Introduction

Through this tutorial, you will learn in the first part how to import, visualise, and extract data from an ODV collection by using the ODV Galaxy interactive tool. In the second part, you will learn how to use DIVAnd using the inputs the outputs from ODV.

Ocean Data View (ODV) is a software package for the interactive exploration, analysis and visualization of oceanographic and other geo-referenced profile, time-series, trajectory, or sequence data. To know more about ODV go check the official page

DIVAnd (Data-Interpolating Variational Analysis in n dimensions) performs an n-dimensional variational analysis/gridding of arbitrarily located observations. Observations will be interpolated/analyzed on a curvilinear grid in 1, 2, 3 or more dimensions. See the official page

Agenda

In this tutorial, we will cover:

1. Introduction
2. Managing ODV Galaxy interactive tool
3. Ocean Data View
   1. Visualise your Data
   2. Subset Data
   3. Save Data
4. DIVAnd: Data-Interpolating Variational Analysis in n dimensions
   1. Launch DIVAnd
5. BONUS: Even more ODV
6. Conclusion
7. Extra information

Managing ODV Galaxy interactive tool

ODV is now integrated in Galaxy as an interactive tool. This kind of tool works differently than classical tools as it allows the user to interact interactively with your data. This kind of tool is used to give access to Jupyter Notebooks, RStudio or R Shiny apps for example.

To use ODV, you need to use the dedicated form, you can specify input datasets from your history you want to use in ODV, then press the execute button to launch an ODV instance. When the graphical user interface of ODV is ready to be used, a URL will be displayed at the top of the Galaxy center panel. If you don’t see it, you can see and access it through the “Active InteractiveTools” space of the “User” menu or you can click on galaxy-eye on the tool in the history.

Once you finish your work on ODV, if you want to retrieve data and/or the entire project, you need to save files in ODV/galaxy/outputs, then quit ODV properly through the “Project” Menu tab.

Details: Short introduction on how Galaxy works

You can come back to where you left off the tutorial anytime by clicking level.

Hands-on: Log in to Galaxy

1. Open your favorite browser (Chrome, Safari or Firefox as your browser, not Internet Explorer!)
2. Browse to your Galaxy instance
3. On the top panel go to Login or Register

The Galaxy homepage is divided into three panels:

• Tools on the left
• Viewing panel in the middle
• History of analysis and files on the right

Open image in new tab

The first time you use Galaxy, there will be no files in your history panel.

Hands-on: Deploy your own ODV instance

1. Create a new history for this tutorial and give it a name (for example “Ocean’s variables”) for you to find it again later if needed.

   Tip: Creating a new history

   Click the new-history icon at the top of the history panel:

   

2. Import an ODV collection as a zip folder.

   Use this link https://github.com/fair-ease/Data-for-Galaxy-/raw/main/Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip in the following instructions. And Name it Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip

   Tip: Importing via links

   • Copy the link location

   • Click galaxy-upload Upload Data at the top of the tool panel

   • Select galaxy-wf-edit Paste/Fetch Data

   • Paste the link(s) into the text field

   • Press Start

   • Close the window

3. Ocean Data View with the following parameters:
   • “Select if you are using an ODV collection in a zip folder or if you have your own raw data”: The data you are using are an ODV collection in a zip folder
   • “ODV collection in a zip folder.”: Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip

   

4. Click on Run Tool

Tip: Open interactive tool

1. Go to User > Active InteractiveTools
2. Wait for the ODV to be running (Job Info)
3. Click on ODV

Details: Some complementary information about your data

The data here are Mediterranean Sea - Eutrophication and Acidity aggregated datasets EMODnet Chemistry aims to provide access to marine chemistry datasets and derived data products concerning eutrophication, acidity, and contaminants. The importance of the selected substances and other parameters relates to the Marine Strategy Framework Directive (MSFD). This aggregated dataset contains all unrestricted EMODnet Chemistry data on eutrophication and acidity and covers the Mediterranean Sea. Data were aggregated and quality controlled by the ‘Hellenic Centre for Marine Research, Hellenic National Oceanographic Data Centre (HCMR/HNODC)’ in Greece. To get more ODV collection and other data please search the sextant catalogue or the EMODnet Chemistry catalogue.

ITS-90 water temperature and water body salinity variables have also been included (‘as are’) to complete the eutrophication and acidity data. If you use these variables for calculations, please refer to SeaDataNet for the quality flags: https://www.seadatanet.org/Products/Aggregated-datasets.

Regional datasets concerning eutrophication and acidity are automatically harvested, and the resulting collections are aggregated and quality-controlled using ODV Software and following a common methodology for all sea regions Lipizer et al. 2023. Parameter names are based on P35 vocabulary, which relates to EMODnet Chemistry aggregated parameter names and is available at: https://vocab.nerc.ac.uk/search_nvs/P35/.

