biodiversity

Tutorials covering biodiversity

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Assembly

Lesson Slides Hands-on Recordings Input dataset Workflows
Assembly of the mitochondrial genome from PacBio HiFi reads
biodiversity
Chloroplast genome assembly
plants nanopore jbrowse1 biodiversity
Decontamination of a genome assembly
biodiversity
ERGA post-assembly QC
plants animals genome assembly QC biodiversity
Genome Assembly Quality Control
assembly quality control biodiversity
Genome assembly using PacBio data
assembly pacbio biodiversity
Large genome assembly and polishing
assembly polishing nanopore plants biodiversity
Unicycler Assembly
prokaryote microgalaxy biodiversity
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
covid19 biodiversity
Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data
pacbio eukaryote VGP biodiversity
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
pacbio eukaryote VGP biodiversity

Climate

Lesson Slides Hands-on Recordings Input dataset Workflows
Getting your hands-on earth data
earth-system ocean land atmosphere biodiversity

Ecology

Lesson Slides Hands-on Recordings Input dataset Workflows
Audio data annotation with NEAL (Nature + Energy Audio labeler)
ecology biodiversity sound media annotation
Biodiversity data exploration
taxonomic data data quality biodiversity
Champs blocs indicators
ecosystem EBV class EBV dataset EBV workflow marine ecosystems biodiversity
Cleaning GBIF data for the use in Ecology
gbif data management data cleaning biodiversity
Cleaning GBIF data using OpenRefine
biodiversity data cleaning
Compute and analyze biodiversity metrics with PAMPA toolsuite
species population EBV class community composition EBV class EBV dataset EBV workflow modeling biodiversity
Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS
metadata EML FAIR data paper biodiversity
Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities
metadata EML ecology biodiversity FAIR data paper
Data submission using ENA upload Tool
biodiversity
Ecoregionalization workflow tutorial
ecology taxonomic data EBV workflow modeling gbif ocean earth-system interactive-tools biodiversity
Life Traits Ecoregionalization workflow
biodiversity ecoregions life traits
Marine Omics identifying biosynthetic gene clusters
earth-system ocean marine omics biodiversity
Metabarcoding/eDNA through Obitools
genetic composition EBV class community composition EBV class EBV dataset EBV workflow eDNA metabarcoding biodiversity
Obis marine indicators
earth-system ocean marine omics biodiversity
Phylodiversity analysis quick tutorial
ecology taxonomic data phylodiversity biodiversity
Preparing genomic data for phylogeny reconstruction
phylogeny data handling functional annotation biodiversity
QGIS Web Feature Services
earth-system GIS Geographical Information System WFS spatial data maps OGC biodiversity
RAD-Seq Reference-based data analysis
RAD-seq genetic composition EBV class species population EBV class EBV dataset EBV workflow biodiversity
RAD-Seq de-novo data analysis
RAD-seq genetic composition EBV class species populations EBV class EBV dataset EBV workflow biodiversity
RAD-Seq to construct genetic maps
RAD-seq genetic composition EBV class EBV dataset EBV workflowz biodiversity
Regional GAM
species populations EBV class species traits EBV class EBV dataset EBV workflow biodiversity
Sentinel 2 biodiversity
Remote sensing biodiversity
Species distribution modeling
interactive-tools modeling gbif species populations EBV class biodiversity
Taxonomic Analysis of eDNA
biodiversity metabarcoding
Object detection with YOLO
object-detection deep-learning ecology biodiversity marine

Genome Annotation

Lesson Slides Hands-on Recordings Input dataset Workflows
Comparison of two annotation tools - Helixer and Braker3
eukaryota Braker3 Helixer jbrowse1 biodiversity
Genome annotation with Braker3
eukaryota Braker3 jbrowse1 biodiversity
Genome annotation with Helixer
eukaryota helixer jbrowse1 biodiversity
Masking repeats with RepeatMasker
eukaryote biodiversity
Refining Genome Annotations with Apollo (prokaryotes)
gmod prokaryote microgalaxy jbrowse1 biodiversity apollo2
Comparative gene analysis in unannotated genomes
evolution annotation vgp cookbook eukaryote prokaryote microgalaxy biodiversity
Genome annotation with Funannotate
gmod eukaryote jbrowse1 biodiversity
Functional annotation of protein sequences
eukaryote biodiversity
Refining Genome Annotations with Apollo (eukaryotes)
gmod eukaryote cyoa jbrowse1 apollo2 biodiversity

