for Europe. +- **🇫🇷 [Earth System French Lab](https://earth-system.usegalaxy.fr/)** +A **test environment** to prove the feasibility of a dedicated subdomain. + - Acts as a **proof of concept** for thematical Galaxy Labs. + - **Interactive tools are currently not working** on this instance. + - Aims to **replicate the model** for other Galaxy instances in the future. - -### 📚 Learning Pathway: Building the European Subdomain +## 📚 Learning Pathway: Building the European Subdomain Discover how we created the **European subdomain** on Galaxy in our dedicated **[Learning Pathway](learning-pathways/dev_tools_training.md)**. This pathway covers: -- Set up your subdomain for your community -- Build a batch tool -- Build an interactive tool +- Set up your subdomain for your community. +- Build a batch tool. +- Build an interactive tool. + ---- # 🌐 Climate and Ecology: Strongly Linked Themes Climate and ecology are **inextricably linked**: - **Climate** drives ecological processes (e.g., temperature affects species distribution). -- **Ecology** influences climate (e.g., forests absorb CO₂, oceans regulate heat). +- **Ecology** influences climate (e.g., forests absorb CO₂, oceans regulate heat). + On Galaxy, you can explore these connections through: + - **Climate Data**: ERA5 reanalysis, Sentinel-5P atmospheric data. - **Ecological Data**: OBIS biodiversity records, Sentinel-2 land cover. - **Integrated Workflows**: Combine climate and ecological datasets to study impacts like habitat loss or carbon cycles. +## 📚 Learn More + +- [Climate 101 Tutorial](topics/climate/tutorials/climate-101/tutorial.md): Introduction to climate science and data. +- [Climate Subdomain](https://climate.usegalaxy.eu/): Dedicated platform for climate data and analysis. +- [Ecology Subdomain](https://ecology.usegalaxy.eu/): Dedicated platform for ecological data and analysis. + + 💬 **Discuss these links in our [Matrix Channel](https://matrix.to/#/#galaxy-earth-system:matrix.org)**! ---- # 🗂️ Explore Earth System Components -Click on the boxes below to dive into dedicated trainings for each component of the Earth System. -Each box includes **data sources, tools, and tutorials** to help you get started. +Choose which Earth System component you want to explore: +**Ocean, Atmosphere, Land, Geosphere (Solid Earth), or Biodiversity**. ---- +{% include _includes/cyoa-choices.html + option1="Ocean" + option2="Atmosphere" + option3="Land" + option4="Geosphere" + option5="Biodiversity" + default="Ocean" + text="Select a component to learn about its data, tools, and tutorials on Galaxy." %} -## 🌊 [Ocean: Monitoring the Blue Planet](topics/climate/tutorials/argo_pangeo/tutorial.md) -**Key Data**: +

-- **Argo Program**: Temperature, salinity, and biogeochemical parameters (chlorophyll, oxygen, nitrate) from floating sensors. -- **Copernicus Sentinel-3**: Sea surface temperature, topography, and color for ocean forecasting. -**Tools**: -- [Argo Data Access](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) -- [Copernicus Data Space Ecosystem (JupyterLab)](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) -**Workflow**: [Full Analyse Argo Data](https://earth-system.usegalaxy.eu/u/marie.josse/w/full-analyse-argo-data) +## 🌊 Ocean 🌊 ---- +The ocean is a key component of the Earth’s climate system. It requires continuous real-time monitoring to help scientists better understand its dynamics and predict its evolution. -## ☁️ [Atmosphere: The Invisible Shield](topics/climate/tutorials/sentinel5_data/tutorial.md) +### On Galaxy -**Key Data**: +🌊 Teaser: Dive into Ocean Data with Galaxy! -- **Sentinel-5P**: Atmospheric composition (SO₂, NO₂, O₃, aerosol index) for air quality and climate studies. -- **ERA5 (Climate Data Store)**: Hourly atmospheric, land, and ocean wave data from 1959–present. -**Tools**: -- [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) -- [Climate Data Store](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0) -**Use Case**: [Volcanic Activity Monitoring (La Soufrière, 2021)](topics/climate/tutorials/sentinel5_data/tutorial.md) +Ever wondered how scientists monitor the **hidden world beneath the waves**? With Galaxy, you can explore **real-time ocean data** from global networks like **Argo**, **Copernicus Sentinel-3**, and **EMODnet Chemistry** to study: +- Ocean currents and temperature (Argo floats). +- Sea surface topography and color (Sentinel-3). +- Marine chemistry and pollutants (EMODnet). +- Climate impacts on marine ecosystems (Copernicus Marine Data Store). ---- +👉[Start your ocean data journey here](topics/climate/tutorials/ocean_101/tutorial.md) and discover how to analyze and visualize ocean data with Galaxy! + + +
+ +
+ +## ☁️ Atmosphere 🌫️ + +The atmosphere is the layer of gas around the Earth, critical for regulating climate and weather. + +### On Galaxy + +☁️ Teaser: Explore the Atmosphere and Its Climate Connections with Galaxy! + +How do scientists monitor the **invisible layer of gas** that surrounds our planet and drives our climate? With Galaxy, you can dive into **atmospheric data** from **Sentinel-5P** and **ERA5** to study: + +- **Atmospheric composition** (e.g., SO₂, NO₂, O₃, aerosol index) and its impact on climate +- **Volcanic activity** (e.g., La Soufrière eruption in the Antilles) and its climate effects +- **Climate reanalysis** (e.g., ERA5 hourly data for past and present climate studies) -## 🏔️ [Solid Earth: The Planet’s Foundation] +💡 **New to atmospheric or climate data?** Our [Where to Start with Atmosphere Data in Galaxy tutorial](topics/climate/tutorials/atmosphere_101/tutorial.md) offer comprehensive guidance! -**Key Data**: +
+
+ +## 🏜️ Land 🏞️ + +Land includes solid Earth, soil, and surface processes like erosion, desertification, and climate change impacts. + +### On Galaxy + +🏜️ Teaser: Explore Land Data and Its Climate Connections with Galaxy! + +How do scientists monitor the **solid surface of our planet** and its interactions with climate? With Galaxy, you can dive into **land data** from **Sentinel-2**, **QGIS**, and **FATES** to study: + +- **Land surface changes** (erosion, desertification, urbanization) +- **Vegetation health** using NDVI and other spectral indices +- **Land-atmosphere interactions** that influence climate +- **Ecosystem modeling** with FATES to understand climate impacts + + +💡 **New to land or climate data?** Our [Where to Start with Land Data in Galaxy tutorial](topics/climate/tutorials/land_101/tutorial.md) offer comprehensive guidance! + +
+ +
+ +## 🌋 Geosphere (Solid Earth) + +The geosphere includes Earth's rocks, minerals, and tectonic processes. + +### On Galaxy - **Seismic and Volcanic Data**: Monitor earthquakes, volcanic eruptions, and tectonic activity. -- **Geodetic Data**: Measure Earth’s shape, gravity, and crustal movements. -**Tools**: -- [QGIS Galaxy Interactive Tool](https://usegalaxy.eu/root?tool_id=interactive_tool_qgis) (for geological maps and WFS services). -**Tutorial**: [Coming Soon!] +- **Geodetic Data**: Measure Earth’s shape, gravity, and crustal movements. +- **Tool**: [QGIS Galaxy Interactive Tool](https://usegalaxy.eu/root?tool_id=interactive_tool_qgis) (for geological maps). ---- +
-## 🌿 [Continental Surfaces: Land in Focus](topics/ecology/tutorials/ndvi_openeo/tutorial.md) +
-**Key Data**: +## 🐙 Biodiversity 🐿️ -- **Sentinel-2**: Multispectral imagery for land cover, vegetation (NDVI), and soil degradation. -- **Scene Classification**: Cloud/snow masks, land cover indices (NDVI, NDSI). -**Tools**: -- [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) -- [QGIS Web Feature Services](topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md) -**Workflow**: [From NDVI to Time Series Visualization](topics/ecology/tutorials/ndvi_openeo/tutorial.md) +Biodiversity encompasses all living organisms in the ocean, atmosphere, and land. ---- +### On Galaxy -## 🐾 [Biodiversity: Life on Earth](topics/ecology/tutorials/obisindicators/tutorial.md) +🐙 Teaser: Explore Biodiversity with Galaxy! -**Key Data**: +Biodiversity is the **web of life** that connects land, ocean, and atmosphere. With Galaxy, you can: +- **Analyze marine biodiversity** using OBIS data and metagenomics tools. +- **Study terrestrial species** with GBIF's billion-record database. +- **Visualize biodiversity patterns** and their environmental correlations. -- **OBIS (Ocean Biodiversity Information System)**: Global marine species occurrence records. -- **Marine Metagenomics**: Microbial biodiversity and environmental correlations. -**Tools**: -- [OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) -**Workflow**: [Marine Omics Visualization](https://usegalaxy.eu/u/marie.josse/w/marine-omics-visualisation) +🔹 **For a deep dive into biodiversity analysis**, start with the **[Intro to Galaxy and Ecology Learning Pathway](learning-pathways/intro-to-galaxy-and-ecology.md)**—your gateway to Galaxy's biodiversity tools and workflows. ---- +🔹 **Explore specific datasets**: +- [OBIS Marine Indicators Tutorial](topics/ecology/tutorials/obisindicators/tutorial.md) +- [Cleaning GBIF Data Tutorial](topics/ecology/tutorials/cleaning-gbif-data/tutorial.md) + +## 🔗 Cross-Domain Connections + +Biodiversity data spans **land, ocean, and atmosphere**. The following tools are **also listed in their respective domain pages**: + +🔹 **Access tools**: +- [OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) +* Also listed in [Where to start with ocean data in galaxy](topics/climate/tutorials/ocean_101/tutorial.md)* +- [Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0) +* Also listed in [Where to start with ocean data in galaxy](topics/climate/tutorials/ocean_101/tutorial.md)* -# 🎯 Conclusion and Next Steps + +💡 **New to biodiversity data?** The **[Ecology Subdomain](https://ecology.usegalaxy.eu/)** is your one-stop shop for all things biodiversity in Galaxy! + +
+ +# 🌟 Conclusion and Next Steps This tutorial introduced the **Earth System** and its five key components, with a focus on **European/French subdomains** and the **links between climate and ecology**. Each component has dedicated trainings, tools, and workflows on Galaxy to help you explore further. -### 🔜 What’s Next? +## 🔜 What’s Next? - **More Tutorials**: Stay tuned for new trainings on Earth System data and analysis! - **Community**: Join our **[Matrix Channel](https://matrix.to/#/#galaxy-earth-system:matrix.org)** to share ideas and get support. - **Feedback**: Help us improve by contributing to the **[Galaxy Training Network](https://training.galaxyproject.org/)**. -🌟 **Keep an eye on Galaxy for updates—happy exploring!