Jekyll 2025-10-22T08:55:48+00:00 https://training.galaxyproject.org/training-material/topics/ecology/feed.xml Recently added tutorials, slides, FAQs, and events in the ecology topic https://training.galaxyproject.org/training-material/assets/images/GTN-60px.png https://training.galaxyproject.org/training-material/events/2025-11-11_ecology.html 2025-10-22T08:55:48+00:00

As colleagues from CCAMLR / Antarctica conservation from Belgium are coming to Concarneau marine station to work on Galaxy Ecology use in their projects, we propose to create an open event, where colleagues from CCAMLR / Antarctica conservation from UK, New Zealand and others are interested to participate remotely, so people wanted to learn how to use and contribute to Galaxy Ecology European Platform during these 3 days.

Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Pauline Seguineau https://training.galaxyproject.org/training-material/hall-of-fame/PaulineSGN/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/NEAL_tutorial/tutorial.html 2025-10-14T14:43:07+00:00

This tutorial is designed to guide you through the annotation of audio data via the NEAL interactive tool.

Pauline Seguineau https://training.galaxyproject.org/training-material/hall-of-fame/PaulineSGN/ Haswane Chei https://training.galaxyproject.org/training-material/hall-of-fame/haswane/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/phylodiversity_workflow/tutorial.html 2025-06-06T14:40:49+00:00

This tutorial is designed to guide you through the Phylodiversity Galaxy workflow, demonstrating how to easily compute phylodiversity and create phyloregions from phylogeny, occupency and spatial files.

Elouan Le Mestric https://training.galaxyproject.org/training-material/hall-of-fame/Morphy427/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html 2025-06-02T19:27:57+00:00

This tutorial is designed to guide you through the Ecoregionalization Galaxy workflow, demonstrating how to create a life traits ecoregionalization map from occurrences and environmental data using a boosted regression tree model for predictions.

Jean Le Cras https://training.galaxyproject.org/training-material/hall-of-fame/jeanlecras/ Pauline Seguineau https://training.galaxyproject.org/training-material/hall-of-fame/PaulineSGN/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Jean Le Cras https://training.galaxyproject.org/training-material/hall-of-fame/jeanlecras/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/eDNA-taxonomic-analysis/workflows/main_workflow.html 2025-06-02T10:39:17+00:00

Final output is a table of Taxa and how many sequences aligned with them. This table can be used to then visualize via a pie chart.

John Beliveau https://training.galaxyproject.org/training-material/topics/ecology/tutorials/eDNA-taxonomic-analysis/tutorial.html 2025-06-02T10:39:17+00:00

Environmental DNA (eDNA) analysis has emerged as a powerful tool in ecological and conservation research. It involves the extraction and analysis of DNA shed by organisms into their surrounding environment without the need to directly observe or capture the species. This non-invasive approach allows us to gain valuable insights into biodiversity, species distribution, and community composition in a wide range of ecosystems, including marine environments, from which the eDNA in this tutorial originates.

John Beliveau https://training.galaxyproject.org/training-material/hall-of-fame/jbeli11/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ John Beliveau https://training.galaxyproject.org/training-material/hall-of-fame/jbeli11/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/openrefine_gbif/tutorial.html 2025-01-21T21:32:43+00:00

In this tutorial we will use OpenRefine tool to clean occurrence records retrieved from GBIF (Global Biodiversity Information Facility).

Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Sophie Pamerlon https://training.galaxyproject.org/training-material/hall-of-fame/sophiepamerlon/ Laura Russell https://training.galaxyproject.org/training-material/hall-of-fame/laurarussell/ Daniela Schneider https://training.galaxyproject.org/training-material/hall-of-fame/Sch-Da/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html 2024-12-13T16:00:52+00:00

This tutorial will guide you through the necessary steps to manage and prepare sequencing files (ab1, FASTQ, FASTA) for submission to the genomic database ENA.