Imaging

Lesson Slides Hands-on Recordings Input dataset Workflows
AI pipeline for annotating marine species (Project Moorev - Marine)
Marine ecosystems biodiversity AI segmentation YOLO deep learning object detection

Contributors

This material was contributed to by:

Tanguy Genthon avatar Tanguy GenthonClara Urfer avatar Clara Urferorcid logoMartin Čech avatar Martin ČechJasper Ouwerkerk avatar Jasper OuwerkerkGiulio Formenti avatar Giulio Formentiorcid logoLaura Leroi avatar Laura Leroiorcid logoAnna Syme avatar Anna SymeOlivier Norvez avatar Olivier Norvezorcid logoSaskia Hiltemann avatar Saskia HiltemannElouan Le Mestric avatar Elouan Le Mestricorcid logoStéphanie Robin avatar Stéphanie RobinMarcella Sozzoni avatar Marcella SozzoniKevin Payet avatar Kevin PayetHaswane Chei avatar Haswane CheiSimon Bray avatar Simon BrayBrandon Pickett avatar Brandon Pickettorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoPauline Seguineau avatar Pauline Seguineauorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoGlinez Thibaud avatar Glinez Thibaudorcid logoNate Coraor avatar Nate CoraorMarie Josse avatar Marie Josseorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBérénice Batut avatar Bérénice Batutorcid logoHelena Rasche avatar Helena RascheJohn Beliveau avatar John Beliveauorcid logoMateo Boudet avatar Mateo Boudetorcid logoTristan Reynolds avatar Tristan ReynoldsArthur Barreau avatar Arthur Barreauorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBrigida Gallone avatar Brigida GalloneNiall Beard avatar Niall Beardorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoSimon Gladman avatar Simon Gladmanorcid logoBjörn Grüning avatar Björn GrüningElisa Michon avatar Elisa Michonorcid logoColine Royaux avatar Coline Royauxorcid logoTom Brown avatar Tom BrownMohammad Joudy avatar Mohammad JoudySimon Benateau avatar Simon Benateauorcid logoNadine Le Bris avatar Nadine Le BrisGildas Le Corguillé avatar Gildas Le Corguilléorcid logoLinelle Abueg avatar Linelle AbuegEric Coissac avatar Eric CoissacMiguel Roncoroni avatar Miguel RoncoroniDominique Pelletier avatar Dominique Pelletierorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoErwan Corre avatar Erwan CorreNathan Dunn avatar Nathan Dunnorcid logoTeresa Müller avatar Teresa Müllerorcid logoCristóbal Gallardo avatar Cristóbal GallardoWilliam Durand avatar William Durandorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSolenne Correard avatar Solenne CorreardNajat Amoukou avatar Najat AmoukouFrédéric Boyer avatar Frédéric BoyerLaura Russell avatar Laura Russellorcid logoAlexandre Cormier avatar Alexandre CormierSophie Pamerlon avatar Sophie PamerlonFabian Recktenwald avatar Fabian Recktenwaldorcid logoWendi Bacon avatar Wendi Baconorcid logoDaniela Schneider avatar Daniela SchneiderAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoAnkerl Yassine avatar Ankerl Yassineorcid logoDeepti Varshney avatar Deepti VarshneyJean Le Cras avatar Jean Le CrasMarius van den Beek avatar Marius van den BeekEnis Afgan avatar Enis AfganJean-Baptiste Mihoub avatar Jean-Baptiste Mihouborcid logoRomane LIBOUBAN avatar Romane LIBOUBANVerena Moosmann avatar Verena MoosmannPerrine Jégousse avatar Perrine Jégousse

Funding

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

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MOOREV
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Antarctic and Southern Ocean Coalition
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EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.
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MNHN
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GBIF
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Australian BioCommons
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
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FNSO
This project (AAPFNSO2019OpenMetaPaper-14026) is funded with the support of the national Fund for Open Science programme of the French Minister of Higher Education, Research and Innovation. Their funding has supported development of data/metadata management tools and related tutorial for Ecology and FAIR topics.
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SU
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Fair-Ease
FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.
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The University of Melbourne
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ELIXIR Europe
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PNDB
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IFB
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ISYEB
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Melbourne Bioinformatics