PNDB
OverviewFrench Biodiversity e-infrastructure
Space: Independent Teams
SEEK ID: https://workflowhub.eu/projects/19
Public web page: https://www.pndb.fr/
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team created: 24th Jul 2020
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Teams: PNDB
Organizations: French Museum of Natural History, ff
https://orcid.org/0000-0003-4308-5617
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, MOLGENIS, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-CBA, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC, CholGen, RNA group, Plant Genomes Pipelines in Galaxy, Pathogen Genomic Laboratory, Chemical Data Lab, JiangLab, Pangenome database project, HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment, Center for Open Bioimage Analysis, Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases, Historical DNA genome skimming, QCDIS, Peter Menzel's Team, NHM Clark group, ESRF Workflow System (Ewoks), Kalbe Bioinformatics, Nextflow4Metabolomics, GBCS, CEMCOF, Jackson Laboratory NGS-Ops, Schwartz Lab, BRAIN - Biomedical Research on Adult Intracranial Neoplasms, Cancer Therapeutics and Drug Safety, Deepdefense, Mid-Ohio Regional Planning Commission, MGSSB, Institute for Human Genetics and Genomic Medicine Aachen, FengTaoSMU, EGA, Plant-Food-Research-Open, KrauthammerLab, Geo Workflows, grassland pDT, FunGIALab, CRIM - Computer Research Institute of Montréal, Medvedeva Lab, Metagenlab, FAIR-EASE, Protein-protein and protein-nucleic acid binding site prediction research, Culhane Lab, IDUN - Drug Delivery and Sensing, Edge Computing DAG Task Scheduling Research Group, Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment, COPO, Taudière group, ErasmusMC Clinical Bioinformatics, interTwin, fluid flow modeling, EnrichDO, WorkflowResearch, Application Security - Test Crypt4GH solutions
Web page: Not specified
Workflow permettant de prendre en entrée les résultats du challenge IA-biodiv par tâche, le fichier de référence par tâche afin de faire tourner un jupyter notebook produisant les scores pour chaque consortium participant.
Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "OBIS marine indicators" .
This workflow allows to compute and visualize marine biodiversity indicators from OBIS data.
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.
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 "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, 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 "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 "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 "Metabarcoding/eDNA through Obitools" .
This workflow allows to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools.
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 ...
Workflow to take DataOne data packages (raw datasets + metadata written in Ecological Metadata Standard) as input and create a DwC occurence.csv file almost ready to put in a Dawrin core Archive using eml-annotations at the attribute level
DownloadGalaxy-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.
