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135 materials found

Content provider: IFB French Institute of Bio... 


FAIR data - Module 4 (share and publish data)

Partager et diffuser les données. Le cadre juridique, les entrepôts et les licences sur les données

Scientific topics: Data management, Biology, Bioinformatics

Keywords: data sharing, Data publishing, legal framework, data warehouse, licensing, data reuse

Resource type: Slides

FAIR data - Module 4 (share and publish data) https://tess.elixir-europe.org/materials/fair-data-module-4-share-and-publish-data Partager et diffuser les données. Le cadre juridique, les entrepôts et les licences sur les données Hélène Chiapello Thomas Denecker Jean-François Dufayard Gautier Sarah Julien Seiler Data management Biology Bioinformatics data sharing, Data publishing, legal framework, data warehouse, licensing, data reuse Biologists bioinformaticians Biomedical researchers
FAIR data - Module 3 (Metadata)

Les Métadonnées : les standards du domaine des données omiques en biologie et séances pratiques d’annotations de jeux de données

Scientific topics: Data management, Biology, Bioinformatics

Operations: Data handling

Keywords: metadata, data annotation, life science standards, data sharing

Resource type: Slides

FAIR data - Module 3 (Metadata) https://tess.elixir-europe.org/materials/fair-data-module-3-metadata Les Métadonnées : les standards du domaine des données omiques en biologie et séances pratiques d’annotations de jeux de données Jean-François Dufayard Gautier Sarah Paulette Lieby Data management Biology Bioinformatics metadata, data annotation, life science standards, data sharing Biologists bioinformaticians Biomedical researchers
FAIR data - Module 2 (data life cycle)

La vie des données pendant le projet : Principe et outils pour organiser, nommer, versionner, stocker, archiver, mes données

Scientific topics: Bioinformatics, Biology, Data management

Operations: Data handling

Keywords: Data preserving, Data storage

Resource type: Slides

FAIR data - Module 2 (data life cycle) https://tess.elixir-europe.org/materials/fair-data-module-2 La vie des données pendant le projet : Principe et outils pour organiser, nommer, versionner, stocker, archiver, mes données Bioinformatics Biology Data management Data preserving, Data storage Biologists bioinformaticians Biomedical researchers
FAIR data - Module 1 (research data)

Research data and their centrality in the research process. This material is mostly in French.

Scientific topics: Biology, Bioinformatics, FAIR data, Open science

Keywords: metadata, Data Life Cycle, Reproducibility, Data management plan

Resource type: Slides

FAIR data - Module 1 (research data) https://tess.elixir-europe.org/materials/fair-data-module-1 Research data and their centrality in the research process. This material is mostly in French. Gautier Sarah Hélène Chiapello Jean-François Dufayard Julien Seiler Lionel Maurel Paulette Lieby Thomas Denecker Biology Bioinformatics FAIR data Open science metadata, Data Life Cycle, Reproducibility, Data management plan Biologists bioinformaticians Biomedical researchers
Plant Phenotyping Data managment Webinar (MIAPPE)

The Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org), has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking...

Scientific topics: Data submission, annotation, and curation, Data quality management, Phenomics, Plant biology

Operations: Standardisation and normalisation

Resource type: Video, Slides

Plant Phenotyping Data managment Webinar (MIAPPE) https://tess.elixir-europe.org/materials/plant-phenotyping-data-managment-webinar-miappe The Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org), has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking between phenotype and genotype datasets, relevant section of MIAPPE are beginning to be used for genotyping standards. This Webinar will give an overview of the current practices and methods for plant phenotyping data standardization, and how to deal with the variability and heterogeneity inherent to research and breeding data sets. Data management approaches at some of the major research organizations will be given as examples. The recording is available [here](https://youtu.be/4FOQPAWl6_M) and the slides are [here](https://drive.google.com/file/d/1FORlCX662T9dxiG4uzQwVXDXnq-sP0FP/view?usp=sharing) Cyril Pommier Anne-Françoise Adam-Blondon Célia Michotey Data submission, annotation, and curation Data quality management Phenomics Plant biology Researchers Biologists, Genomicists, Computer Scientists Biologists software developers, bioinformaticians
IFB Shiny training

Shiny package training (in french)

Keywords: R-programming, Reproducible Science

IFB Shiny training https://tess.elixir-europe.org/materials/ifb-shiny-training Shiny package training (in french) Hélène Chiapello Jacques van Helden R-programming, Reproducible Science bioinformaticians statisticians
FAIR principles applied to bioinformatics

Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure...

Keywords: FAIR, Reproducible Science, Open science, Data analysis, Data processing

Resource type: Training materials

FAIR principles applied to bioinformatics https://tess.elixir-europe.org/materials/fair-principles-applied-to-bioinformatics Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure the traceability of analysis using Notebooks. The training material is in french Hélène Chiapello FAIR, Reproducible Science, Open science, Data analysis, Data processing bioinformaticians software developers, bioinformaticians computational scientists Researchers
Plant Phenotyping Data managment (MIAPPE)

This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners...