** 🌟 - Climate 101 Introduction +> Before diving into land data, it's important to understand the basics of climate science and its connection to land surfaces. +> Check out our **[Climate 101 Tutorial](topics/climate/tutorials/climate-101/tutorial.md)** to learn about: +> - The difference between weather and climate +> - Essential Climate Variables (ECVs) related to land +> - How land surfaces interact with climate systems +{: .comment} + +The **land** component encompasses the solid part of Earth, including rocks, soils, and surface processes. It plays a **critical role in the Earth's climate system** through: +- **Carbon storage** in soils and vegetation +- **Albedo effects** (reflectivity of land surfaces) +- **Water cycle** interactions +- **Land-atmosphere exchanges** of energy, water, and greenhouse gases + +This component aims at assessing **land and soil degradation**, such as: +- Erosion +- Loss of organic matter and soil biodiversity +- Compaction +- Salinization +- Landslides +- Contamination +- Sealing +- Desertification +- **Climate change impacts** + + +## 📌 Key Data Sources and Tools + +### Copernicus Data Space Ecosystem +- **Data**: The **Copernicus Sentinel-2 mission** consists of two polar-orbiting satellites in sun-synchronous orbit (180° phase difference). + - **Capabilities**: Wide swath width (290 km) and high revisit time for monitoring land surface changes. + - **Applications**: Supports **land monitoring, agriculture, emergency management, risk mapping, forestry, climate change studies, disaster control, and humanitarian relief operations**. + - **Strong Climate Connection**: Sentinel-2 data is essential for studying land cover changes that affect climate patterns. + +- **Scene Classification Algorithm**: + - Uses reflective properties to detect clouds and snow. + - Based on threshold tests using TOA reflectance, band ratios, and indices like: + - **Normalised Difference Vegetation Index (NDVI)**: Measures vegetation health and density. + - **Normalised Difference Snow and Ice Index (NDSI)**: Detects snow and ice cover. + - Produces probabilistic cloud and snow mask quality indicators. + - **Climate Relevance**: NDVI is crucial for studying vegetation changes related to climate variability. + +- **Tool**: [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) +- **Tutorial**: [From NDVI data with OpenEO to time series visualisation with Holoviews](topics/ecology/tutorials/ndvi_openeo/tutorial.md) + + +### QGIS (Geographical Information System) +- **Functionality**: Access, filter, and import GIS data through **WFS (Web Feature Services)** and **WMS (Web Map Services)**. + - **WMS**: Allows users to access and display maps stored remotely. + - **WFS**: Provides access to data features for modification and custom map creation. + - **Strong Climate Connection**: GIS tools help analyze spatial patterns of land degradation and their climate impacts. + +- **Tool**: [QGIS Galaxy Interactive Tool](https://usegalaxy.eu/root?tool_id=interactive_tool_qgis) +- **Tutorial**: [QGIS Web Feature Services](topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md) + + +### FATES (Functionally Assembled Terrestrial Ecosystem Simulator) +- **Purpose**: Advanced modeling of terrestrial ecosystems and their interactions with climate. +- **Tutorials**: + - [FATES JupyterLab Tutorial](topics/climate/tutorials/fates-jupyterlab/tutorial.md) + - [FATES Tutorial](topics/climate/tutorials/fates/tutorial.md) +- **Strong Climate Connection**: FATES helps study how land ecosystems respond to and influence climate change. + +## 🔗 Cross-Domain Connections + +The following tools and resources are **also relevant to other Earth System domains**: + +### **Biodiversity Tools (Terrestrial Focus)** +- **[Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0)** + *Also listed in: [Biodiversity](topics/climate/tutorials/earth_system/tutorial.md)* + - Access GBIF's global biodiversity records for terrestrial species. diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md new file mode 100644 index 00000000000000..ccf39232ed1b18 --- /dev/null +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -0,0 +1,77 @@ +--- +layout: tutorial_hands_on +title: Where to Start with Ocean Data in Galaxy +zenodo_link: '' # Add Zenodo DOI if available +questions: + - What ocean data is available in Galaxy? + - How can I access and analyze ocean datasets? + - What tools are available for oceanography, marine chemistry, and climate interactions? +objectives: + - Discover key ocean datasets (Argo, Copernicus, EMODnet, etc.) + - Learn how to use Galaxy tools for ocean data analysis + - Explore tutorials and workflows for ocean data visualization +time_estimation: 1H +key_points: + - Ocean as a key component of the Earth’s climate system + - Real-time monitoring with Argo, Sentinel-3, and EMODnet + - Tools for ocean data access, analysis, and visualization +tags: + - earth-system + - ocean + - climate +contributors: + - Marie59 +funders: + - gaiadata + - gallantries + - fairease + - eurosciencegateway +--- + +# 🌊 Where to Start with Ocean Data in Galaxy + +The ocean is a key component of the Earth’s climate system, requiring **continuous real-time monitoring** to understand its dynamics and predict its evolution. Galaxy provides access to a variety of ocean datasets, tools, and tutorials to help you explore oceanography, marine chemistry, and climate interactions. + + +## 📌 Key Data Sources and Tools + +### **Argo Program** +- **Data**: Latitude, longitude, time, water temperature, pressure, salinity, chlorophyll, oxygen, and nitrate. +- **Tool**: [Argo Data Access (Galaxy version 0.1.15+galaxy0)](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) +- **Tutorial**: [Analyse Argo Data](topics/climate/tutorials/argo_pangeo/tutorial.md) +- **Workflow**: [Full Analyse Argo Data](https://earth-system.usegalaxy.eu/u/marie.josse/w/full-analyse-argo-data) + + +### **Copernicus Data Space Ecosystem** +- **Data**: Sea surface topography, sea and land surface temperature, ocean and land surface color (Sentinel-3 mission). +- **Tool**: [Copernicus Data Space Ecosystem (JupyterLab)](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) +- **Tutorial**: [Sentinel-5P Data Visualisation](topics/climate/tutorials/sentinel5_data/tutorial.md) +- **Example**: In JupyterLab, navigate to `samples > openeo > Sentinel_3.ipynb` for a Sentinel-3 data example. + + +### **EMODnet Chemistry** +- **Data**: Standardized, harmonized, and validated marine chemical data for European sea basins (eutrophication, contaminants). +- **Tool**: [Ocean Data View (ODV)](https://usegalaxy.eu/root?tool_id=interactive_tool_odv) +- **Tutorials & Workflows**: + - [Ocean’s Variables Study](topics/climate/tutorials/ocean_qcv_analysis/tutorial.md) + - [Workflow: Ocean’s Variables Study](https://usegalaxy.eu/u/marie.josse/w/oceans-var-v2) + - [Ocean Data View (ODV) Tutorial](topics/climate/tutorials/ocean_qcv_analysis/workflows/) + + +### **Copernicus Marine Data Store** +- **Data**: Ocean product catalog with ~15 variables (hindcast, current, and forecast data). +- **Tool**: [Copernicus Marine Data Store retrieve marine data ](toolshed.g2.bx.psu.edu/repos/ecology/copernicusmarine/copernicusmarine/2.3.0+galaxy0) + +## 🔗 Cross-Domain Connections + +The following tools and resources are **also relevant to other Earth System domains**: + +### **Biodiversity Tools (Marine Focus)** +- **[OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2)** + *Also listed in: [Biodiversity](topics/climate/tutorials/earth_system/tutorial.md)* + - Access global marine biodiversity data for science and conservation. + +- **[Marine Omics Visualization Workflow](https://usegalaxy.eu/u/marie.josse/w/marine-omics-visualisation)** + *Also listed in: [Biodiversity](topics/climate/tutorials/earth_system/tutorial.md)* + - Analyze marine microbial metagenomics datasets. + From f844c944c1f39648f2d87bf2c9d269687447faef Mon Sep 17 00:00:00 2001 From: mjosse Date: Wed, 15 Apr 2026 10:50:42 +0200 Subject: [PATCH 03/61] minor updates --- topics/climate/tutorials/atmosphere_101/tutorial.md | 2 +- topics/climate/tutorials/earth_system/tutorial.md | 1 + topics/climate/tutorials/land_101/tutorial.md | 11 ++++++++++- topics/climate/tutorials/ocean_101/tutorial.md | 13 ++++++++++++- 4 files changed, 24 insertions(+), 3 deletions(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index 53c72cc44716a3..c8cdbaf7f25ff2 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -82,7 +82,7 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help The following atmospheric tools and resources **support climate studies** that may overlap with other domains: -### **Climate Tools (Relevant to All Domains)** +### Climate Tools (Relevant to All Domains) - **[Climate Data Store (ERA5)](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0)** *Relevant for: Ocean, Land, Biodiversity* - Hourly atmospheric, land, and ocean wave data for climate studies. diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index d529d6a0662b30..f39d9283cb8e3f 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -141,6 +141,7 @@ Ever wondered how scientists monitor the **hidden world beneath the waves**? Wit - Sea surface topography and color (Sentinel-3). - Marine chemistry and pollutants (EMODnet). - Climate impacts on marine ecosystems (Copernicus Marine Data Store). +- Nitrate calibration and quality control for Argo floats. 👉[Start your ocean data journey here](topics/climate/tutorials/ocean_101/tutorial.md) and discover how to analyze and visualize ocean data with Galaxy! diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index 70d858a25241a5..26c44c92bdcfdb 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -98,11 +98,20 @@ This component aims at assessing **land and soil degradation**, such as: - [FATES Tutorial](topics/climate/tutorials/fates/tutorial.md) - **Strong Climate Connection**: FATES helps study how land ecosystems respond to and influence climate change. + +### 3D Trees Analysis +A suite of tools for processing and visualizing **LiDAR point cloud data** to study forest structure, biomass, and ecosystem dynamics. + +- **[3DTrees: LAS/LAZ Standardization](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/las_laz_standardization/las_laz_standardization/1.0.0)**: Standardize LAS/LAZ files or validate collections for consistency. +- **[3DTrees: Potree Converter](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/potree_converter/potree_converter/1.0.0)**: Convert LAS/LAZ point clouds to Potree octree format for web visualization. + +🔜 **Upcoming**: Public workflow and training materials for 3D tree analysis. + ## 🔗 Cross-Domain Connections The following tools and resources are **also relevant to other Earth System domains**: -### **Biodiversity Tools (Terrestrial Focus)** +### Biodiversity Tools (Terrestrial Focus) - **[Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0)** *Also listed in: [Biodiversity](topics/climate/tutorials/earth_system/tutorial.md)* - Access GBIF's global biodiversity records for terrestrial species. diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index ccf39232ed1b18..8739329781d633 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -41,6 +41,17 @@ The ocean is a key component of the Earth’s climate system, requiring **contin - **Tutorial**: [Analyse Argo Data](topics/climate/tutorials/argo_pangeo/tutorial.md) - **Workflow**: [Full Analyse Argo Data](https://earth-system.usegalaxy.eu/u/marie.josse/w/full-analyse-argo-data) +### **Nitrate DMQC for Argo Floats** +- **Description**: Focuses on **Quality Control (QC) and calibration** of nitrate sensors mounted on Argo floats. This includes **Data Management Quality Control (DMQC)** and **Qualified Control Validation (QCV)** analysis to ensure accurate nitrate measurements. +- **Tutorial**: [Nitrate DMQC for Autonomous Platforms such as Argo Floats](https://github.com/Marie59/training-material/tree/main/topics/climate/tutorials/ocean_qcv_analysis) +- **Workflow**: [Argo-Glider Nitrate QCV](https://usegalaxy.eu/published/workflow?id=44827462c065bae3) +- **Tools Used**: + - **QCV Harmonizer**: Harmonizes vocabulary and format for input files. + - **ODV Collection Manager**: Creates ODV spreadsheet collections for visualization and qualification. + - **Ocean Data View (ODV)**: Interactive tool for visualizing and qualifying data. + - **ODV History Manager**: Reports QC flags and data edits. + - **Biogeochemical Calibration**: Calibrates nitrate using reference datasets and methods. + ### **Copernicus Data Space Ecosystem** - **Data**: Sea surface topography, sea and land surface temperature, ocean and land surface color (Sentinel-3 mission). @@ -66,7 +77,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin The following tools and resources are **also relevant to other Earth System domains**: -### **Biodiversity Tools (Marine Focus)** +### Biodiversity Tools (Marine Focus) - **[OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2)** *Also listed in: [Biodiversity](topics/climate/tutorials/earth_system/tutorial.md)* - Access global marine biodiversity data for science and conservation. From dcde0c6c334bed595ccd61cc437ef43c8b67d4dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 11:35:00 +0200 Subject: [PATCH 04/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 8739329781d633..68ef7557c27a32 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -35,7 +35,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin ## 📌 Key Data Sources and Tools -### **Argo Program** +### Argo