diff --git a/_layouts/contributor_index.html b/_layouts/contributor_index.html
index e8d7133b26b197..9220784e441936 100644
--- a/_layouts/contributor_index.html
+++ b/_layouts/contributor_index.html
@@ -359,7 +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 }}
diff --git a/topics/climate/tutorials/atmosphere_101/tutorial.md b/topics/climate/tutorials/atmosphere_101/tutorial.md
new file mode 100644
index 00000000000000..9eeaffc7845c20
--- /dev/null
+++ b/topics/climate/tutorials/atmosphere_101/tutorial.md
@@ -0,0 +1,93 @@
+---
+layout: tutorial_hands_on
+title: Where to Start with Atmosphere Data in Galaxy
+zenodo_link: '' # Add Zenodo DOI if available
+questions:
+ - What atmospheric data is available in Galaxy?
+ - 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: 1H
+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 (SOโ, Aerosol Index) and its climate impacts
+ - Using Pangeo for advanced atmospheric data analysis
+tags:
+ - earth-system
+ - atmosphere
+ - climate
+contributions:
+ authorship:
+ - Marie59
+ funding:
+ - gaiadata
+ - gallantries
+ - fairease
+ - eurosciencegateway
+---
+
+# โ๏ธ 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]( {% 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
+{: .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.
+
+
+## ๐ 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]( {% 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 ๐ Use Case
+- **Data**: Subset of Sentinel-5P L2 data (e.g., April 1 to May 30, 2021) for the **Antilles region**, focusing on **La Soufriรจre Saint Vincent** (eruption on April 9, 2021).
+ - **Variables**: Sulfur dioxide (SOโ) 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 1950โ1958).
+ - **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**: {% 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).
+
+## ๐ Cross-Domain Connections
+
+The following atmospheric tools and resources **support climate studies** that may overlap with other domains:
+
+### Climate Tools (Relevant to All Domains)
+- **{% 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.
+
+- **[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 (SOโ, NOโ, Oโ, aerosol index).
diff --git a/topics/climate/tutorials/earth_system/tutorial.md b/topics/climate/tutorials/earth_system/tutorial.md
index bb0f24f6eab3d9..575b680989c932 100644
--- a/topics/climate/tutorials/earth_system/tutorial.md
+++ b/topics/climate/tutorials/earth_system/tutorial.md
@@ -1,37 +1,41 @@
---
-layout: tutorial_hands_on
-title: Getting your hands-on earth data
-subtopic: introduction
-questions:
-- What is the Earth System?
-- What type of data is available?
-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
-key_points:
-- Earth System
-- Essential variables
-- Observations, reanalysis, visualisation
-tags:
- - earth-system
- - ocean
- - land
- - atmosphere
- - biodiversity
-contributions:
- authorship:
- - Marie59
- funding:
- - gallantries
- - fairease
- - eurosciencegateway
----
-
+layout: tutorial_hands_on
+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: 2H
+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:
+ - Marie59
+ funding:
+ - gaiadata
+ - 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.
+---
>
>
@@ -42,165 +46,213 @@ anyone interested in learning about Earth system.
>
{: .agenda}
-๐๐๐
+# ๐ 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 componentsโ**atmosphere, hydrosphere (ocean), geosphere (solid earth), biosphere (biodiversity), and continental surfaces (land)**โthat interact to shape our planetโs climate, weather, and life. Understanding these interactions is critical for addressing global challenges like climate change, biodiversity loss, and natural disasters.
-Next we will see for each compartiment which kind of data (and how to get them) are availabe on Galaxy 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.
+
+## ๐ 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/)**.
+
+## ๐ European and French Subdomains
-# ๐ Ocean ๐
+The **Galaxy Earth System** platform includes two dedicated spaces for regional analysis:
-The ocean is a key component of the Earthโs climate system. Thus, it needs continuous real-time monitoring to help scientists better understand its dynamics and predict its evolution.
+- **๐ช๐บ [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.
+- **๐ซ๐ท [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.
-## 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.
+## ๐ Learning Pathway: Building the European Subdomain
-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
+Discover how we created the **European subdomain** on Galaxy in our dedicated **[Learning Pathway]( {% link learning-pathways/dev_tools_training.md %} )**. This pathway covers:
-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.
+- Set up your subdomain for your community.
+- Build a batch tool.
+- Build an interactive 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
+# ๐ Climate and Ecology: Strongly Linked Themes
-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.
+Climate and ecology are **inextricably linked**:
-To access those data you can use the [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) tool.
+- **Climate** drives ecological processes (e.g., temperature affects species distribution).
+- **Ecology** influences climate (e.g., forests absorb COโ, oceans regulate heat).
