Champs blocs indicators

Overview
Creative Commons License: CC-BY Questions:
  • Which biological questions are addressed by the tutorial?

  • Which bioinformatics techniques are important to know for this type of data?

Objectives:
  • Calculate IVR (Visual Rollover Indicator)

  • Compute dissimilarity indice

  • Vizualize some diversity indices

Requirements:
Time estimation: 1 hour
Supporting Materials:
Published: Jan 4, 2023
Last modification: Jan 19, 2024
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
purl PURL: https://gxy.io/GTN:T00127
version Revision: 29

This tutorial will allow you to better apprehend the workflow for indicators on boulder fields. This will help you understand the effects of global and local changes on marine habitats, and the effectiveness of the management measures adopted, requires standardized monitoring and robust and sensitive indicators reflecting the state of the habitats.

The “mediolittoral boulder fields” habitat harbors a high diversity of micro-habitats and species due to its high structural heterogeneity and its intermediate position on the foreshore, which makes it one of the most diversified mediolittoral habitats and of high ecological interest along the French Channel-Atlantic coast. It is also a very attractive habitat for recreational fishing, which, through the reworking of the blocks, can impact the communities. Thus, the “mediolittoral boulder fields” habitat has been the subject of several national and local initiatives (including LIFE+ “Experimentation for a sustainable and concerted management of recreational foot fishing in France” 2013-2017) to better assess its status and relate it to the pressure of foot fishing with a view to adapting local management, particularly through the network of Marine Protected Areas (Natura 2000, PNM, PNR etc.).

In particular, these projects have made it possible to develop a network of involved field players and managers and tools for evaluating the ecological status and pressure of fishing on foot:

  • the Visual Boulder Turning Indicator (VTI), which is similar to a “landscape” indicator to assess fishing pressure based on architectural criteria;
  • the Boulder Field Ecological Quality Index (BFEQ) - the subject of this report - based on biotic and abiotic variables that respond to the disturbance “boulder turning”.

Here we will go over the different steps in order to get those 2 indicators and more.

Agenda

In this tutorial, we will cover:

  1. Get data
  2. Computing the Visual Boulder turning Indicator for each site
    1. IVR
  3. Computing dissimilarity coefficient for each site
    1. Dissimilarity
    2. Diversity indicators
  4. Conclusion

You can leave the tutorial and go bask on the main screen by clicking outside of the tutorial screen. 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. Log in or register
Screenshot of Galaxy interface with the register or login button highlighted. Open image in new tab

Figure 1: Galaxy homepage

This is an image of Galaxy Ecology, located at usegalaxy.eu

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
Screenshot of the Galaxy interface, the tools panel is on the left, the main panel is in the center, and the history is on the right.Open image in new tab

Figure 2: Galaxy interface explanation

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

Now let’s focus on our workflow on boulder field ecological state

Workflow for boulder field ecological state analysis. Open image in new tab

Figure 3: Workflow

Get 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

Are your ESTAMP data ready ?

  1. Download your data on ESTAMP estamp.afbiodiversite.fr website, clicking on “Accédez aux données” at the bottom of the page. You will get a zip folder.
  2. Unzip your folder. In the folder three files .csv will interest us :

    • champbloc_ivr.csv
    • champbloc_qecb.csv
    • ficheterrain.csv
Hands-on: Data upload
  1. Import the data into Galaxy
  • Open the Galaxy Upload Manager galaxy-upload
  • Select Choose local files
    Choose local files. Open image in new tab

    Figure 4: upload your data
  • Browse in your computer and get your ESTAMP files (select all three of them : champbloc_ivr.csv, champbloc_qecb.csv and ficheterrain.csv)

  • Press Start
    Start charging your data. Open image in new tab

    Figure 5: Start
  • Press Close
    Close upload your data. Open image in new tab

    Figure 6: Close

    You need to wait for the data to become green on the right panel

    Data ready. Open image in new tab

    Figure 7: Data ready

Create a new history for this tutorial and give it a name (example: “Champs blocs indicators”) for you to find it again later if needed. <p>Click the new-history icon at the top of the history panel.</p> <p>If the new-history is missing:</p> <ol> <li>Click on the galaxy-gear icon (History options) on the top of the history panel</li> <li>Select the option Create New from the menu</li> </ol>

Computing the Visual Boulder turning Indicator for each site

Based on the proportion of “turned” and “not turned” blocs this indicator vary from 0 to 5 and can be quickly used.