Program - **Data**: Latitude, longitude, time, water temperature, pressure, salinity, chlorophyll, oxygen, and nitrate. - **Tool**: [Argo Data Access (Galaxy version 0.1.15+galaxy0)](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) - **Tutorial**: [Analyse Argo Data](topics/climate/tutorials/argo_pangeo/tutorial.md) From ee2b6857aef47d44836af68b433b60f5b316b5fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 11:35:09 +0200 Subject: [PATCH 05/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 68ef7557c27a32..7228c96fa7cfa8 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -41,7 +41,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin - **Tutorial**: [Analyse Argo Data](topics/climate/tutorials/argo_pangeo/tutorial.md) - **Workflow**: [Full Analyse Argo Data](https://earth-system.usegalaxy.eu/u/marie.josse/w/full-analyse-argo-data) -### **Nitrate DMQC for Argo Floats** +### Nitrate DMQC for Argo Floats - **Description**: Focuses on **Quality Control (QC) and calibration** of nitrate sensors mounted on Argo floats. This includes **Data Management Quality Control (DMQC)** and **Qualified Control Validation (QCV)** analysis to ensure accurate nitrate measurements. - **Tutorial**: [Nitrate DMQC for Autonomous Platforms such as Argo Floats](https://github.com/Marie59/training-material/tree/main/topics/climate/tutorials/ocean_qcv_analysis) - **Workflow**: [Argo-Glider Nitrate QCV](https://usegalaxy.eu/published/workflow?id=44827462c065bae3) From d710f8e65547ec5ce2cd5da5b3a6924c0853bf05 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 11:35:21 +0200 Subject: [PATCH 06/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 7228c96fa7cfa8..170765d3e7af88 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -53,7 +53,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin - **Biogeochemical Calibration**: Calibrates nitrate using reference datasets and methods. -### **Copernicus Data Space Ecosystem** +### Copernicus Data Space Ecosystem - **Data**: Sea surface topography, sea and land surface temperature, ocean and land surface color (Sentinel-3 mission). - **Tool**: [Copernicus Data Space Ecosystem (JupyterLab)](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) - **Tutorial**: [Sentinel-5P Data Visualisation](topics/climate/tutorials/sentinel5_data/tutorial.md) From 560d871422d78d6225c1210f573c2522fbf6c777 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 11:35:29 +0200 Subject: [PATCH 07/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 170765d3e7af88..6f25746d2d71c1 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -60,7 +60,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin - **Example**: In JupyterLab, navigate to `samples > openeo > Sentinel_3.ipynb` for a Sentinel-3 data example. -### **EMODnet Chemistry** +### EMODnet Chemistry - **Data**: Standardized, harmonized, and validated marine chemical data for European sea basins (eutrophication, contaminants). - **Tool**: [Ocean Data View (ODV)](https://usegalaxy.eu/root?tool_id=interactive_tool_odv) - **Tutorials & Workflows**: From 6491660c5b99775605f66f68bbd80df86edfd43a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 11:35:51 +0200 Subject: [PATCH 08/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 6f25746d2d71c1..06c708897b8db6 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -69,7 +69,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin - [Ocean Data View (ODV) Tutorial](topics/climate/tutorials/ocean_qcv_analysis/workflows/) -### **Copernicus Marine Data Store** +### Copernicus Marine Data Store - **Data**: Ocean product catalog with ~15 variables (hindcast, current, and forecast data). - **Tool**: [Copernicus Marine Data Store retrieve marine data ](toolshed.g2.bx.psu.edu/repos/ecology/copernicusmarine/copernicusmarine/2.3.0+galaxy0) From b04c7ad798df073fc93101f55e3e02bb9c8ab798 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 12:00:24 +0200 Subject: [PATCH 09/61] fix links --- .../tutorials/earth_system/tutorial.md | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index f39d9283cb8e3f..c4f79b03863905 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -80,7 +80,7 @@ A **test environment** to prove the feasibility of a dedicated subdomain. ## 📚 Learning Pathway: Building the European Subdomain -Discover how we created the **European subdomain** on Galaxy in our dedicated **[Learning Pathway](learning-pathways/dev_tools_training.md)**. This pathway covers: +Discover how we created the **European subdomain** on Galaxy in our dedicated **[Learning Pathway]( {% link learning-pathways/dev_tools_training.md %} )**. This pathway covers: - Set up your subdomain for your community. - Build a batch tool. @@ -103,7 +103,7 @@ On Galaxy, you can explore these connections through: ## 📚 Learn More -- [Climate 101 Tutorial](topics/climate/tutorials/climate-101/tutorial.md): Introduction to climate science and data. +- [Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md %} ): Introduction to climate science and data. - [Climate Subdomain](https://climate.usegalaxy.eu/): Dedicated platform for climate data and analysis. - [Ecology Subdomain](https://ecology.usegalaxy.eu/): Dedicated platform for ecological data and analysis. @@ -143,7 +143,7 @@ Ever wondered how scientists monitor the **hidden world beneath the waves**? Wit - Climate impacts on marine ecosystems (Copernicus Marine Data Store). - Nitrate calibration and quality control for Argo floats. -👉[Start your ocean data journey here](topics/climate/tutorials/ocean_101/tutorial.md) and discover how to analyze and visualize ocean data with Galaxy! +👉[Start your ocean data journey here]( {% link topics/climate/tutorials/ocean_101/tutorial.md %} ) and discover how to analyze and visualize ocean data with Galaxy! @@ -164,7 +164,7 @@ How do scientists monitor the **invisible layer of gas** that surrounds our plan - **Volcanic activity** (e.g., La Soufrière eruption in the Antilles) and its climate effects - **Climate reanalysis** (e.g., ERA5 hourly data for past and present climate studies) -💡 **New to atmospheric or climate data?** Our [Where to Start with Atmosphere Data in Galaxy tutorial](topics/climate/tutorials/atmosphere_101/tutorial.md) offer comprehensive guidance! +💡 **New to atmospheric or climate data?** Our [Where to Start with Atmosphere Data in Galaxy tutorial]( {% link topics/climate/tutorials/atmosphere_101/tutorial.md %} ) offer comprehensive guidance! @@ -186,7 +186,7 @@ How do scientists monitor the **solid surface of our planet** and its interactio - **Ecosystem modeling** with FATES to understand climate impacts -💡 **New to land or climate data?** Our [Where to Start with Land Data in Galaxy tutorial](topics/climate/tutorials/land_101/tutorial.md) offer comprehensive guidance! +💡 **New to land or climate data?** Our [Where to Start with Land Data in Galaxy tutorial]( {% link topics/climate/tutorials/land_101/tutorial.md %} ) offer comprehensive guidance! @@ -218,11 +218,11 @@ Biodiversity is the **web of life** that connects land, ocean, and atmosphere. W - **Study terrestrial species** with GBIF's billion-record database. - **Visualize biodiversity patterns** and their environmental correlations. -🔹 **For a deep dive into biodiversity analysis**, start with the **[Intro to Galaxy and Ecology Learning Pathway](learning-pathways/intro-to-galaxy-and-ecology.md)**—your gateway to Galaxy's biodiversity tools and workflows. +🔹 **For a deep dive into biodiversity analysis**, start with the **[Intro to Galaxy and Ecology Learning Pathway]( {% link learning-pathways/intro-to-galaxy-and-ecology.md} )**—your gateway to Galaxy's biodiversity tools and workflows. 🔹 **Explore specific datasets**: -- [OBIS Marine Indicators Tutorial](topics/ecology/tutorials/obisindicators/tutorial.md) -- [Cleaning GBIF Data Tutorial](topics/ecology/tutorials/cleaning-gbif-data/tutorial.md) +- [OBIS Marine Indicators Tutorial]( {% link topics/ecology/tutorials/obisindicators/tutorial.md %} ) +- [Cleaning GBIF Data Tutorial]( {% link topics/ecology/tutorials/cleaning-gbif-data/tutorial.md %} ) ## 🔗 Cross-Domain Connections @@ -232,7 +232,7 @@ Biodiversity data spans **land, ocean, and atmosphere**. The following tools are - [OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) * Also listed in [Where to start with ocean data in galaxy](topics/climate/tutorials/ocean_101/tutorial.md)* - [Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0) -* Also listed in [Where to start with ocean data in galaxy](topics/climate/tutorials/ocean_101/tutorial.md)* +* Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md} )* 💡 **New to biodiversity data?** The **[Ecology Subdomain](https://ecology.usegalaxy.eu/)** is your one-stop shop for all things biodiversity in Galaxy! @@ -254,4 +254,4 @@ This tutorial introduced the **Earth System** and its five key components, with Coming up soon even more tutorials on and other Earth-System related trainings. Keep an {% icon galaxy-eye %} open if you are interested! -🌟 \ No newline at end of file +🌟 From 1b01ec10bb807918fe5caa16ab4e5217d1fbc7f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 12:03:47 +0200 Subject: [PATCH 10/61] fix link --- topics/climate/tutorials/ocean_101/tutorial.md | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 06c708897b8db6..2fc925f0b4b83b 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -38,12 +38,12 @@ The ocean is a key component of the Earth’s climate system, requiring **contin ### Argo Program - **Data**: Latitude, longitude, time, water temperature, pressure, salinity, chlorophyll, oxygen, and nitrate. - **Tool**: [Argo Data Access (Galaxy version 0.1.15+galaxy0)](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) -- **Tutorial**: [Analyse Argo Data](topics/climate/tutorials/argo_pangeo/tutorial.md) +- **Tutorial**: [Analyse Argo Data]( {% link topics/climate/tutorials/argo_pangeo/tutorial.md} ) - **Workflow**: [Full Analyse Argo Data](https://earth-system.usegalaxy.eu/u/marie.josse/w/full-analyse-argo-data) ### Nitrate DMQC for Argo Floats - **Description**: Focuses on **Quality Control (QC) and calibration** of nitrate sensors mounted on Argo floats. This includes **Data Management Quality Control (DMQC)** and **Qualified Control Validation (QCV)** analysis to ensure accurate nitrate measurements. -- **Tutorial**: [Nitrate DMQC for Autonomous Platforms such as Argo Floats](https://github.com/Marie59/training-material/tree/main/topics/climate/tutorials/ocean_qcv_analysis) +- **Tutorial**: [Nitrate DMQC for Autonomous Platforms such as Argo Floats]( {% link topics/climate/tutorials/ocean_qcv_analysis/tutorial.md} ) - **Workflow**: [Argo-Glider Nitrate QCV](https://usegalaxy.eu/published/workflow?id=44827462c065bae3) - **Tools Used**: - **QCV Harmonizer**: Harmonizes vocabulary and format for input files. @@ -56,7 +56,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin ### Copernicus Data Space Ecosystem - **Data**: Sea surface topography, sea and land surface temperature, ocean and land surface color (Sentinel-3 mission). - **Tool**: [Copernicus Data Space Ecosystem (JupyterLab)](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) -- **Tutorial**: [Sentinel-5P Data Visualisation](topics/climate/tutorials/sentinel5_data/tutorial.md) +- **Tutorial**: [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md} ) - **Example**: In JupyterLab, navigate to `samples > openeo > Sentinel_3.ipynb` for a Sentinel-3 data example. @@ -64,10 +64,8 @@ The ocean is a key component of the Earth’s climate system, requiring **contin - **Data**: Standardized, harmonized, and validated marine chemical data for European sea basins (eutrophication, contaminants). - **Tool**: [Ocean Data View (ODV)](https://usegalaxy.eu/root?tool_id=interactive_tool_odv) - **Tutorials & Workflows**: - - [Ocean’s Variables Study](topics/climate/tutorials/ocean_qcv_analysis/tutorial.md) + - [Ocean’s Variables Study]( {% link topics/climate/tutorials/ocean-variables/tutorial.md }) - [Workflow: Ocean’s Variables Study](https://usegalaxy.eu/u/marie.josse/w/oceans-var-v2) - - [Ocean Data View (ODV) Tutorial](topics/climate/tutorials/ocean_qcv_analysis/workflows/) - ### Copernicus Marine Data Store - **Data**: Ocean product catalog with ~15 variables (hindcast, current, and forecast data). @@ -79,10 +77,10 @@ The following tools and resources are **also relevant to other Earth System doma ### Biodiversity Tools (Marine Focus) - **[OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2)** - *Also listed in: [Biodiversity](topics/climate/tutorials/earth_system/tutorial.md)* + *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md} )* - Access global marine biodiversity data for science and conservation. - **[Marine Omics Visualization Workflow](https://usegalaxy.eu/u/marie.josse/w/marine-omics-visualisation)** - *Also listed in: [Biodiversity](topics/climate/tutorials/earth_system/tutorial.md)* + *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md} )* - Analyze marine microbial metagenomics datasets. From b84ea7247073fb10b8ead66c5633e8a3b7484959 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 12:05:18 +0200 Subject: [PATCH 11/61] fix links --- topics/climate/tutorials/land_101/tutorial.