Najat Amoukou https://training.galaxyproject.org/training-material/hall-of-fame/Najatamk/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Pauline Seguineau https://training.galaxyproject.org/training-material/hall-of-fame/PaulineSGN/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Verena Moosmann https://training.galaxyproject.org/training-material/hall-of-fame/VerenaMoo/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/lotus2-identifying-fungi/workflows/lotus2-fungi-workflow.html 2024-09-30T13:53:59+00:00

Workflow for running LotuS2 tool on fungal ITS paired-end sequencing data, to identify the fungi present in the samples

Society for the Protection of Underground Networks Sujai Kumar Bethan Manley https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.html 2024-09-30T13:53:59+00:00

Introduction

Sujai Kumar https://training.galaxyproject.org/training-material/hall-of-fame/sujaikumar/ Bethan Manley https://training.galaxyproject.org/training-material/hall-of-fame/bethanmanley/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Sujai Kumar https://training.galaxyproject.org/training-material/hall-of-fame/sujaikumar/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Ecoregionalization_tutorial/workflows/Ecoregionalization_workflow.html 2024-09-16T09:54:51+00:00

Pauline Seguineau https://training.galaxyproject.org/training-material/hall-of-fame/PaulineSGN/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html 2024-09-16T09:54:51+00:00

This tutorial is designed to guide you through the Ecoregionalization Galaxy workflow, demonstrating how to create an ecoregionalization map from occurrences and environmental data using a boosted regression trees model for predictions.

Pauline Seguineau https://training.galaxyproject.org/training-material/hall-of-fame/PaulineSGN/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Ankerl Yassine https://training.galaxyproject.org/training-material/hall-of-fame/Rassine/ Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/marine_omics_bgc/workflows/main_workflow.html 2024-08-19T13:25:15+00:00

Secondary metabolite biosynthetic gene cluster (SMBGC) Annotation using Neural Networks Trained on Interpro Signatures

Marie Jossé https://training.galaxyproject.org/training-material/topics/ecology/tutorials/marine_omics_bgc/tutorial.html 2024-08-19T13:25:15+00:00

Introduction

Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/events/galaxy-academy-2024.html 2024-06-11T15:07:31+00:00

The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day. <button id="program-button" class="btn btn-info" onclick="$('#program-tab').tab('show');">Start the Course!</button>

Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Natalie Whitaker-Allen https://training.galaxyproject.org/training-material/hall-of-fame/natalie-wa/ Natalie Kucher https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/ Anika Erxleben https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/ Anna Syme https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/ Anton Nekrutenko https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/ Dannon Baker https://training.galaxyproject.org/training-material/hall-of-fame/dannon/ Delphine Lariviere https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/ Gareth Price https://training.galaxyproject.org/training-material/hall-of-fame/GarethPrice-Aus/ John Davis https://training.galaxyproject.org/training-material/hall-of-fame/jdavcs/ Michael Schatz https://training.galaxyproject.org/training-material/hall-of-fame/mschatz/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Ahmed Hamid Awan https://training.galaxyproject.org/training-material/hall-of-fame/ahmedhamidawan/ Anup Kumar https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Clea Siguret https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/ Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ Deepti Varshney https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/ Eli Chadwick https://training.galaxyproject.org/training-material/hall-of-fame/elichad/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Emmanuel Augustine https://training.galaxyproject.org/training-material/hall-of-fame/emmaustin20/ Igor Makunin https://training.galaxyproject.org/training-material/hall-of-fame/igormakunin/ Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ Matthias Bernt https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/ Melanie Föll https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/ Nate Coraor https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Polina Polunina https://training.galaxyproject.org/training-material/hall-of-fame/plushz/ Pratik Jagtap https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/ Rand Zoabi https://training.galaxyproject.org/training-material/hall-of-fame/RZ9082/ Romane LIBOUBAN https://training.galaxyproject.org/training-material/hall-of-fame/rlibouba/ Saim Momin https://training.galaxyproject.org/training-material/hall-of-fame/SaimMomin12/ Stéphanie Robin https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/ Subina Mehta https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/ Timothy J. Griffin https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/ Tyler Collins https://training.galaxyproject.org/training-material/hall-of-fame/tcollins2011/ Wendi Bacon https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/MetaShARK_tutorial/tutorial.html 2024-03-04T15:18:02+00:00

This tutorial aims to teach how to use functionalities of the EML Assembly Line R package to produce rich metadata using the Ecological Metadata Language (EML) international metadata standard. Here, we will notably propose a concrete example on how to use Galaxy Ecology tools to create, evaluate and modify EML metadata content using both EML Assemby Line metadata template tabular files, easily readable and editable by humans, and XML file, devoted to machine.

Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Glinez Thibaud https://training.galaxyproject.org/training-material/hall-of-fame/ThibaudGlinez/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Glinez Thibaud https://training.galaxyproject.org/training-material/hall-of-fame/ThibaudGlinez/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.html 2024-03-04T11:07:10+00:00

Checking expected species and contamination in bacterial isolate

Pierre https://training.galaxyproject.org/training-material/hall-of-fame/Pierre/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html 2024-03-04T11:07:10+00:00

Sequencing (determining of DNA/RNA nucleotide sequence) is used all over the world for all kinds of analysis. The product of these sequencers are reads, which are sequences of detected nucleotides.

Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Clea Siguret https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.html 2024-01-24T19:43:59+00:00

Marie Jossé https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/workflows/NDVI-with-OpenEO.html 2024-01-24T19:43:59+00:00

Marie Jossé https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/tutorial.html 2024-01-24T19:43:59+00:00

Through this tutorial you will learn here how to access and download Copernicus Data Space Ecosystem (CDSE) data through a jupyterlab Galaxy interactive tool :

Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.html 2024-01-22T09:50:51+00:00

This tutorial aims to teach how to use the interactive tool MetaShRIMPS, available on Galaxy Ecology,

Tanguy Genthon https://training.galaxyproject.org/training-material/hall-of-fame/TanguyGen/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.html 2023-10-11T11:50:32+00:00

Based on this QGIS official tutorial, you will learn here how to access, filter and import GIS data through WFS web service using QGIS Galaxy interactive tool:

Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-ecology.html 2023-05-03T10:16:01+00:00

This learning path aims to teach you the basics of Galaxy and analysis of ecological data. You will learn how to use Galaxy for analysis, and will be guided through the common steps of biodiversity data analysis: download, check, filter and explore biodiversity data and analyze abundance data through modeling.

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/remote-sensing/workflows/Sentinel-2-example.html 2023-04-13T09:11:06+00:00

Marie Josse https://training.galaxyproject.org/training-material/topics/ecology/tutorials/remote-sensing/tutorial.html 2023-04-13T09:11:06+00:00

This tutorial will guide you on getting Sentinel 2 data and processing them in order to calculate and visualize biodiversity indicators. This workflow made of 6 tools will allow you to explore Sentinel 2 data in the view of making biodiversity analyses.

Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Wendi Bacon https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/obisindicators/workflows/Obis-indicators.html 2023-04-11T09:13:43+00:00

From Obis data to Biodiversity indicators

Marie Jossé https://training.galaxyproject.org/training-material/topics/ecology/tutorials/obisindicators/tutorial.html 2023-04-11T09:13:43+00:00

OBIS is a global open-access data and information clearing-house on marine biodiversity for science, conservation and sustainable development. In order to visualize their marine data OBIS created the package obisindicators.

Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/champs-blocs/tutorial_FR.html 2023-03-21T16:27:58+00:00

Ce tutoriel vous permettra de mieux appréhender le workflow des indicateurs “champs de blocs”. Cela vous aidera à comprendre les effets des changements globaux et locaux sur les habitats marins, et l’efficacité des mesures de gestion adoptées, nécessite un suivi standardisé et des indicateurs robustes et sensibles reflétant l’état des habitats.

Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Mehmet Tekman https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/ Pablo Moreno https://training.galaxyproject.org/training-material/hall-of-fame/pcm32/ Julia Jakiela https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/champs-blocs/workflows/main_workflow.html 2023-01-04T09:55:12+00:00

Compute indicators for Champs blocs

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/champs-blocs/tutorial.html 2023-01-04T09:55:12+00:00

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.

Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/panoply_ebv/tutorial.html 2022-10-28T12:54:51+00:00

The practical aims at familiarzing you with the Panoply Galaxy interactive tool. Panoply is among the most popular tool to visualize geo-referenced data stored in Network Common Data Form (netCDF). It provides a graphical interface for inspecting (show metadata) and visualizing netCDF data. It supports many features to customize your plots and we will introduce some of them in this lesson.

