TeSS Training eSupport System

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://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module4.html 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 Frédéric de Lamotte Paulette Lieby Lionel Maurel 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://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module3.html 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 Frédéric de Lamotte Hélène Chiapello Thomas Denecker 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://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module2.html 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 Frédéric de Lamotte Julien Seiler 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://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module1.html 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. Frédéric de Lamotte 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://youtu.be/4FOQPAWl6_M 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 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://ifb-elixirfr.github.io/IFB_Shiny_training/ https://tess.elixir-europe.org/materials/ifb-shiny-training Shiny package training (in french) Frederic Schütz Cédric Midoux Christophe Malabat 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://github.com/IFB-ElixirFr/IFB-FAIR-bioinfo-training 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 Thomas Denecker Claire Toffano-Nioche Céline Hernandez Julien Seiler Gildas Le Corguillé 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://github.com/MIAPPE/training/tree/master/Paris-Feb-2020 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. Cyril Pommier Daniel Faria Evangelia Papoutsoglou Célia Michotey Elizabeth Arnaud Anne-Françoise Adam-Blondon Data management Plant biology Phenomics Plant Phenotyping, Data-format, data sharing Biologists geneticists plant researchers software engineers database managers

Initiation to R programming and descriptive statistics

On-line course support for the initiation to R programming and descriptive statistics given to PhD students at Institut Pasteur (Paris, France).

Keywords: R-programming, Descriptive statistics, Statistics, Bioinformatics

Initiation to R programming and descriptive statistics https://hub-courses.pages.pasteur.fr/R_pasteur_phd/index.html https://tess.elixir-europe.org/materials/initiation-to-r-programming-and-descriptive-statistics On-line course support for the initiation to R programming and descriptive statistics given to PhD students at Institut Pasteur (Paris, France). Institut Pasteur, Bioinformatics and Biostatistics Hub Blaise Li Étienne Kornobis Sébastien Mella Vincent Guillemot R-programming, Descriptive statistics, Statistics, Bioinformatics PhD students Post-Doctoral Fellows Biologists

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://wheat-urgi.versailles.inrae.fr/About-us/News/WheatIS-webinar-replay 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). Raphaël Flores Cyril Pommier Nicolas Francillonne Hadi Quesneville Anne-Françoise Adam-Blondon Michael Alaux 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://bioschemas.gitbook.io/training-portal/ 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