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.
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
Open your favorite browser (Chrome, Safari or Firefox as your browser, not Internet Explorer!)
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 ?
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.
Unzip your folder. In the folder three files .csv will interest us :
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>To create a new history simply click the new-history icon at the top of the history panel:</p> <p></p>
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
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
IVR ( Galaxy version 0.0.0) with the following parameters:
In the top of the History panel (on the right) go on the search box
Click on the double arrows to display more filter options
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
Further information, including links to documentation and original publications, regarding the tools, analysis techniques and the interpretation of results described in this tutorial can be found here.
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Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012
@misc{ecology-champs-blocs,
author = "Marie Josse and Yvan Le Bras",
title = "Champs blocs indicators (Galaxy Training Materials)",
year = "",
month = "",
day = ""
url = "\url{https://training.galaxyproject.org/training-material/topics/ecology/tutorials/champs-blocs/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
Marie Josse
Yvan Le Bras
Questions:
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