KG-Microbe -- Knowledge graph construction for microbial traits and beyond

KG-Microbe preprint

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Associated Tutorial

This workflows is part of the tutorial Sentinel 2 biodiversity, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Marie Josse

Tutorial Author(s): [Marie ...

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

This Galaxy-E workflow was made from the "Cleaning GBIF data for the use in biogeography" tutorial and allows to:

• Use CoordinateCleaner to automatically flag problematic records
• Use GBIF provided meta-data to improve coordinate quality, tailored to your downstream analyses
• Use automated cleaning algorithms of CoordinateCleaner to identify problematic contributing datasets
• Visualize data ...

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Metabarcoding/eDNA through Obitools" .

This workflow allows to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools.

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Biodiversity data exploration"

This workflow allows to explore biodiversity data looking at homoscedasticity, normality or collinearity of presences-absence or abundance data and at comparing beta diversity taking into account space, time and species components ...

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Sentinel 2 biodiversity" .

This workflow allows to analyze remote sensing sentinel 2 satellites data to compute spectral indices such as the NDVI and visualizing biodiversity indicators

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Antarctic sea ecoregionalization" .

This workflow allows to analyze marine benthic biodiversity data to compute ecoregions regarding environmental data.

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Deep learning to predict animal behavior" .

This workflow allows to analyze animal behavior data through deep learning.

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, to analyze crowdsourcing results of the SPIPOLL hoverflies GAPARS European project activity on MMOS server.

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Champs blocs" .

This workflow allows to produce Visual Rollover Indicator and dissimilarity as diversity indices on boulder fields.

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 7.95 km2 large Salisbury Plain in the United Kingdom (1.866189 W, 51.220814 N). The work has been performed in the context of the EU project MAMBO (Modern Approaches to the Monitoring ...

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 54 km2 large Oostvaardersplassen in the Netherlands (5.418842 E, 52.456870 N). The work has been performed in the context of the EU project MAMBO (Modern Approaches to the Monitoring ...

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 0.08 km2 large Monks Wood in the United Kingdom (10.478393 E, 56.289050 N). The work has been performed in the context of the EU project MAMBO (Modern Approaches to the Monitoring ...

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 1.29 km2 large Mols Bjerge National Park in Denmark (10.478393 E, 56.289050 N). The work has been performed in the context of the EU project MAMBO (Modern Approaches to the Monitoring ...

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 5.55 km2 large Knepp Estate in the United Kingdom (0.3758 W, 50.969859 N). The work has been performed in the context of the EU project MAMBO (Modern Approaches to the Monitoring ...

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 3.5 km2 large island of Comino in Malta (36.0113 E, 14.3362 N). The work has been performed in the context of the EU project MAMBO (Modern Approaches to the Monitoring of Biоdiversity, ...

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.

Associated Tutorial

This workflows is part of the tutorial Taxonomic Analysis of eDNA, available in the GTN

Features

• Includes a Galaxy Workflow Report ...

Regional GAM

Associated Tutorial

This workflows is part of the tutorial Regional GAM, available in the GTN

Thanks to...

Tutorial Author(s): Clara Urfer, Elisa Michon, [Yvan Le ...

Regional GAM

Associated Tutorial

This workflows is part of the tutorial Regional GAM, available in the GTN

Thanks to...

Tutorial Author(s): Clara Urfer, Elisa Michon, [Yvan Le ...

Regional GAM

Associated Tutorial

This workflows is part of the tutorial Regional GAM, available in the GTN

Thanks to...

Tutorial Author(s): Clara Urfer, Elisa Michon, [Yvan Le ...

Regional GAM

Associated Tutorial

This workflows is part of the tutorial Regional GAM, available in the GTN

Thanks to...

Tutorial Author(s): Clara Urfer, Elisa Michon, [Yvan Le ...

Metabarcoding/eDNA through Obitools

Associated Tutorial

This workflows is part of the tutorial Metabarcoding/eDNA through Obitools, available in the GTN

Thanks to...

Tutorial Author(s): Coline Royaux, [Olivier ...