When not present in the original data, water body nitrate plus nitrite was calculated by summing all nitrate and nitrite parameters. The same procedure was applied for water body dissolved inorganic nitrogen (DIN), which was calculated by summing all nitrate, nitrite, and ammonium parameters. Concentrations per unit mass were converted to a unit volume using a constant density of 1.025 kg/L. Hellenic Centre for Marine Research, Hellenic National Oceanographic Data Centre (HCMR/HNODC) 2022

Ocean Data View

Visualise your Data

Tip: Copy pasting between computer and ODV

You can expand the ODV left panel (where there are 3 dots, vertically) to access the “clipboard” menu and paste the content you want to paste on an ODV form. From there you can copy-paste everything from one side to the other. Then, click outside of this panel to collapse it.

Tip: ODV - Disconnected

If at one point your ODV interface becomes grey with a red panel on the top “X ODV - Disconnected”, do NOT panic ;) you just need to reload your tab (circular arrow top left)

Hands-on: Loading data

1. Click on close of the pop-up screen for the check for Updates
2. Go the top left and click on File, then on Open…
3. On the pop-up screen on the left panel select ODV, then the folder galaxy, then data. You should see a folder open it (double clicking)
4. Select the file with a .odv extension
5. Click on Open in the bottom right

There your data should be opening an you can now visualise them!

Question

1. What are the longitude and latitude of the red dot?

Solution

1. On the to right window you can read Longitude 34°E and Latitude 32.332°N.

Subset Data

Hands-on: Create a subset

1. On the left smaller map right click and select Zoom
2. Then move your cursor on the map you should see a red rectangle moving along
3. Reduce the rectangular to have the selection you want on the map. It can be something similar to the following image (no need to be exactly the same)
4. Once you’re happy with your selection click on Enter on your keyboard.

Here you have created a a subset of your data.

Tip: Change your visualisation properties

1. Go to the central map
2. Click right and select Properties…
3. For example, make your data dots bigger in “Display Style” increase the number below “Symbol Size” to 50, and click OK

You can now see bigger dots representing your data.

If you already saved it once you just have to click left on the save icon (top left) when it’s red.

Save Data

Hands-on: Choose Your Own Tutorial

This is a "Choose Your Own Tutorial" section, where you can select between multiple paths. Click one of the buttons below to select how you want to follow the tutorial

Here you can choose if you want to save your view as an ODV view in xview format (you will not able to directly visualise it on Galaxy) or if you want to save it in png which you can visualise on Galaxy.

xview png

Hands-on: Extract your variables in netcdf data

Now we want to extract and save the right parameters of your data in netcdf format.

1. Go to the the left and click on Export, Data and NetCDF File…
2. In the pop-up screen go to the folder ODV, galaxy, outputs.
3. Click Save
4. A new pop-up window opens “Select Extended Metadata Variables for Export” Let the 56 items selected and click OK
5. “Select Data Variables for Export” here you need to select 1: Depth[m], ̀4: Water body dissolved oxygen concentration [umol/l], 6: Water body phosphate [umol/l] and click OK
6. “NetCDF File Properties” change the Longitude range to [-180 ... 180] degrees_E, then select Export metadata quality flags and Export data quality flags and OK.
7. And OK again

You now know how to export and save the right variables on ODV to netCDF data.

Now, if you have finished with your analysis you can exit ODV. To do so you need to do it properly.

Hands-on: Exit ODV and go back on Galaxy

1. On the top left click on File select Exit
2. If you want to save the other window also click on Yes. Here we don’t need it so click No.

You can now go back to your Galaxy instance. Now, after waiting for everything to turn green in your history, you can see 2 new outputs

In the history panel in the output ODV all outputs click on the galaxy-eye (eye) icon of your output.

You can now visualize the outputs in Galaxy middle panel.

DIVAnd: Data-Interpolating Variational Analysis in n dimensions

Tip: Check Datatype

Go to your output ‘data_from_Eutrophication_Med_profiles_2022_unrestricted’

Check if the datatype is netcdf if not :

Tip: Changing the datatype

• Click on the galaxy-pencil pencil icon for the dataset to edit its attributes
• In the central panel, click galaxy-chart-select-data Datatypes tab on the top
• In the galaxy-chart-select-data Assign Datatype, select your desired datatype from “New type” dropdown
  • Tip: you can start typing the datatype into the field to filter the dropdown menu
• Click the Save button

Launch DIVAnd

Use ODV outputs as DIVAnd input.