Scientific topics: Data management, Plant biology, Phenomics

Operations: Formatting, Annotation

Keywords: Plant Phenotyping, Data-format, data sharing

Resource type: Training materials

Plant Phenotyping Data managment (MIAPPE) https://tess.elixir-europe.org/materials/plant-phenotyping-data-managment-miappe This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners will know how to use standards and ontologies, how to describe their measurment protocole and practices how to fill a template with their data and how to apply the standards concept in some data managment tools. Data management Plant biology Phenomics Plant Phenotyping, Data-format, data sharing Biologists geneticists plant researchers software engineers database managers
WheatIS DataDiscovery webinar

The [WheatIS project](http://www.wheatis.org/) aims at building an International Wheat Information System to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools. The project is...

Scientific topics: Data management

Keywords: wheat, information system, data discovery

Resource type: Webinar, Slides, Video

WheatIS DataDiscovery webinar https://tess.elixir-europe.org/materials/wheatis-datadiscovery-webinar The [WheatIS project](http://www.wheatis.org/) aims at building an International Wheat Information System to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools. The project is endorsed by the [Wheat Initiative](https://www.wheatinitiative.org/). The [WheatIS DataDiscovery tool](https://urgi.versailles.inrae.fr/wheatis/) allows to search data in all the wheat resources around the world. This Webinar described how to use the tool, what data are available, how to join, etc. The replay is available on [Youtube](https://youtu.be/FoVXBhO8arY). Taner Sen Data management wheat, information system, data discovery Researchers Scientists
Getting started with Bioschemas

### "How to do" guidelines about: * What and why schema.org * What and why bioschemas.org * How-to select the right profile for your resource * How-to mark up your own resource with Bioschemas

Keywords: Bioschemas, Standards

Getting started with Bioschemas https://tess.elixir-europe.org/materials/getting-started-with-bioschemas ### "How to do" guidelines about: * What and why schema.org * What and why bioschemas.org * How-to select the right profile for your resource * How-to mark up your own resource with Bioschemas Bioschemas, Standards
bio.tools & EDAM drop-in hackathon & discussions

bio.tools, EDAM drop-in hackathon and discussions

Keywords: biohackaton 2018

bio.tools & EDAM drop-in hackathon & discussions https://tess.elixir-europe.org/materials/bio-tools-edam-drop-in-hackathon-discussions bio.tools, EDAM drop-in hackathon and discussions biohackaton 2018
Application of RDF-based models and tools for enhancing interoperable

Application of RDF-based models and tools for enhancing interoperable use of biomedical resources

Keywords: biohackaton 2018

Application of RDF-based models and tools for enhancing interoperable https://tess.elixir-europe.org/materials/application-of-rdf-based-models-and-tools-for-enhancing-interoperable Application of RDF-based models and tools for enhancing interoperable use of biomedical resources biohackaton 2018
Development of a GA4GH-compliant, language-agnostic workflow execution service

Development of a GA4GH-compliant, language-agnostic workflow execution service

Keywords: biohackaton 2018

Development of a GA4GH-compliant, language-agnostic workflow execution service https://tess.elixir-europe.org/materials/development-of-a-ga4gh-compliant-language-agnostic-workflow-execution-service Development of a GA4GH-compliant, language-agnostic workflow execution service biohackaton 2018
Exploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships

Exploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships

Keywords: biohackaton 2018

Exploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships https://tess.elixir-europe.org/materials/exploring-pharmacogenomic-lod-for-molecular-explanations-of-gene-drug-relationships Exploring Pharmacogenomic LOD for Molecular Explanations of Gene-Drug Relationships biohackaton 2018
From Biotea to Bioschemas: definition of profiles required to represent scholarly publications

From Biotea to Bioschemas: definition of profiles required to represent scholarly publications

Keywords: biohackaton 2018

From Biotea to Bioschemas: definition of profiles required to represent scholarly publications https://tess.elixir-europe.org/materials/from-biotea-to-bioschemas-definition-of-profiles-required-to-represent-scholarly-publications From Biotea to Bioschemas: definition of profiles required to represent scholarly publications biohackaton 2018
Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases

Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases

Keywords: biohackaton 2018

Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases https://tess.elixir-europe.org/materials/data-clearinghouse-validation-and-curation-of-biosamples-ena-breeding-api-endpoints-mar-databases Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases biohackaton 2018
Import workflows into TeSS Concept Maps

Import workflows into TeSS Concept Maps

Keywords: biohackaton 2018

Import workflows into TeSS Concept Maps https://tess.elixir-europe.org/materials/import-workflows-into-tess-concept-maps Import workflows into TeSS Concept Maps biohackaton 2018
Assessing the FAIRness of Training Materials