Compute and analyze biodiversity metrics with PAMPA toolsuite

Associated Tutorial

This workflows is part of the tutorial Compute and analyze biodiversity metrics with PAMPA toolsuite, available in the GTN

Thanks to...

Tutorial Author(s): Coline Royaux, ...

Biodiversity data exploration

Associated Tutorial

This workflows is part of the tutorial Biodiversity data exploration, available in the GTN

Thanks to...

Tutorial Author(s): Olivier Norvez, Marie Josse, ...

Compute indicators for Champs blocs

Associated Tutorial

This workflows is part of the tutorial Champs blocs indicators, available in the GTN

Thanks to...

Tutorial Author(s): Marie Josse, Yvan Le Bras ...

Species distribution modeling

Associated Tutorial

This workflows is part of the tutorial Species distribution modeling, available in the GTN

Thanks to...

Tutorial Author(s): Elisa Michon, Yvan Le Bras, ...

RAD-Seq to construct genetic maps

Associated Tutorial

This workflows is part of the tutorial RAD-Seq to construct genetic maps, available in the GTN

Thanks to...

Tutorial Author(s): Yvan Le Bras

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Checking expected species and contamination in bacterial isolate

Associated Tutorial

This workflows is part of the tutorial Checking expected species and contamination in bacterial isolate, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Cleaning GBIF data for the use in Ecology

Associated Tutorial

This workflows is part of the tutorial Cleaning GBIF data for the use in Ecology, available in the GTN

Thanks to...

Tutorial Author(s): Yvan Le Bras, [Simon ...

RAD-Seq de-novo data analysis

Associated Tutorial

This workflows is part of the tutorial RAD-Seq de-novo data analysis, available in the GTN

Thanks to...

Tutorial Author(s): Yvan Le Bras

Tutorial Contributor(s): [Verena ...

RAD-Seq Reference-based data analysis

Associated Tutorial

This workflows is part of the tutorial RAD-Seq Reference-based data analysis, available in the GTN

Thanks to...

Tutorial Author(s): Yvan Le Bras

Tutorial Contributor(s): [Verena ...

RAD-Seq Reference-based data analysis

Associated Tutorial

This workflows is part of the tutorial RAD-Seq Reference-based data analysis, available in the GTN

Thanks to...

Tutorial Author(s): Yvan Le Bras

Tutorial Contributor(s): [Verena ...

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 ...

Visualization of Climate Data using NetCDF Xarray Map Plotting

Associated Tutorial

This workflows is part of the tutorial Visualization of Climate Data using NetCDF xarray Map Plotting, available in the GTN

Thanks to...

Workflow Author(s): Soumya Jha

Tutorial Author(s): Soumya Jha ...

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

Associated Tutorial

This workflows is part of the tutorial Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2, available in the GTN

Features

• Includes [Galaxy Workflow ...

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 7.5 km2 large Reserve Naturelle Nationale du Bagnas ('Bagnas') in France (3.514360 E, 43.314332 N). The work has been performed in the context of the EU project MAMBO (Modern ...

Second part of the ecoregionalization

This workflow allows you to create an ecoregionalization map from occurrences and environmental data using a boosted regression trees model for predictions.

The workflow is intended for processing occurrence data, which should include latitude, longitude and species presence or absence. You can use example test data available with the workflow, highlighting a use case centered on the Dumont d'Urville sea region and benthic invertebrates. The primary goal of ...

Part 1 of ecoregionalization workflow

This workflow allows you to create an ecoregionalization map from occurrences and environmental data using a boosted regression trees model for predictions.

The workflow is intended for processing occurrence data, which should include latitude, longitude and species presence or absence. You can use example test data available with the workflow, highlighting a use case centered on the Dumont d'Urville sea region and benthic invertebrates. The primary goal of ...

NDVI data with OpenEO to time series visualisation with HoloViz

Calculating and visualizing marine biodiversity indicators

Galaxy-E (ecology.usegalaxy.eu) workflow to calculate species presence / absence, community metrics and compute generalized linear models to identify effects and significativity of these effects on biodiversity.