Pôle National de Données de Biodiversité https://training.galaxyproject.org/training-material/hall-of-fame/pndb/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Anne Fouilloux https://training.galaxyproject.org/training-material/hall-of-fame/annefou/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/gbif_cleaning/workflows/Galaxy-Workflow-GBIF_data_Quality_check_and_filtering_workflow.html 2022-10-28T10:17:19+00:00

Cleaning GBIF data for the use in Ecology

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/gbif_cleaning/tutorial.html 2022-10-28T10:17:19+00:00

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.

Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Simon Benateau https://training.galaxyproject.org/training-material/hall-of-fame/sbenateau/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/x-array-map-plot/workflows/main-workflow.html 2022-10-26T18:20:31+00:00

Visualization of Climate Data using NetCDF Xarray Map Plotting

Soumya Jha https://training.galaxyproject.org/training-material/topics/ecology/tutorials/x-array-map-plot/tutorial.html 2022-10-26T18:20:31+00:00

The data used in this tutorial is ECMWF Reanalysis 5 hourly data on single levels. We are interested in the following variables: air temperature at 2 metres, latitude, longitude and time. Our main objective is to plot the global air temperature at 2 metres with respect to time. For this we will be using the netCDF xarray tool available in the Galaxy Europe (or your favourite Galaxy Instance) server.

Soumya Jha https://training.galaxyproject.org/training-material/hall-of-fame/Quickbeasts51429/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/phylogeny-data-prep/workflows/main_workflow.html 2022-10-21T11:45:57+00:00

This workflow begins from a set of genome assemblies of different samples, strains, species. The genome is first annotated with Funnanotate. Predicted proteins are furtner annotated with Busco. Next, 'ProteinOrtho' finds orthologs across the samples and makes orthogroups. Orthogroups where all samples are represented are extracted. Orthologs in each orthogroup are aligned with ClustalW. The alignments are cleaned with ClipKIT and the concatenation matrix is built using PhyKit. This can be used for phylogeny reconstruction.

Miguel Roncoroni https://training.galaxyproject.org/training-material/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html 2022-10-21T11:45:57+00:00

A robust and well-resolved phylogenetic classification is essential to understand genetic relationships within and between species and the evolution of their phenotypic diversity. In the last decade the genomic revolution has represented a drastic change in the amount of data used for phylogenetic inference. The single-gene approach using universal phylogenetic markers for the different lineages across the tree of life, is now being replaced by the assembly of taxon-rich and genome-scale data matrices, the so called phylogenomic approach.

Miguel Roncoroni https://training.galaxyproject.org/training-material/hall-of-fame/roncoronimiguel/ Brigida Gallone https://training.galaxyproject.org/training-material/hall-of-fame/brigidagallone/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Miguel Roncoroni https://training.galaxyproject.org/training-material/hall-of-fame/roncoronimiguel/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/biodiversity-data-exploration/recordings/#tutorial-recording-3-march-2022 2022-03-03T00:00:00+00:00

A 1H long recording is now available.

Olivier Norvez https://training.galaxyproject.org/training-material/hall-of-fame/onorvez/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/recordings/#tutorial-recording-3-march-2022 2022-03-03T00:00:00+00:00

A 2H long recording is now available.

Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Obitools-metabarcoding/recordings/#tutorial-recording-3-march-2022 2022-03-03T00:00:00+00:00

A 1H15M long recording is now available.

Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/faqs/account_exists.html 2022-03-02T15:46:20+00:00

The ecology.usegalaxy.eu (and any other Galaxy server ending in usegalaxy.eu) is the SAME server as the regular usegalaxy.eu server, just modified for Ecology analyses.

Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/biodiversity-data-exploration/workflows/main_workflow.html 2022-03-01T10:23:23+00:00

Biodiversity data exploration

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html 2022-03-01T10:23:23+00:00

This tutorial will guide you on the exploration of biodiversity data having taxonomic, spatial and temporal informations.