-For more information follow the tutorial related to it called [Sentinel 5P data visualisation]({% link topics/climate/tutorials/sentinel5_data/tutorial.md %}).
+On Galaxy, you can explore these connections through:
-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.
+- **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.
-## EMODnet Chemistry
+## ๐ Learn More
-[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 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.
-### A focus on ODV (Ocean Data View) collections
-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)
+๐ฌ **Discuss these links in our [Matrix Channel](https://matrix.to/#/#galaxy-earth-system:matrix.org)**!
-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 %})
+# ๐๏ธ Explore Earth System Components
+Choose which Earth System component you want to explore:
+**Ocean, Atmosphere, Land, Geosphere (Solid Earth), or Biodiversity**.
-## Copernicus Marine Data Store
+{% 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." %}
-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.
+
+## ๐ Ocean ๐
+The ocean is a key component of the Earthโs climate system. It requires continuous real-time monitoring to help scientists better understand its dynamics and predict its evolution.
-# ๐๏ธ Land ๐๏ธ
+### On Galaxy
-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.
+๐ Teaser: Dive into Ocean Data with Galaxy!
-## Copernicus Data Space Ecosystem
+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).
+- Nitrate calibration and quality control for Argo floats.
-The Copernicus Data Space Ecosystem provides access to Earth observation data.
+๐[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!
-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 180ยฐ.
-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 Sentinel-2 twin satellites provide image data that largely contribute to existing and ongoing multispectral observations.
+
-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
+## โ๏ธ Atmosphere ๐ซ๏ธ
-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 atmosphere is the layer of gas around the Earth, critical for regulating climate and weather.
-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.
+### On Galaxy
-To access those data you can use the [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) tool.
+โ๏ธ Teaser: Explore the Atmosphere and Its Climate Connections with Galaxy!
-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 %}).
+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., SOโ, NOโ, Oโ, aerosol index) and its impact on climate
+- **Volcanic activity** (e.g., La Soufriรจre eruption in the Antilles) and its climate effects
+- **Climate reanalysis** (e.g., ERA5 hourly data for past and present climate studies)
-## QGIS (Geographical Information System)
+๐ก **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!
-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)
+
-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.
+
-To learn more on how to do that folow [QGIS Web Feature Services]({% link topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md %})
+## ๐๏ธ Land ๐๏ธ
-# โ๏ธ Atmosphere ๐ซ๏ธ
+Land includes solid Earth, soil, and surface processes like erosion, desertification, and climate change impacts.
-This component represents the layer of gas around the Earth.
+### On Galaxy
-## Copernicus Data Space Ecosystem
+๐๏ธ Teaser: Explore Land Data and Its Climate Connections with Galaxy!
-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.
+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:
-To access those data you can use the [Copernicus Data Space Ecosystem](https://usegalaxy.eu/root?tool_id=interactive_tool_copernicus_notebook) tool.
+- **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
-### Volcano ๐
-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 %}).
+๐ก **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!
+
-## Climate Data Store
+
-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.
+## ๐ Geosphere (Solid Earth)
+The geosphere includes Earth's rocks, minerals, and tectonic processes.
-# ๐ Biodiversity ๐ฟ๏ธ
+### On Galaxy
+- **Seismic and Volcanic Data**: Monitor earthquakes, volcanic eruptions, and tectonic activity.
+- **Geodetic Data**: Measure Earthโs shape, gravity, and crustal movements.
+- **Tool**: [QGIS Galaxy Interactive Tool](https://usegalaxy.eu/root?tool_id=interactive_tool_qgis) (for geological maps).
-This englobes the part of the land, ocean, and athmosphere in which organisms are able to live.
+
-## Marine biodiversity ๐ณ
+
-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.
+## ๐ Biodiversity ๐ฟ๏ธ
-### OBIS Ocean Biodiversity Information System
+Biodiversity encompasses all living organisms in the ocean, atmosphere, and land.
-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.
+### On Galaxy
-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`
+๐ Teaser: Explore Biodiversity with Galaxy!
-## Land biodiversity ๐ฆค
+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.
-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).
+๐น **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 %} )**โyour gateway to Galaxy's biodiversity tools and workflows.
+๐น **Explore specific datasets**:
+- [OBIS Marine Indicators Tutorial]( {% link topics/ecology/tutorials/obisindicators/tutorial.md %} )
+- [Cleaning GBIF Data Tutorial]( {% link topics/ecology/tutorials/gbif_cleaning/tutorial.md %} )
+## ๐ Cross-Domain Connections
-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.
+Biodiversity data spans **land, ocean, and atmosphere**. The following tools are **also listed in their respective domain pages**:
-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 %}).
