Module: Ecology

Galaxy is not just for Biology!

Lecture Video

Description:

This tutorial aims to present the PAMPA Galaxy workflow, how to use it to compute common biodiversity metrics from species abundance data and analyse it through generalized linear (mixed) models (GLM and GLMM). This workflow made up of 5 tools will allow you to process temporal series data that include at least year, location and species sampled along with abundance value and, finally, generate article-ready data products.
Length: 2 hours
Captions: Coline Royaux
Created: 3 March 2022
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Upload data from DATRAS portal of ICES
  • Pre-process population data with Galaxy
  • Learning how to use an ecological analysis workflow from raw data to graphical representations
  • Learning how to construct a Generalized Linear (Mixed) Model from a usual ecological question
  • Learning how to interpret a Generalized Linear (Mixed) Model
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Speaker

Lecture Video

Description:

Based on this OBITools official tutorial, you will learn here how to analyze DNA metabarcoding data produced on Illumina sequencers
Length: 1 hour 15 minutes
Captions: Yvan Le Bras
Created: 3 March 2022
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Deal with paired-end data to create consensus sequences
  • Clean, filter and anlayse data to obtain strong results
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Speaker

Lecture Video

Length: 1 hour
Captions: Olivier Norvez
Created: 3 March 2022
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Explore Biodiversity data with taxonomic, temporal and geographical informations
  • Have an idea about quality content of the data regarding statistical tests like normality or homoscedasticity and coverage like temporal or geographical coverage
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Speaker