Hands-on: Run DIVANnd

1. Use DIVAnd with the following parameters:
   • “Do you already have a notebook”: Start with a fresh notebook
   • “Include data into the environment”: ODV netcdf outputs (output of Ocean Data View tool)
2. Run tool

3. Tip: Open interactive tool

   1. Go to User > Active InteractiveTools
   2. Wait for the DIVAnd to be running (Job Info)
   3. Click on DIVAnd

Hands-on: Navigate the jupyterlab

1. Once in the Jupyterlab, go to the Notebooks folder.
2. There open a terminal window and write :

   wget https://raw.githubusercontent.com/fair-ease/Divand-Galaxy-ext/main/90-analysis-shorten.ipynb
   

3. Run the entire notebook.

In the first ‘outputs’ folder (at the root of the Jupyterlab folders), you should now have one netcdf file “Water_body_Phosphate_Mediterranean”.

So, you can now properly close the Jupyter notebook.

1. On the top left click on files and then on Shut down.
2. Go back to your Galaxy instance.

After a couple of minutes, your outputs should appear in your Galaxy history.

BONUS: Even more ODV

Do you want to go even further and visualise your new netcdf data? (Because this tutorial is fascinating and you want to keep reading ;))

Hands-on: Open your Netcdf data in ODV

Ocean Data View with the following parameters:

• “Select if you are using an ODV collection in a zip folder or if you have your own raw data”: The data you are using are Netcdf or text tabular files
• “Netcdf or tabular text file. For text file, odv format is recommanded.”: DIVAnd netcdf outputs (output of DIVAnd tool)

Click on Run Tool

Tip: Open interactive tool

1. Go to User > Active InteractiveTools
2. Wait for the ODV to be running (Job Info)
3. Click on ODV

1. Click on close of the pop-up screen for the check for Updates
2. Go the top left and click on File, then on Open…
3. On the pop-up screen on the left panel select ODV, then the folder galaxy, then data. You should see a file open it (double clicking)
4. Click on Open in the bottom right. Then click on Next*$ until you can click on **Finish you can keep everything by default.

There your data should be opening and you can now visualise them!

Hands-on: Visualise your Phosphate variable

1. Go on the big + on the top left
2. Select “1 SURFACE Window”
3. Press right on the new plot and select Properties…
4. In the tab “Display Style” increase the “Symbol size” to 22 for instance
5. In the tab “Color Mapping” increase the level of the “Median” part and lower the “Nonlinearity” such as in the following picture

6. Then, click on OK, and you can see the Phosphate repartition.

7. Click right on the map and select Save Plot As…
8. In the pop-up screen go to the folder ODV, galaxy, outputs.
9. In Files of type select PNG (*.png *.PNG) and Save then OK and OK.

If you want to have a visualisation of the Phosphate according to the depth, you can do the following.

1. Go on the big + on the top left
2. Select “1 STATION Window” in the new tab, in the plot press enter on your keyboard.
3. Same as before to save it, click right on the map and select Save Plot As…
4. In Files of type select PNG (*.png *.PNG) and Save then OK and OK.

You can now safely exit ODV.

1. On the top left click on File select Exit
2. If you want to save the other window also click on Yes. Here we don’t need it so click No.

Conclusion

Great you now know how to extract ocean variables from an ODV collection and use these extracted data in DIVAnd. From there you can grid the phosphate variable on the subset extracted create a netcdf file and visualise it on ODV again. We finished with the last results visible on the galaxy instance in the output ODV all outputs :

Extra information

Coming up soon even more tutorials on and other Earth-System related trainings. Keep an galaxy-eye open if you are interested!

Key points

• Manage ODV collection’s data.

• Learn to extract data and visualize them on ODV

• Learn to chain ODV and DIVAnd

Frequently Asked Questions

References

1. Hellenic Centre for Marine Research, Hellenic National Oceanographic Data Centre (HCMR/HNODC), 2022 Mediterranean Sea - Eutrophication and Acidity aggregated datasets 1911/2022 v2022. 10.13120
2. Lipizer, M., E. Molina Jack M., K. Wesslander, L. Fyrberg, M. Tsompanou et al., 2023 EMODnet Chemistry Regional sea eutrophication data collection and Quality Control loop. 10.13120/8XM0-5M67 https://nodc.ogs.it/catalogs/doidetails?doi=10.13120/8xm0-5m67

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Citing this Tutorial

1. Marie Josse, Ocean's variables study (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/climate/tutorials/ocean-variables/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{climate-ocean-variables,
author = "Marie Josse",
	title = "Ocean's variables study (Galaxy Training Materials)",
	year = "",
	month = "",
	day = ""
	url = "\url{https://training.galaxyproject.org/training-material/topics/climate/tutorials/ocean-variables/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol} Computational Biology}
}

                   

Funding

These individuals or organisations provided funding support for the development of this resource

See Funder Profile

See Funder Profile

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-variables/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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