+๐น **Access tools**:
+- {% 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) %}
+* Also listed in [Where to start with ocean data in galaxy]( {% link topics/climate/tutorials/ocean_101/tutorial.md %} )*
+๐ก **New to biodiversity data?** The **[Ecology Subdomain](https://ecology.usegalaxy.eu/)** is your one-stop shop for all things biodiversity in Galaxy!
-# 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 !
+
-# Extra information
+# ๐ 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.
+
+## ๐ Whatโs 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/)**.
+
+
+## Extra information
Coming up soon even more tutorials on and other Earth-System related trainings. Keep an {% icon galaxy-eye %} open if you are interested!
+
+๐
diff --git a/topics/climate/tutorials/land_101/tutorial.md b/topics/climate/tutorials/land_101/tutorial.md
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+---
+layout: tutorial_hands_on
+title: Where to Start with Land Data in Galaxy
+zenodo_link: '' # Add Zenodo DOI if available
+questions:
+ - What land data is available in Galaxy for climate and ecology studies?
+ - How can I monitor land surface changes and degradation?
+ - What tools are available for analyzing land cover, vegetation, and soil data?
+ - How is land data connected to climate change?
+objectives:
+ - Understand the role of land surfaces in the Earth's climate system
+ - Discover key land datasets (Sentinel-2, QGIS, etc.)
+ - 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: 1H
+key_points:
+ - Land as a critical component of the Earth's climate system
+ - Monitoring land surface changes with Sentinel-2
+ - Assessing land degradation (erosion, salinization, desertification)
+ - Using NDVI and other indices for vegetation and climate studies
+ - GIS tools for land data analysis and visualization
+tags:
+ - earth-system
+ - land
+ - climate
+contributions:
+ authorship:
+ - Marie59
+ funding:
+ - gaiadata
+ - gallantries
+ - fairease
+ - eurosciencegateway
+---
+
+# ๐๏ธ Where to Start with Land Data in Galaxy
+
+> 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:
+> - 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**
+
+
+## ๐ 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 (180ยฐ 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]( {% link 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]( {% 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]( {% 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.
+
+
+### 3D Trees Analysis
+A suite of tools for processing and visualizing **LiDAR point cloud data** to study forest structure, biomass, and ecosystem dynamics.
+
+- **{% 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.
+
+๐ **Upcoming**: Public workflow and training materials for 3D tree analysis.
+
+## ๐ Cross-Domain Connections
+
+The following tools and resources are **also relevant to other Earth System domains**:
+
+### Biodiversity Tools (Terrestrial Focus)
+- **{% 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.
diff --git a/topics/climate/tutorials/ocean_101/tutorial.md b/topics/climate/tutorials/ocean_101/tutorial.md
new file mode 100644
index 00000000000000..b4177b5a653192
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+++ b/topics/climate/tutorials/ocean_101/tutorial.md
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+---
+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 Earthโs climate system
+ - Real-time monitoring with Argo, Sentinel-3, and EMODnet
+ - Tools for ocean data access, analysis, and visualization
+tags:
+ - earth-system
+ - ocean
+ - climate
+contributions:
+ authorship:
+ - Marie59
+ funding:
+ - gaiadata
+ - gallantries
+ - fairease
+ - eurosciencegateway
+---
+
+# ๐ Where to Start with Ocean Data in Galaxy
+
+The ocean is a key component of the Earthโs 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.
+
+
+## ๐ Key Data Sources and Tools
+
+### Argo Program
+- **Data**: Latitude, longitude, time, water temperature, pressure, salinity, chlorophyll, oxygen, and nitrate.
+- **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)
+
+### 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 %} )
+- **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).
+- **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 %} )
+- **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**:
+ - [Oceanโs Variables Study]{% link topics/climate/tutorials/ocean-variables/tutorial.md %})
+ - [Workflow: Oceanโs Variables Study](https://usegalaxy.eu/u/marie.josse/w/oceans-var-v2)
+
+### Copernicus Marine Data Store
+- **Data**: Ocean product catalog with ~15 variables (hindcast, current, and forecast data).
+- **Tool**: {% tool [Copernicus Marine Data Store retrieve marine data ](toolshed.g2.bx.psu.edu/repos/ecology/copernicusmarine/copernicusmarine/2.3.0+galaxy0) %}
+
+## ๐ Cross-Domain Connections
+
+The following tools and resources are **also relevant to other Earth System domains**:
+
+### Biodiversity Tools (Marine Focus)
+- **{% 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.
+
+- **[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 %} )*
+ - Analyze marine microbial metagenomics datasets.
+