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index 26c44c92bdcfdb..c41fce2beceaed 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -37,7 +37,7 @@ funders: > Climate 101 Introduction > Before diving into land data, it's important to understand the basics of climate science and its connection to land surfaces. -> Check out our **[Climate 101 Tutorial](topics/climate/tutorials/climate-101/tutorial.md)** to learn about: +> Check out our **[Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md} )** to learn about: > - The difference between weather and climate > - Essential Climate Variables (ECVs) related to land > - How land surfaces interact with climate systems @@ -78,7 +78,7 @@ This component aims at assessing **land and soil degradation**, such as: - **Climate Relevance**: NDVI is crucial for studying vegetation changes related to climate variability. - **Tool**: [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) -- **Tutorial**: [From NDVI data with OpenEO to time series visualisation with Holoviews](topics/ecology/tutorials/ndvi_openeo/tutorial.md) +- **Tutorial**: [From NDVI data with OpenEO to time series visualisation with Holoviews]( {% link topics/ecology/tutorials/ndvi_openeo/tutorial.md}) ### QGIS (Geographical Information System) @@ -88,14 +88,14 @@ This component aims at assessing **land and soil degradation**, such as: - **Strong Climate Connection**: GIS tools help analyze spatial patterns of land degradation and their climate impacts. - **Tool**: [QGIS Galaxy Interactive Tool](https://usegalaxy.eu/root?tool_id=interactive_tool_qgis) -- **Tutorial**: [QGIS Web Feature Services](topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md) +- **Tutorial**: [QGIS Web Feature Services]( {% link topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md} ) ### FATES (Functionally Assembled Terrestrial Ecosystem Simulator) - **Purpose**: Advanced modeling of terrestrial ecosystems and their interactions with climate. - **Tutorials**: - [FATES JupyterLab Tutorial](topics/climate/tutorials/fates-jupyterlab/tutorial.md) - - [FATES Tutorial](topics/climate/tutorials/fates/tutorial.md) + - [FATES Tutorial]( {% link topics/climate/tutorials/fates/tutorial.md} ) - **Strong Climate Connection**: FATES helps study how land ecosystems respond to and influence climate change. @@ -113,5 +113,5 @@ The following tools and resources are **also relevant to other Earth System doma ### Biodiversity Tools (Terrestrial Focus) - **[Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0)** - *Also listed in: [Biodiversity](topics/climate/tutorials/earth_system/tutorial.md)* + *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md} )* - Access GBIF's global biodiversity records for terrestrial species. From 5eeed0b219e05169d2cfb583148be5c1634205d8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 12:06:49 +0200 Subject: [PATCH 12/61] fix links --- topics/climate/tutorials/atmosphere_101/tutorial.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index c8cdbaf7f25ff2..76ee4c3585561c 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -37,7 +37,7 @@ funders: > Climate 101 Introduction > Before diving into atmospheric data, it's important to understand the basics of climate science. -> Check out our **[Climate 101 Tutorial](topics/climate/tutorials/climate-101/tutorial.md)** to learn about: +> Check out our **[Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md} )** to learn about: > - The difference between weather and climate > - Essential Climate Variables (ECVs) > - Observations, reanalysis, predictions, and projections @@ -59,9 +59,9 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help - **Strong Climate Connection**: Sentinel-5P data is essential for studying atmospheric components that drive climate change. - **Tool**: [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) - **Tutorials**: - - [Sentinel-5P Data Visualisation](topics/climate/tutorials/sentinel5_data/tutorial.md) - - [Pangeo Tutorial](topics/climate/tutorials/pangeo/tutorial.md) - - [Pangeo Notebook Tutorial](topics/climate/tutorials/pangeo-notebook/tutorial.md) + - [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md} ) + - [Pangeo Tutorial]( {% link topics/climate/tutorials/pangeo/tutorial.md} ) + - [Pangeo Notebook Tutorial]( {% link topics/climate/tutorials/pangeo-notebook/tutorial.md} ) #### Volcano 🌋 Use Case - **Data**: Subset of Sentinel-5P L2 data (e.g., April 1 to May 30, 2021) for the **Antilles region**, focusing on **La Soufrière Saint Vincent** (eruption on April 9, 2021). @@ -76,7 +76,7 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help - **Features**: Includes uncertainty estimates to highlight the evolution of observing systems. - **Strong Climate Connection**: ERA5 is one of the most comprehensive datasets for studying past and present climate. - **Tool**: [Climate Data Store (Galaxy version 0.2.0)](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0) -- **Tutorial**: [Panoply Tutorial](topics/climate/tutorials/panoply/tutorial.md) (for visualizing atmospheric and climate data). +- **Tutorial**: [Panoply Tutorial]( {% link topics/climate/tutorials/panoply/tutorial.md} ) (for visualizing atmospheric and climate data). ## 🔗 Cross-Domain Connections @@ -89,4 +89,4 @@ The following atmospheric tools and resources **support climate studies** that m - **[Sentinel-5P Data](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook)** *Relevant for: Ocean (marine atmosphere), Land (air quality over land)* - - Atmospheric composition data (SO₂, NO₂, O₃, aerosol index). \ No newline at end of file + - Atmospheric composition data (SO₂, NO₂, O₃, aerosol index). From 978bcc54e5a9b6c7058f06ce5492c531451dbe29 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 12:09:24 +0200 Subject: [PATCH 13/61] Update time --- topics/climate/tutorials/atmosphere_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index 76ee4c3585561c..233486d02835ff 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -13,7 +13,7 @@ objectives: - Learn how to use Galaxy tools for atmospheric data analysis - Explore the strong connections between atmospheric data and climate studies - Access tutorials for visualizing and analyzing atmospheric data -time_estimation: 1H30 +time_estimation: 1H key_points: - Atmosphere as a layer of gas around the Earth, strongly connected to climate - Monitoring atmospheric composition with Sentinel-5P From 1c8e49c8a394216c32994603d201f0337c5bc0d8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 12:09:57 +0200 Subject: [PATCH 14/61] Update time --- topics/climate/tutorials/land_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index c41fce2beceaed..12cf19477efef7 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -13,7 +13,7 @@ objectives: - Learn how to use Galaxy tools for land data analysis - Explore the connections between land degradation and climate change - Access tutorials for visualizing and analyzing land data -time_estimation: 1H30 +time_estimation: 1H key_points: - Land as a critical component of the Earth's climate system - Monitoring land surface changes with Sentinel-2 From 719a51460d6095cc91ba675666175438c839a91d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 12:10:21 +0200 Subject: [PATCH 15/61] Update time --- topics/climate/tutorials/earth_system/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index c4f79b03863905..a7dd1d27d424f5 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -11,7 +11,7 @@ objectives: - Discover the terminology and data sources for Earth science - Learn about Earth observations, reanalysis, and visualization tools on Galaxy - Explore European and French subdomains, and their relevance to climate and ecology -time_estimation: 1H30 +time_estimation: 2H key_points: - Earth System as a complex, interconnected system - Essential variables and data types (observations, reanalysis, models) From 42fe8b4f126e95e0af02d9e429cf95cde38e91a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:25:47 +0200 Subject: [PATCH 16/61] Update topics/climate/tutorials/atmosphere_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/atmosphere_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index 233486d02835ff..65352db60fab16 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -37,7 +37,7 @@ funders: > Climate 101 Introduction > Before diving into atmospheric data, it's important to understand the basics of climate science. -> Check out our **[Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md} )** to learn about: +> Check out our **[Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md%} )** to learn about: > - The difference between weather and climate > - Essential Climate Variables (ECVs) > - Observations, reanalysis, predictions, and projections From cbdc8662b9cb48cdc7439ec9e74433cce20d68c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:26:22 +0200 Subject: [PATCH 17/61] Update topics/climate/tutorials/atmosphere_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/atmosphere_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index 65352db60fab16..004617652d5713 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -59,7 +59,7 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help - **Strong Climate Connection**: Sentinel-5P data is essential for studying atmospheric components that drive climate change. - **Tool**: [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) - **Tutorials**: - - [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md} ) + - [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md%} ) - [Pangeo Tutorial]( {% link topics/climate/tutorials/pangeo/tutorial.md} ) - [Pangeo Notebook Tutorial]( {% link topics/climate/tutorials/pangeo-notebook/tutorial.md} ) From 27f79089fd973a1d91b5a39640003fb7065182bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:26:34 +0200 Subject: [PATCH 18/61] Update topics/climate/tutorials/atmosphere_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/atmosphere_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index 004617652d5713..57d4fd38002c1b 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -60,7 +60,7 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help - **Tool**: [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) - **Tutorials**: - [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md%} ) - - [Pangeo Tutorial]( {% link topics/climate/tutorials/pangeo/tutorial.md} ) + - [Pangeo Tutorial]( {% link topics/climate/tutorials/pangeo/tutorial.md%} ) - [Pangeo Notebook Tutorial]( {% link topics/climate/tutorials/pangeo-notebook/tutorial.md} ) #### Volcano 🌋 Use Case From 3b9ebe945749c9d90d8c86d42f32707c8561a7b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:26:44 +0200 Subject: [PATCH 19/61] Update topics/climate/tutorials/atmosphere_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/atmosphere_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index 57d4fd38002c1b..62432e5c0418f3 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -61,7 +61,7 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help - **Tutorials**: - [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md%} ) - [Pangeo Tutorial]( {% link topics/climate/tutorials/pangeo/tutorial.md%} ) - - [Pangeo Notebook Tutorial]( {% link topics/climate/tutorials/pangeo-notebook/tutorial.md} ) + - [Pangeo Notebook Tutorial]( {% link topics/climate/tutorials/pangeo-notebook/tutorial.md%} ) #### Volcano 🌋 Use Case - **Data**: Subset of Sentinel-5P L2 data (e.g., April 1 to May 30, 2021) for the **Antilles region**, focusing on **La Soufrière Saint Vincent** (eruption on April 9, 2021). From c0eb05733166467d46f2b9122c7b0679044ca371 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:27:01 +0200 Subject: [PATCH 20/61] Update topics/climate/tutorials/atmosphere_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/atmosphere_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index 62432e5c0418f3..76e2f885ba3cf6 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -76,7 +76,7 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help - **Features**: Includes uncertainty estimates to highlight the evolution of observing systems. - **Strong Climate Connection**: ERA5 is one of the most comprehensive datasets for studying past and present climate. - **Tool**: [Climate Data Store (Galaxy version 0.2.0)](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0) -- **Tutorial**: [Panoply Tutorial]( {% link topics/climate/tutorials/panoply/tutorial.md} ) (for visualizing atmospheric and climate data). +- **Tutorial**: [Panoply Tutorial]( {% link topics/climate/tutorials/panoply/tutorial.md%} ) (for visualizing atmospheric and climate data). ## 🔗 Cross-Domain Connections From 9e94fce21d5769e786ae43349b1c1866ade6cd0e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:27:10 +0200 Subject: [PATCH 21/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 2fc925f0b4b83b..eb89d4e95ff7c6 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -43,7 +43,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin ### Nitrate DMQC for Argo Floats - **Description**: Focuses on **Quality Control (QC) and calibration** of nitrate sensors mounted on Argo floats. This includes **Data Management Quality Control (DMQC)** and **Qualified Control Validation (QCV)** analysis to ensure accurate nitrate measurements. -- **Tutorial**: [Nitrate DMQC for Autonomous Platforms such as Argo Floats]( {% link topics/climate/tutorials/ocean_qcv_analysis/tutorial.md} ) +- **Tutorial**: [Nitrate DMQC for Autonomous Platforms such as Argo Floats]( {% link topics/climate/tutorials/ocean_qcv_analysis/tutorial.md%} ) - **Workflow**: [Argo-Glider Nitrate QCV](https://usegalaxy.eu/published/workflow?id=44827462c065bae3) - **Tools Used**: - **QCV Harmonizer**: Harmonizes vocabulary and format for input files. From d479d713d25c30f11c017ab0eec91b91e5f18be7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:27:41 +0200 Subject: [PATCH 22/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index eb89d4e95ff7c6..585e85fac85aad 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -56,7 +56,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin ### Copernicus Data Space Ecosystem - **Data**: Sea surface topography, sea and land surface temperature, ocean and land surface color (Sentinel-3 mission). - **Tool**: [Copernicus Data Space Ecosystem (JupyterLab)](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) -- **Tutorial**: [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md} ) +- **Tutorial**: [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md%} ) - **Example**: In JupyterLab, navigate to `samples > openeo > Sentinel_3.ipynb` for a Sentinel-3 data example. From 1184b447c27fefc246c2c095fbd7f7f73e89002e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:27:54 +0200 Subject: [PATCH 23/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 585e85fac85aad..191c2f8543d1ef 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -64,7 +64,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin - **Data**: Standardized, harmonized, and validated marine chemical data for European sea basins (eutrophication, contaminants). - **Tool**: [Ocean Data View (ODV)](https://usegalaxy.eu/root?tool_id=interactive_tool_odv) - **Tutorials & Workflows**: - - [Ocean’s Variables Study]( {% link topics/climate/tutorials/ocean-variables/tutorial.md }) + - [Ocean’s Variables Study]{% link topics/climate/tutorials/ocean-variables/tutorial.md %d }) - [Workflow: Ocean’s Variables Study](https://usegalaxy.eu/u/marie.josse/w/oceans-var-v2) ### Copernicus Marine Data Store From 7943210bde6e563df24a0b4489d8042a7d8c8b43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:28:03 +0200 Subject: [PATCH 24/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 191c2f8543d1ef..7f9b73f27c3979 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -77,7 +77,7 @@ The following tools and resources are **also relevant to other Earth System doma ### Biodiversity Tools (Marine Focus) - **[OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2)** - *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md} )* + *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md%} )* - Access global marine biodiversity data for science and conservation. - **[Marine Omics Visualization Workflow](https://usegalaxy.eu/u/marie.josse/w/marine-omics-visualisation)** From fcd8c6441df56e41dbb5a8582670d3212ae72416 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:28:33 +0200 Subject: [PATCH 25/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 7f9b73f27c3979..114892c93ef3ae 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -81,6 +81,6 @@ The following tools and resources are **also relevant to other Earth System doma - Access global marine biodiversity data for science and conservation. - **[Marine Omics Visualization Workflow](https://usegalaxy.eu/u/marie.josse/w/marine-omics-visualisation)** - *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md} )* + *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md%} )* - Analyze marine microbial metagenomics datasets. From b9b08115430bd2dac04f354e5c0fb8ec6a688e78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:28:51 +0200 Subject: [PATCH 26/61] Update topics/climate/tutorials/earth_system/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/earth_system/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index a7dd1d27d424f5..d06aec8c09fa9b 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -218,7 +218,7 @@ Biodiversity is the **web of life** that connects land, ocean, and atmosphere. W - **Study terrestrial species** with GBIF's billion-record database. - **Visualize biodiversity patterns** and their environmental correlations. -🔹 **For a deep dive into biodiversity analysis**, start with the **[Intro to Galaxy and Ecology Learning Pathway]( {% link learning-pathways/intro-to-galaxy-and-ecology.md} )**—your gateway to Galaxy's biodiversity tools and workflows. +🔹 **For a deep dive into biodiversity analysis**, start with the **[Intro to Galaxy and Ecology Learning Pathway{% link learning-pathways/intro-to-galaxy-and-ecology.md%.md} )**—your gateway to Galaxy's biodiversity tools and workflows. 🔹 **Explore specific datasets**: - [OBIS Marine Indicators Tutorial]( {% link topics/ecology/tutorials/obisindicators/tutorial.md %} ) From 822ce4abe94be3a61c068429012bdd6932d57857 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:29:05 +0200 Subject: [PATCH 27/61] Update topics/climate/tutorials/earth_system/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/earth_system/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index d06aec8c09fa9b..50aa11eee09544 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -232,7 +232,7 @@ Biodiversity data spans **land, ocean, and atmosphere**. The following tools are - [OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) * Also listed in [Where to start with ocean data in galaxy](topics/climate/tutorials/ocean_101/tutorial.md)* - [Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0) -* Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md} )* +* Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md%} )* 💡 **New to biodiversity data?** The **[Ecology Subdomain](https://ecology.usegalaxy.eu/)** is your one-stop shop for all things biodiversity in Galaxy! From 2c7ffedbb6c9aab0aa1c23d45df54dd3c77a68c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:29:18 +0200 Subject: [PATCH 28/61] Update topics/climate/tutorials/land_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/land_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index 12cf19477efef7..701108d57ee7ea 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -37,7 +37,7 @@ funders: > Climate 101 Introduction > Before diving into land data, it's important to understand the basics of climate science and its connection to land surfaces. -> Check out our **[Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md} )** to learn about: +> Check out our **[Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md%} )** to learn about: > - The difference between weather and climate > - Essential Climate Variables (ECVs) related to land > - How land surfaces interact with climate systems From 91677834f24ee9d0fd8fb0c6933c69331a9f04a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:29:32 +0200 Subject: [PATCH 29/61] Update topics/climate/tutorials/land_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/land_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index 701108d57ee7ea..4fcaaf9627b4e9 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -78,7 +78,7 @@ This component aims at assessing **land and soil degradation**, such as: - **Climate Relevance**: NDVI is crucial for studying vegetation changes related to climate variability. - **Tool**: [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) -- **Tutorial**: [From NDVI data with OpenEO to time series visualisation with Holoviews]( {% link topics/ecology/tutorials/ndvi_openeo/tutorial.md}) +- **Tutorial**: [From NDVI data with OpenEO to time series visualisation with Holoviews]( {% link topics/ecology/tutorials/ndvi_openeo/tutorial.md%}) ### QGIS (Geographical Information System) From 6f2ea5f0f23e0e1c19a1034c575bdbcbab921acc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:29:45 +0200 Subject: [PATCH 30/61] Update topics/climate/tutorials/land_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/land_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index 4fcaaf9627b4e9..424b1617870029 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -88,7 +88,7 @@ This component aims at assessing **land and soil degradation**, such as: - **Strong Climate Connection**: GIS tools help analyze spatial patterns of land degradation and their climate impacts. - **Tool**: [QGIS Galaxy Interactive Tool](https://usegalaxy.eu/root?tool_id=interactive_tool_qgis) -- **Tutorial**: [QGIS Web Feature Services]( {% link topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md} ) +- **Tutorial**: [QGIS Web Feature Services]( {% link topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md%} ) ### FATES (Functionally Assembled Terrestrial Ecosystem Simulator) From 54d0ee0b93223dbc67c7b81d579bcdb00fbb2dd2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:30:00 +0200 Subject: [PATCH 31/61] Update topics/climate/tutorials/land_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/land_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index 424b1617870029..c472d0fe148157 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -95,7 +95,7 @@ This component aims at assessing **land and soil degradation**, such as: - **Purpose**: Advanced modeling of terrestrial ecosystems and their interactions with climate. - **Tutorials**: - [FATES JupyterLab Tutorial](topics/climate/tutorials/fates-jupyterlab/tutorial.md) - - [FATES Tutorial]( {% link topics/climate/tutorials/fates/tutorial.md} ) + - [FATES Tutorial]( {% link topics/climate/tutorials/fates/tutorial.md%} ) - **Strong Climate Connection**: FATES helps study how land ecosystems respond to and