Olivier Norvez https://training.galaxyproject.org/training-material/hall-of-fame/onorvez/ Marie Josse https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/ Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Obitools-metabarcoding/workflows/main_workflow.html 2022-02-28T12:32:09+00:00

Metabarcoding/eDNA through Obitools

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html 2022-02-28T12:32:09+00:00

Based on this OBITools official tutorial, you will learn here how to analyze DNA metabarcoding data produced on Illumina sequencers using:

Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Olivier Norvez https://training.galaxyproject.org/training-material/hall-of-fame/onorvez/ Eric Coissac https://training.galaxyproject.org/training-material/hall-of-fame/ecoissac/ Frédéric Boyer https://training.galaxyproject.org/training-material/hall-of-fame/fboyer/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Anne Fouilloux https://training.galaxyproject.org/training-material/hall-of-fame/annefou/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/workflows/Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.html 2021-02-24T16:21:43+00:00

Compute and analyze biodiversity metrics with PAMPA toolsuite

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html 2020-11-19T16:31:09+00:00

This tutorial aims to present the PAMPA Galaxy workflow, how to use it to compute common

Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Dominique Pelletier https://training.galaxyproject.org/training-material/hall-of-fame/dpelletier/ Jean-Baptiste Mihoub https://training.galaxyproject.org/training-material/hall-of-fame/jbmihoub/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Coline Royaux https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/species-distribution-modeling/workflows/Galaxy-Workflow-Species_Distribution_Modeling_with_Wallace_from_GBIF_-_Training_material.html 2019-12-05T14:23:28+00:00

Species distribution modeling

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/regionalGAM/workflows/Galaxy-Workflow-Tutorial_training_regionalGAM_complete_workflow.html 2019-07-04T07:32:28+00:00

Regional GAM

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/regionalGAM/workflows/Galaxy-Workflow-Tutorial_regionalGAM_complete_Multispecies.html 2019-07-04T07:32:28+00:00

Regional GAM

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/regionalGAM/workflows/Galaxy-Workflow-Phenology__stacked__visualization_creation.html 2019-07-04T07:32:28+00:00

Regional GAM

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/regionalGAM/workflows/Galaxy-Workflow-Abundance_index__stacked__visualization_creation.html 2019-07-04T07:32:28+00:00

Regional GAM

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/regionalGAM/tutorial.html 2019-07-04T07:32:28+00:00

This tutorial will show you how to study species abundance through the computation of a flight curve, abundance index, and trends. It will explain you how to use different regionalGAM tools on Galaxy allowing you to deal with datasets containing abundance information for various species per site and per date through a couple of years.

Clara Urfer https://training.galaxyproject.org/training-material/hall-of-fame/claraurf/ Elisa Michon https://training.galaxyproject.org/training-material/hall-of-fame/emichn/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Simon Benateau https://training.galaxyproject.org/training-material/hall-of-fame/sbenateau/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/species-distribution-modeling/tutorial.html 2019-07-04T07:32:28+00:00

Species Distribution Modeling (SDM) can help understand a species distribution in relation to its environment. It can also attempt to quantify the impact of climate change on the species’ habitat, direct conservation efforts and predict invasive species distributions. This is acheived by associating species occurrence (observations) data with a set of environmental data (such as temperature and precipitation).

Elisa Michon https://training.galaxyproject.org/training-material/hall-of-fame/emichn/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Anthony Bretaudeau https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ Nate Coraor https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/ Martin Čech https://training.galaxyproject.org/training-material/hall-of-fame/martenson/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.html 2018-11-15T14:31:11+00:00

RAD-Seq Reference-based data analysis

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.html 2018-11-15T08:09:30+00:00

RAD-Seq de-novo data analysis

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.html 2017-12-14T16:46:45+00:00

RAD-Seq to construct genetic maps

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/workflows/workflow.html 2017-06-12T08:10:40+00:00

RAD-Seq Reference-based data analysis

https://training.galaxyproject.org/training-material/topics/ecology/tutorials/de-novo-rad-seq/tutorial.html 2017-02-14T14:09:17+00:00

In the study of Hohenlohe et al. 2010, a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback Gasterosteus aculeatus was conducted. Authors used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations.

Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Verena Moosmann https://training.galaxyproject.org/training-material/hall-of-fame/VerenaMoo/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/genetic-map-rad-seq/tutorial.html 2017-02-14T14:09:17+00:00

This tutorial is based on the analysis described in publication.

Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html 2017-02-14T14:09:17+00:00

In the study of Hohenlohe et al. 2010, a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback Gasterosteus aculeatus was conducted. Authors used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations.

Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Verena Moosmann https://training.galaxyproject.org/training-material/hall-of-fame/VerenaMoo/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/