Hands-on: Use a tool
  1. click on for example the IVR ( Galaxy version 0.0.0) tool or type ivr in the tools panel search box (top left) The tool form will be displayed in the central Galaxy panel.

IVR

Go on the tool IVR

Hands-on: Calculating IVR
  1. IVR ( Galaxy version 0.0.0) with the following parameters:
    • param-file “Input champbloc_ivr.csv”: input (champbloc_ivr.csv)
    • param-file “Input ficheterrain.csv”: input (ficheterrain.csv)
  2. Press Run Tool (it can take some minutes to process it’s normal if you have to wait a bit especially if your internet connection is weak)

  3. Three outputs will appear in your history panel on the right.

  4. View graphs
    • Once it’s green, click on IVR plot
    • Then, click on the galaxy-eye (eye) icon of your output in the history panel.

The information is displayed in the central panel

IVR. Open image in new tab

Figure 8: IVR for Bilfot
  1. In the top of the History panel (on the right) go on the search box
  2. Click on the double arrows to display more filter options
  3. Type the name of your site (for instance “Bilfot”) on the “Filter by name:” criteria then click on “No” for the “Visible:” criteria, as plots are created in a data collection and not directly visible on the history
Bilfot filter. Open image in new tab

Figure 9: Filter IVR for Bilfot

For your reports you need to download the ones you want. You won’t be able to vizualise them directly on Galaxy center panel !

  1. Download results
  • Click on the output you are interested in for instance Reports
  • Click on galaxy-save (download)

Computing dissimilarity coefficient for each site

Dissimilarity

Cleaning out your data in order and then compute de dissimilarity coefficient. Get the Dissimilarity ( Galaxy version 0.0.0) tool

Hands-on: Calculate dissimilarity index
  1. Dissimilarity ( Galaxy version 0.0.0) with the following parameters:
    • param-file “Input champbloc_qecb.csv”: input (champbloc_qecb.csv)
    • param-file “Input ficheterrain.csv”: input (ficheterrain.csv)

    • param-select “Do you have data after the year 2021 ?”: No
    • param-text “Until when do you have data (write only the YEAR) ?”: 2021
  2. Press Run Tool (it can take some minutes to process it’s normal if you have to wait a bit especially if your internet connection is weak)

  3. View graphs
    • Once it’s green, click on type of plot you want to see
    • Then, click on the galaxy-eye (eye) icon of your output in the history panel.

The information is displayed in the central panel

Dissim fs fi. Open image in new tab

Figure 10: face sup and inf dissimilarity
Dissim bf bm. Open image in new tab

Figure 11: bloc fixed and mobile dissimilarity
  1. Download your results
  • Click on the output you are interested in
  • Click on galaxy-save (download)

Diversity indicators

Taking as input cleaned data from the Dissimilarity step tocompute diversity indicators. Get the Diversity indicators ( Galaxy version 0.0.0) tool

Hands-on: Calculate diversity indicators
  1. Diversity indicators ( Galaxy version 0.0.0) with the following parameters:
    • param-file “Input clean data”: input (Clean Rdata)
  2. Press Execute

  3. View graphs
    • Once it’s green, click on type of plot you want to see
    • Then, click on the galaxy-eye (eye) icon of your output in the history panel.

The information is displayed in the central panel

Div . Open image in new tab

Figure 12: Simpson indicator
  1. Download your results
  • Click on the output you are interested in
  • Click on galaxy-save (download)

Conclusion

Here you have finished your study on your boulder fields biodiversity state.