influence climate change. From 7b0ffd90dddb43774af132beb3d15d5a99456182 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:30:13 +0200 Subject: [PATCH 32/61] Update topics/climate/tutorials/land_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/land_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index c472d0fe148157..c4a45007c5e5c3 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -113,5 +113,5 @@ The following tools and resources are **also relevant to other Earth System doma ### Biodiversity Tools (Terrestrial Focus) - **[Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0)** - *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md} )* + *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md%} )* - Access GBIF's global biodiversity records for terrestrial species. From 0a098d7045160a0571021371aef9b165cbaca5c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 13:30:27 +0200 Subject: [PATCH 33/61] Update topics/climate/tutorials/ocean_101/tutorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 114892c93ef3ae..162da354225fd3 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -38,7 +38,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin ### Argo Program - **Data**: Latitude, longitude, time, water temperature, pressure, salinity, chlorophyll, oxygen, and nitrate. - **Tool**: [Argo Data Access (Galaxy version 0.1.15+galaxy0)](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) -- **Tutorial**: [Analyse Argo Data]( {% link topics/climate/tutorials/argo_pangeo/tutorial.md} ) +- **Tutorial**: [Analyse Argo Data]( {% link topics/climate/tutorials/argo_pangeo/tutorial.md%} ) - **Workflow**: [Full Analyse Argo Data](https://earth-system.usegalaxy.eu/u/marie.josse/w/full-analyse-argo-data) ### Nitrate DMQC for Argo Floats From 4b4ac89f32f16e4656d070feec5b6fe3f6e876d3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 14:18:32 +0200 Subject: [PATCH 34/61] Update tutorial.md --- topics/climate/tutorials/ocean_101/tutorial.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 162da354225fd3..3cbce193d05bf6 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -38,12 +38,12 @@ The ocean is a key component of the Earth’s climate system, requiring **contin ### Argo Program - **Data**: Latitude, longitude, time, water temperature, pressure, salinity, chlorophyll, oxygen, and nitrate. - **Tool**: [Argo Data Access (Galaxy version 0.1.15+galaxy0)](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) -- **Tutorial**: [Analyse Argo Data]( {% link topics/climate/tutorials/argo_pangeo/tutorial.md%} ) +- **Tutorial**: [Analyse Argo Data]( {% link topics/climate/tutorials/argo_pangeo/tutorial.md %} ) - **Workflow**: [Full Analyse Argo Data](https://earth-system.usegalaxy.eu/u/marie.josse/w/full-analyse-argo-data) ### Nitrate DMQC for Argo Floats - **Description**: Focuses on **Quality Control (QC) and calibration** of nitrate sensors mounted on Argo floats. This includes **Data Management Quality Control (DMQC)** and **Qualified Control Validation (QCV)** analysis to ensure accurate nitrate measurements. -- **Tutorial**: [Nitrate DMQC for Autonomous Platforms such as Argo Floats]( {% link topics/climate/tutorials/ocean_qcv_analysis/tutorial.md%} ) +- **Tutorial**: [Nitrate DMQC for Autonomous Platforms such as Argo Floats]( {% link topics/climate/tutorials/ocean_qcv_analysis/tutorial.md %} ) - **Workflow**: [Argo-Glider Nitrate QCV](https://usegalaxy.eu/published/workflow?id=44827462c065bae3) - **Tools Used**: - **QCV Harmonizer**: Harmonizes vocabulary and format for input files. @@ -56,7 +56,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin ### Copernicus Data Space Ecosystem - **Data**: Sea surface topography, sea and land surface temperature, ocean and land surface color (Sentinel-3 mission). - **Tool**: [Copernicus Data Space Ecosystem (JupyterLab)](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) -- **Tutorial**: [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md%} ) +- **Tutorial**: [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md %} ) - **Example**: In JupyterLab, navigate to `samples > openeo > Sentinel_3.ipynb` for a Sentinel-3 data example. @@ -64,7 +64,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin - **Data**: Standardized, harmonized, and validated marine chemical data for European sea basins (eutrophication, contaminants). - **Tool**: [Ocean Data View (ODV)](https://usegalaxy.eu/root?tool_id=interactive_tool_odv) - **Tutorials & Workflows**: - - [Ocean’s Variables Study]{% link topics/climate/tutorials/ocean-variables/tutorial.md %d }) + - [Ocean’s Variables Study]{% link topics/climate/tutorials/ocean-variables/tutorial.md %}) - [Workflow: Ocean’s Variables Study](https://usegalaxy.eu/u/marie.josse/w/oceans-var-v2) ### Copernicus Marine Data Store @@ -77,10 +77,10 @@ The following tools and resources are **also relevant to other Earth System doma ### Biodiversity Tools (Marine Focus) - **[OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2)** - *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md%} )* + *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md %} )* - Access global marine biodiversity data for science and conservation. - **[Marine Omics Visualization Workflow](https://usegalaxy.eu/u/marie.josse/w/marine-omics-visualisation)** - *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md%} )* + *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md %} )* - Analyze marine microbial metagenomics datasets. From baadd09db3be3fc0fea9b5c653fd19ba90082d39 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 15:15:18 +0200 Subject: [PATCH 35/61] Update tutorial.md --- topics/climate/tutorials/earth_system/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index 50aa11eee09544..33db08b2a79f61 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -218,7 +218,7 @@ Biodiversity is the **web of life** that connects land, ocean, and atmosphere. W - **Study terrestrial species** with GBIF's billion-record database. - **Visualize biodiversity patterns** and their environmental correlations. -🔹 **For a deep dive into biodiversity analysis**, start with the **[Intro to Galaxy and Ecology Learning Pathway{% link learning-pathways/intro-to-galaxy-and-ecology.md%.md} )**—your gateway to Galaxy's biodiversity tools and workflows. +🔹 **For a deep dive into biodiversity analysis**, start with the **[Intro to Galaxy and Ecology Learning Pathway{% link learning-pathways/intro-to-galaxy-and-ecology.md %} )**—your gateway to Galaxy's biodiversity tools and workflows. 🔹 **Explore specific datasets**: - [OBIS Marine Indicators Tutorial]( {% link topics/ecology/tutorials/obisindicators/tutorial.md %} ) @@ -230,7 +230,7 @@ Biodiversity data spans **land, ocean, and atmosphere**. The following tools are 🔹 **Access tools**: - [OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) -* Also listed in [Where to start with ocean data in galaxy](topics/climate/tutorials/ocean_101/tutorial.md)* +* Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md %} )* - [Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0) * Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md%} )* From 66fb53d9dc09c807964c9b1efe353811320e5395 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 15:19:56 +0200 Subject: [PATCH 36/61] Update tutorial.md --- topics/climate/tutorials/land_101/tutorial.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index c4a45007c5e5c3..71b60c901e87da 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -37,7 +37,7 @@ funders: > Climate 101 Introduction > Before diving into land data, it's important to understand the basics of climate science and its connection to land surfaces. -> Check out our **[Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md%} )** to learn about: +> Check out our **[Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md %} )** to learn about: > - The difference between weather and climate > - Essential Climate Variables (ECVs) related to land > - How land surfaces interact with climate systems @@ -78,7 +78,7 @@ This component aims at assessing **land and soil degradation**, such as: - **Climate Relevance**: NDVI is crucial for studying vegetation changes related to climate variability. - **Tool**: [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) -- **Tutorial**: [From NDVI data with OpenEO to time series visualisation with Holoviews]( {% link topics/ecology/tutorials/ndvi_openeo/tutorial.md%}) +- **Tutorial**: [From NDVI data with OpenEO to time series visualisation with Holoviews]( {% link topics/ecology/tutorials/ndvi_openeo/tutorial.md %}) ### QGIS (Geographical Information System) @@ -88,14 +88,14 @@ This component aims at assessing **land and soil degradation**, such as: - **Strong Climate Connection**: GIS tools help analyze spatial patterns of land degradation and their climate impacts. - **Tool**: [QGIS Galaxy Interactive Tool](https://usegalaxy.eu/root?tool_id=interactive_tool_qgis) -- **Tutorial**: [QGIS Web Feature Services]( {% link topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md%} ) +- **Tutorial**: [QGIS Web Feature Services]( {% link topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md %} ) ### FATES (Functionally Assembled Terrestrial Ecosystem Simulator) - **Purpose**: Advanced modeling of terrestrial ecosystems and their interactions with climate. - **Tutorials**: - [FATES JupyterLab Tutorial](topics/climate/tutorials/fates-jupyterlab/tutorial.md) - - [FATES Tutorial]( {% link topics/climate/tutorials/fates/tutorial.md%} ) + - [FATES Tutorial]( {% link topics/climate/tutorials/fates/tutorial.md %} ) - **Strong Climate Connection**: FATES helps study how land ecosystems respond to and influence climate change. From 22eb7ebd621a99893d83bea59d092bb1c3595c74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 15:21:55 +0200 Subject: [PATCH 37/61] Update tutorial.md --- topics/climate/tutorials/atmosphere_101/tutorial.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index 76e2f885ba3cf6..714b87af88e2e0 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -37,7 +37,7 @@ funders: > Climate 101 Introduction > Before diving into atmospheric data, it's important to understand the basics of climate science. -> Check out our **[Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md%} )** to learn about: +> Check out our **[Climate 101 Tutorial]( {% link topics/climate/tutorials/climate-101/tutorial.md %} )** to learn about: > - The difference between weather and climate > - Essential Climate Variables (ECVs) > - Observations, reanalysis, predictions, and projections @@ -59,9 +59,9 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help - **Strong Climate Connection**: Sentinel-5P data is essential for studying atmospheric components that drive climate change. - **Tool**: [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) - **Tutorials**: - - [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md%} ) - - [Pangeo Tutorial]( {% link topics/climate/tutorials/pangeo/tutorial.md%} ) - - [Pangeo Notebook Tutorial]( {% link topics/climate/tutorials/pangeo-notebook/tutorial.md%} ) + - [Sentinel-5P Data Visualisation]( {% link topics/climate/tutorials/sentinel5_data/tutorial.md %} ) + - [Pangeo Tutorial]( {% link topics/climate/tutorials/pangeo/tutorial.md %} ) + - [Pangeo Notebook Tutorial]( {% link topics/climate/tutorials/pangeo-notebook/tutorial.md %} ) #### Volcano 🌋 Use Case - **Data**: Subset of Sentinel-5P L2 data (e.g., April 1 to May 30, 2021) for the **Antilles region**, focusing on **La Soufrière Saint Vincent** (eruption on April 9, 2021). @@ -76,7 +76,7 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help - **Features**: Includes uncertainty estimates to highlight the evolution of observing systems. - **Strong Climate Connection**: ERA5 is one of the most comprehensive datasets for studying past and present climate. - **Tool**: [Climate Data Store (Galaxy version 0.2.0)](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0) -- **Tutorial**: [Panoply Tutorial]( {% link topics/climate/tutorials/panoply/tutorial.md%} ) (for visualizing