Assessing the FAIRness of Training Materials

Keywords: biohackaton 2018

Assessing the FAIRness of Training Materials https://tess.elixir-europe.org/materials/assessing-the-fairness-of-training-materials Assessing the FAIRness of Training Materials biohackaton 2018
Alternative episodes for the 4 Open Source Software

Alternative episodes for the 4 Open Source Software (4OSS) lesson focused on different Open Source technologies: Github, Docker, Jupyter Notebook and so on

Keywords: biohackaton 2018

Alternative episodes for the 4 Open Source Software https://tess.elixir-europe.org/materials/alternative-episodes-for-the-4-open-source-software Alternative episodes for the 4 Open Source Software (4OSS) lesson focused on different Open Source technologies: Github, Docker, Jupyter Notebook and so on biohackaton 2018
JSON schema validation with ontologies

JSON schema validation with ontologies

Keywords: biohackaton 2018

JSON schema validation with ontologies https://tess.elixir-europe.org/materials/json-schema-validation-with-ontologies JSON schema validation with ontologies biohackaton 2018
Development of a catalog of federated SPARQL queries in the field of Rare Diseases

Development of a catalog of federated SPARQL queries in the field of Rare Diseases

Keywords: biohackaton 2018

Development of a catalog of federated SPARQL queries in the field of Rare Diseases https://tess.elixir-europe.org/materials/development-of-a-catalog-of-federated-sparql-queries-in-the-field-of-rare-diseases Development of a catalog of federated SPARQL queries in the field of Rare Diseases biohackaton 2018
Building a semantic search engine for biology publications using event stream processing

Building a semantic search engine for biology publications using event stream processing

Keywords: biohackaton 2018

Building a semantic search engine for biology publications using event stream processing https://tess.elixir-europe.org/materials/c-sparql-powered-querying-pipeline-of-biorxiv-publications Building a semantic search engine for biology publications using event stream processing biohackaton 2018
Adding bioschemas markup to data repository

Adding bioschemas markup to data repository

Keywords: biohackaton

Adding bioschemas markup to data repository https://tess.elixir-europe.org/materials/adding-bioschemas-markup-to-data-repository Adding bioschemas markup to data repository biohackaton
Bioconda packaging of the Regulatory Sequence Analysis Tools (RSAT)

Bioconda packaging of the Regulatory Sequence Analysis Tools (RSAT)

Keywords: biohackaton 2018

Bioconda packaging of the Regulatory Sequence Analysis Tools (RSAT) https://tess.elixir-europe.org/materials/bioconda-packaging-of-the-regulatory-sequence-analysis-tools-rsat Bioconda packaging of the Regulatory Sequence Analysis Tools (RSAT) biohackaton 2018
Improve Orphanet disease description knowledge by phenotypic automated recognition using scrapping toolkits

Improve Orphanet disease description knowledge by phenotypic automated recognition using scrapping toolkits

Keywords: biohackaton 2018

Improve Orphanet disease description knowledge by phenotypic automated recognition using scrapping toolkits https://tess.elixir-europe.org/materials/improve-orphanet-disease-description-knowledge-by-phenotypic-automated-recognition-using-scrapping-toolkits Improve Orphanet disease description knowledge by phenotypic automated recognition using scrapping toolkits biohackaton 2018
CWL support in Galaxy

CWL support in Galaxy

Keywords: biohackaton 2018

CWL support in Galaxy https://tess.elixir-europe.org/materials/cwl-support-in-galaxy CWL support in Galaxy biohackaton 2018
Transfer of Research Assets between FAIRDOM SEEKs

Transfer of Research Assets between FAIRDOM SEEKs

Keywords: biohackaton 2018

Transfer of Research Assets between FAIRDOM SEEKs https://tess.elixir-europe.org/materials/transfer-of-research-assets-between-fairdom-seeks Transfer of Research Assets between FAIRDOM SEEKs biohackaton 2018
Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment

Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment

Keywords: biohackaton 2018

Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment https://tess.elixir-europe.org/materials/improve-shiny-and-rstudio-integration-within-galaxy-using-galaxy-interactive-environment Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment biohackaton 2018
Galaxy training material improvement and extension

Galaxy training material improvement and extension

Keywords: biohackaton 2018

Galaxy training material improvement and extension https://tess.elixir-europe.org/materials/galaxy-training-material-improvement-and-extension Galaxy training material improvement and extension biohackaton 2018
Pathway effect prediction for protein targets

Pathway effect prediction for protein targets

Keywords: biohackaton 2018

Pathway effect prediction for protein targets https://tess.elixir-europe.org/materials/pathway-effect-prediction-for-protein-targets Pathway effect prediction for protein targets biohackaton 2018