atmospheric and climate data). +- **Tutorial**: [Panoply Tutorial]( {% link topics/climate/tutorials/panoply/tutorial.md %} ) (for visualizing atmospheric and climate data). ## 🔗 Cross-Domain Connections From 06f6efe7c23ad7c6459fb89558c9b001989dbf3e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 15:44:26 +0200 Subject: [PATCH 38/61] Update tutorial.md --- topics/climate/tutorials/land_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index 71b60c901e87da..85a1f1b00c1976 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -94,7 +94,7 @@ This component aims at assessing **land and soil degradation**, such as: ### FATES (Functionally Assembled Terrestrial Ecosystem Simulator) - **Purpose**: Advanced modeling of terrestrial ecosystems and their interactions with climate. - **Tutorials**: - - [FATES JupyterLab Tutorial](topics/climate/tutorials/fates-jupyterlab/tutorial.md) + - [FATES JupyterLab Tutorial]( {% link topics/climate/tutorials/fates-jupyterlab/tutorial.md %} ) - [FATES Tutorial]( {% link topics/climate/tutorials/fates/tutorial.md %} ) - **Strong Climate Connection**: FATES helps study how land ecosystems respond to and influence climate change. From 953cfc83b8a73757996dc535ddd125805795649f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 15:48:53 +0200 Subject: [PATCH 39/61] Update tutorial.md --- topics/climate/tutorials/earth_system/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index 33db08b2a79f61..d03451be0691f8 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -232,7 +232,7 @@ Biodiversity data spans **land, ocean, and atmosphere**. The following tools are - [OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) * Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md %} )* - [Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0) -* Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md%} )* +* Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md %} )* 💡 **New to biodiversity data?** The **[Ecology Subdomain](https://ecology.usegalaxy.eu/)** is your one-stop shop for all things biodiversity in Galaxy! From ebec710bca300c79bafb300e753189ba094e1e35 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 16:01:21 +0200 Subject: [PATCH 40/61] fix tool lonks --- topics/climate/tutorials/earth_system/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index d03451be0691f8..0d4fdf6a54716f 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -229,9 +229,9 @@ Biodiversity is the **web of life** that connects land, ocean, and atmosphere. W Biodiversity data spans **land, ocean, and atmosphere**. The following tools are **also listed in their respective domain pages**: 🔹 **Access tools**: -- [OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) +- {% tool [OBIS Occurrences](toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2)} * Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md %} )* -- [Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0) +- {% tool [Get Species Occurrences Data](toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0)} * Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md %} )* From f313c80d7de5d52f5a4162eccd3902a64e994578 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 16:02:36 +0200 Subject: [PATCH 41/61] Update tutorial.md --- topics/climate/tutorials/atmosphere_101/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index 714b87af88e2e0..85b551da820921 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -75,7 +75,7 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help - **Data**: **ERA5 reanalysis data** providing hourly snapshots of the atmosphere, land surface, and ocean waves from **1959 onwards** (preliminary data available for 1950–1958). - **Features**: Includes uncertainty estimates to highlight the evolution of observing systems. - **Strong Climate Connection**: ERA5 is one of the most comprehensive datasets for studying past and present climate. -- **Tool**: [Climate Data Store (Galaxy version 0.2.0)](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0) +- **Tool**: {% tool [Climate Data Store (Galaxy version 0.2.0)](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0) %} - **Tutorial**: [Panoply Tutorial]( {% link topics/climate/tutorials/panoply/tutorial.md %} ) (for visualizing atmospheric and climate data). ## 🔗 Cross-Domain Connections @@ -83,7 +83,7 @@ Galaxy provides access to **atmospheric datasets, tools, and tutorials** to help The following atmospheric tools and resources **support climate studies** that may overlap with other domains: ### Climate Tools (Relevant to All Domains) -- **[Climate Data Store (ERA5)](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0)** +- **{% tool [Climate Data Store (ERA5)](toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0) %}** *Relevant for: Ocean, Land, Biodiversity* - Hourly atmospheric, land, and ocean wave data for climate studies. From 8a537debadb25139a2c1642b2b13a39be103bca8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 16:04:15 +0200 Subject: [PATCH 42/61] Update tutorial.md --- topics/climate/tutorials/ocean_101/tutorial.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 3cbce193d05bf6..8a0e5199dec15a 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -37,7 +37,7 @@ The ocean is a key component of the Earth’s climate system, requiring **contin ### Argo Program - **Data**: Latitude, longitude, time, water temperature, pressure, salinity, chlorophyll, oxygen, and nitrate. -- **Tool**: [Argo Data Access (Galaxy version 0.1.15+galaxy0)](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) +- **Tool**: {% tool [Argo Data Access (Galaxy version 0.1.15+galaxy0)](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) %} - **Tutorial**: [Analyse Argo Data]( {% link topics/climate/tutorials/argo_pangeo/tutorial.md %} ) - **Workflow**: [Full Analyse Argo Data](https://earth-system.usegalaxy.eu/u/marie.josse/w/full-analyse-argo-data) @@ -69,14 +69,14 @@ The ocean is a key component of the Earth’s climate system, requiring **contin ### Copernicus Marine Data Store - **Data**: Ocean product catalog with ~15 variables (hindcast, current, and forecast data). -- **Tool**: [Copernicus Marine Data Store retrieve marine data ](toolshed.g2.bx.psu.edu/repos/ecology/copernicusmarine/copernicusmarine/2.3.0+galaxy0) +- **Tool**: {% tool [Copernicus Marine Data Store retrieve marine data ](toolshed.g2.bx.psu.edu/repos/ecology/copernicusmarine/copernicusmarine/2.3.0+galaxy0) %} ## 🔗 Cross-Domain Connections The following tools and resources are **also relevant to other Earth System domains**: ### Biodiversity Tools (Marine Focus) -- **[OBIS Occurrences](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2)** +- **{% tool [OBIS Occurrences](toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) %}** *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md %} )* - Access global marine biodiversity data for science and conservation. From 8dfdba7f7e88a26ad70bb2f40b4e8c595f252bff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 16:05:43 +0200 Subject: [PATCH 43/61] Update tutorial.md --- topics/climate/tutorials/land_101/tutorial.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index 85a1f1b00c1976..b5c3878f5186fb 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -102,8 +102,8 @@ This component aims at assessing **land and soil degradation**, such as: ### 3D Trees Analysis A suite of tools for processing and visualizing **LiDAR point cloud data** to study forest structure, biomass, and ecosystem dynamics. -- **[3DTrees: LAS/LAZ Standardization](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/las_laz_standardization/las_laz_standardization/1.0.0)**: Standardize LAS/LAZ files or validate collections for consistency. -- **[3DTrees: Potree Converter](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/potree_converter/potree_converter/1.0.0)**: Convert LAS/LAZ point clouds to Potree octree format for web visualization. +- **{% tool [3DTrees: LAS/LAZ Standardization](toolshed.g2.bx.psu.edu/repos/ecology/las_laz_standardization/las_laz_standardization/1.0.0) %}**: Standardize LAS/LAZ files or validate collections for consistency. +- **{% tool [3DTrees: Potree Converter](toolshed.g2.bx.psu.edu/repos/ecology/potree_converter/potree_converter/1.0.0) %}**: Convert LAS/LAZ point clouds to Potree octree format for web visualization. 🔜 **Upcoming**: Public workflow and training materials for 3D tree analysis. @@ -112,6 +112,6 @@ A suite of tools for processing and visualizing **LiDAR point cloud data** to st The following tools and resources are **also relevant to other Earth System domains**: ### Biodiversity Tools (Terrestrial Focus) -- **[Get Species Occurrences Data](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0)** +- **{% tool [Get Species Occurrences Data](toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0) %}** *Also listed in: [Biodiversity]( {% link topics/climate/tutorials/earth_system/tutorial.md%} )* - Access GBIF's global biodiversity records for terrestrial species. From d8d10774527974fc7e8d3ccb8989deba706e63b6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 15 Apr 2026 16:06:57 +0200 Subject: [PATCH 44/61] Update tutorial.md --- topics/climate/tutorials/earth_system/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index 0d4fdf6a54716f..76c89b89ee37ee 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -229,9 +229,9 @@ Biodiversity is the **web of life** that connects land, ocean, and atmosphere. W Biodiversity data spans **land, ocean, and atmosphere**. The following tools are **also listed in their respective domain pages**: 🔹 **Access tools**: -- {% tool [OBIS Occurrences](toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2)} +- {% tool [OBIS Occurrences](toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2) %} * Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md %} )* -- {% tool [Get Species Occurrences Data](toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0)} +- {% tool [Get Species Occurrences Data](toolshed.g2.bx.psu.edu/repos/ecology/gbif_data/gbif_data/0.9.0) %} * Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md %} )* From 6a768530c9f70adeff481b5babb28cd9aacd1ce4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:26:59 +0200 Subject: [PATCH 45/61] Update tutorial.md --- topics/climate/tutorials/earth_system/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index 76c89b89ee37ee..206421fd01e6a6 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -222,7 +222,7 @@ Biodiversity is the **web of life** that connects land, ocean, and atmosphere. W 🔹 **Explore specific datasets**: - [OBIS Marine Indicators Tutorial]( {% link topics/ecology/tutorials/obisindicators/tutorial.md %} ) -- [Cleaning GBIF Data Tutorial]( {% link topics/ecology/tutorials/cleaning-gbif-data/tutorial.md %} ) +- [Cleaning GBIF Data Tutorial]( {% link topics/ecology/tutorials/gbif_cleaning/tutorial.md %} ) ## 🔗 Cross-Domain Connections From 4cef077dbdb3cb0dfc007fe6147a967bac3d4fb0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:28:42 +0200 Subject: [PATCH 46/61] fix funding --- topics/climate/tutorials/ocean_101/tutorial.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 8a0e5199dec15a..bc6828e8970117 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -20,12 +20,13 @@ tags: - ocean - climate contributors: + authorship: - Marie59 -funders: - - gaiadata - - gallantries - - fairease - - eurosciencegateway + funding: + - gaiadata + - gallantries + - fairease + - eurosciencegateway --- # 🌊 Where to Start with Ocean Data in Galaxy From 13654caf4cac69adba72ba801caa7a374ebe1e96 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:29:01 +0200 Subject: [PATCH 47/61] Update tutorial.md --- topics/climate/tutorials/atmosphere_101/tutorial.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index 85b551da820921..e212a01485e496 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -25,8 +25,9 @@ tags: - atmosphere - climate contributors: + authorship: - Marie59 -funders: + funding: - gaiadata - gallantries - fairease From ab3f404eefb4fc1820bd4dd954c8718ed30c7410 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:29:20 +0200 Subject: [PATCH 48/61] Update tutorial.md --- topics/climate/tutorials/land_101/tutorial.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index b5c3878f5186fb..3c447e1e0913ff 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -25,8 +25,9 @@ tags: - land - climate contributors: + authorship: - Marie59 -funders: + funding: - gaiadata - gallantries - fairease From 947944a8632ace35da9ac0437f1cc2c5d4266523 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:29:48 +0200 Subject: [PATCH 49/61] Update tutorial.md --- topics/climate/tutorials/earth_system/tutorial.md | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index 206421fd01e6a6..656f3634950988 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -27,12 +27,13 @@ tags: - climate - ecology contributors: - - Marie59 -funders: - - gaiadata - - gallantries - - fairease - - eurosciencegateway + authorship: + - Marie59 + funding: + - gaiadata + - gallantries + - fairease + - eurosciencegateway --- From 478cbb6fd0b27f885d51dc256755f2dfe2cf54dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:30:08 +0200 Subject: [PATCH 50/61] fix indent --- topics/climate/tutorials/atmosphere_101/tutorial.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index e212a01485e496..b3ba7328a26ac6 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -26,12 +26,12 @@ tags: - climate contributors: authorship: - - Marie59 + - Marie59 funding: - - gaiadata - - gallantries - - fairease - - eurosciencegateway + - gaiadata + - gallantries + - fairease + - eurosciencegateway --- # ☁️ Where to Start with Atmosphere Data in Galaxy From 83333ff3c823ffdb8a76b0533feb6450ae732b64 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:30:25 +0200 Subject: [PATCH 51/61] Update tutorial.md --- topics/climate/tutorials/land_101/tutorial.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index 3c447e1e0913ff..f9102411139a8c 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -26,12 +26,12 @@ tags: - climate contributors: authorship: - - Marie59 + - Marie59 funding: - - gaiadata - - gallantries - - fairease - - eurosciencegateway + - gaiadata + - gallantries + - fairease + - eurosciencegateway --- # 🏜️ Where to Start with Land Data in Galaxy From 7e893f133bbd0d0c2da2b1bd944c826f5fb7469c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:30:43 +0200 Subject: [PATCH 52/61] Update tutorial.md --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index bc6828e8970117..5f4640a47cf4f6 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -21,7 +21,7 @@ tags: - climate contributors: authorship: - - Marie59 + - Marie59 funding: - gaiadata - gallantries From 5c5224a927e10009bcb02a7ca7d5211e8f61c98d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:39:41 +0200 Subject: [PATCH 53/61] contributors-> contributions --- topics/climate/tutorials/atmosphere_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md index b3ba7328a26ac6..9eeaffc7845c20 100644 --- a/topics/climate/tutorials/atmosphere_101/tutorial.md +++ b/topics/climate/tutorials/atmosphere_101/tutorial.md @@ -24,7 +24,7 @@ tags: - earth-system - atmosphere - climate -contributors: +contributions: authorship: - Marie59 funding: From 998dcec5d5ebe139eeb6efa839dd0d1d39dd0db0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:39:55 +0200 Subject: [PATCH 54/61] Update tutorial.md --- topics/climate/tutorials/earth_system/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index 656f3634950988..a195b0a5b757e1 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -26,7 +26,7 @@ tags: - biodiversity - climate - ecology -contributors: +contributions: authorship: - Marie59 funding: From ef21f4091df5ccf34c4b93e2c6f9dea9034f7c71 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:40:11 +0200 Subject: [PATCH 55/61] Update tutorial.md --- topics/climate/tutorials/land_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md index f9102411139a8c..5c62f11ce56bd0 100644 --- a/topics/climate/tutorials/land_101/tutorial.md +++ b/topics/climate/tutorials/land_101/tutorial.md @@ -24,7 +24,7 @@ tags: - earth-system - land - climate -contributors: +contributions: authorship: - Marie59 funding: From be14a71ee17e21ec584e3118124ae6699befa88b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 16 Apr 2026 09:40:27 +0200 Subject: [PATCH 56/61] Update tutorial.md --- topics/climate/tutorials/ocean_101/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md index 5f4640a47cf4f6..b4177b5a653192 100644 --- a/topics/climate/tutorials/ocean_101/tutorial.md +++ b/topics/climate/tutorials/ocean_101/tutorial.md @@ -19,7 +19,7 @@ tags: - earth-system - ocean - climate -contributors: +contributions: authorship: - Marie59 funding: From 2cf83b09c6a9d445b095fcb0d0e0c466e9abea3f Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Mon, 27 Apr 2026 10:04:38 +0200 Subject: [PATCH 57/61] Update GRANTS.yaml try add openaire and correct id --- GRANTS.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/GRANTS.yaml b/GRANTS.yaml index a8ce4e7c1d729c..caf7ac69c4a299 100644 --- a/GRANTS.yaml +++ b/GRANTS.yaml @@ -321,8 +321,8 @@ gaiadata: joined: 2022-06 avatar: "/training-material/assets/images/gaia_data.png" url: https://www.gaia-data.org/ - funding_id: "21-ESRE-0010" - funding_database: ANR- 21-ESRE-0010 + funding_id: "ANR-21-ESRE-0010" + funding_database: OpenAIRE funding_statement: | This work was supported by the Agence Nationale de la Recherche as part of the “Investissements d’Avenir” Equipex+ Gaia Data program n°ANR-21ESRE-0010. From aad0b03aff6b7db7bca15cb4c4b8b6c2a71af3ac Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Wed, 29 Apr 2026 12:32:31 +0200 Subject: [PATCH 58/61] support ANR as funding body --- GRANTS.yaml | 11 ++++++----- _includes/funding-statement-short.md | 2 +- _layouts/contributor_index.html | 5 +++-- _plugins/gtn/contributors.rb | 2 ++ bin/schema-grants.yaml | 8 +++++++- 5 files changed, 19 insertions(+), 9 deletions(-) diff --git a/GRANTS.yaml b/GRANTS.yaml index caf7ac69c4a299..5c62ae595dbd39 100644 --- a/GRANTS.yaml +++ b/GRANTS.yaml @@ -17,9 +17,9 @@ # url: "https://example.com" # homepage of the project # funding_statement: "This project is funded with the support of .." # optional, if you want a specific bit of text to appear # funding_id: 2020-1-NL01-KA203-064717 # id of your grant, will be used in combination with funding_database to link to offical grant page -# funding_database: cordis|highergov|ukri|erasmusplus # Database where your project/grant is listed, -# # EU grants are often listed in cordis, US grants in highergov, UK grants in ukri -# # If your project is not present in one of these databases, please ping us. +# funding_database: cordis|highergov|ukri|dfg|erasmusplus|anr # Database where your project/grant is listed, +# # EU grants are often listed in cordis, US grants in highergov, UK grants in ukri +# # If your project is not present in one of these databases, please ping us. # # Please add in alphabetical order of the key (id) @@ -321,8 +321,9 @@ gaiadata: joined: 2022-06 avatar: "/training-material/assets/images/gaia_data.png" url: https://www.gaia-data.org/ - funding_id: "ANR-21-ESRE-0010" - funding_database: OpenAIRE + funding_id: "ProjetIA-21-ESRE-0010" + funding_id_display: "21-ESRE-0010" + funding_database: anr funding_statement: | This work was supported by the Agence Nationale de la Recherche as part of the “Investissements d’Avenir” Equipex+ Gaia Data program n°ANR-21ESRE-0010. diff --git a/_includes/funding-statement-short.md b/_includes/funding-statement-short.md index b1748fdefdcc2d..2dd9340356d3bf 100644 --- a/_includes/funding-statement-short.md +++ b/_includes/funding-statement-short.md @@ -11,7 +11,7 @@
{% if site.data.contributors[id].funding_id %} - {{ site.data.contributors[id].funding_id }} + {{ site.data.contributors[id].funding_id_display | default: site.data.contributors[id].funding_id }} {% endif %}
diff --git a/_layouts/contributor_index.html b/_layouts/contributor_index.html index 9bc689c6dae508..90a3dcc689c9d9 100644 --- a/_layouts/contributor_index.html +++ b/_layouts/contributor_index.html @@ -359,10 +359,11 @@

External Links

{% if entity.funding_database %} {% assign url = entity | fetch_funding_url %} - {{ entity.funding_id }} + {{ entity.funding_id_display + default: entity.funding_id }} {% else %} -
{{ entity.funding_id }} +
{{ entity.funding_id_display | default: entity.funding_id }} {% endif %}

diff --git a/_plugins/gtn/contributors.rb b/_plugins/gtn/contributors.rb index c99f6b1ef08bf6..dbd61c00aac638 100644 --- a/_plugins/gtn/contributors.rb +++ b/_plugins/gtn/contributors.rb @@ -237,6 +237,8 @@ def self.fetch_funding_url(contributor) "https://www.highergov.com/contract/#{contributor['funding_id']}/" when 'dfg' "https://gepris-extern.dfg.de/gepris/projekt/#{contributor['funding_id']}?language=en" + when 'anr' + "https://anr.fr/#{contributor['funding_id']}" else Jekyll.logger.error "Unknown funding system #{contributor['funding_database']}. Please let us know so we can add support for it!" 'ERROR' diff --git a/bin/schema-grants.yaml b/bin/schema-grants.yaml index f393d282916de6..fc99e21c748e28 100644 --- a/bin/schema-grants.yaml +++ b/bin/schema-grants.yaml @@ -106,9 +106,15 @@ mapping: funding_id: type: str required: true - description: The short identifier for your grant. + description: The short identifier for your grant. This will be used to construct the URL to your project page on the funding body's website. _examples: - 2020-1-NL01-KA203-064717 + funding_id_display: + type: str + required: false + description: The short identifier for your grant. Only needed if the funding_id cannot be used to construct a url for to your project page. For example for ANR. Then put the id that should be shown to the user here. + _examples: + - 21-ESRE-0010 url: type: str description: associated webpage From 0ff1000d88e667bb78b9b3328ceb863e35e24716 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Wed, 29 Apr 2026 12:39:44 +0200 Subject: [PATCH 59/61] add anr to funding_database enum --- bin/schema-grants.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/schema-grants.yaml b/bin/schema-grants.yaml index fc99e21c748e28..a280035a91eaf3 100644 --- a/bin/schema-grants.yaml +++ b/bin/schema-grants.yaml @@ -129,6 +129,7 @@ mapping: - ukri - highergov - dfg + - anr funder_name: type: str description: A name for the agency providing the funding. From 803689e87cb2d081e0f9bdae97326eb5649c799b Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Wed, 29 Apr 2026 12:45:56 +0200 Subject: [PATCH 60/61] fix --- _layouts/contributor_index.html | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/_layouts/contributor_index.html b/_layouts/contributor_index.html index 90a3dcc689c9d9..9220784e441936 100644 --- a/_layouts/contributor_index.html +++ b/_layouts/contributor_index.html @@ -359,8 +359,7 @@

External Links

{% if entity.funding_database %} {% assign url = entity | fetch_funding_url %} - {{ entity.funding_id_display - default: entity.funding_id }} + {{ entity.funding_id_display | default: entity.funding_id }} {% else %}
{{ entity.funding_id_display | default: entity.funding_id }} From 03271d7ae613afe2cfee104276e430d3f595a9dd Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Wed, 29 Apr 2026 13:04:56 +0200 Subject: [PATCH 61/61] fix link --- topics/climate/tutorials/earth_system/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md index a195b0a5b757e1..575b680989c932 100644 --- a/topics/climate/tutorials/earth_system/tutorial.md +++ b/topics/climate/tutorials/earth_system/tutorial.md @@ -144,7 +144,7 @@ Ever wondered how scientists monitor the **hidden world beneath the waves**? Wit - Climate impacts on marine ecosystems (Copernicus Marine Data Store). - Nitrate calibration and quality control for Argo floats. -👉[Start your ocean data journey here]( {% link topics/climate/tutorials/ocean_101/tutorial.md %} ) and discover how to analyze and visualize ocean data with Galaxy! +👉[Start your ocean data journey here]({% link topics/climate/tutorials/ocean_101/tutorial.md %}) and discover how to analyze and visualize ocean data with Galaxy!