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1561 materials found

BridgeDb-Matlab Usage Instructions

Instructions on how to install and use the BridgeDb functionality in Matlab.

Keywords: ELIXIR RIR, BridgeDb

BridgeDb-Matlab Usage Instructions https://tess.elixir-europe.org/materials/bridgedb-matlab-usage-instructions Instructions on how to install and use the BridgeDb functionality in Matlab. ELIXIR RIR, BridgeDb
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
Elaboración de un Plan de Gestión de Datos (DMP): teoria y práctica

PDF with slides of the course in Spanish - Data management definitions - DMP Objectives - DMP Content and structure - Competencies needed - Practical session: DMP content analysis and evaluation

Scientific topics: FAIR data, Data management

Keywords: ELIXIR-CONVERGE, DMP, DMP tools, DMP templates, DMP evaluation, Data managment plan, research data management, FAIR principles, tools, template, competency, evaluation, online, e-learning, Spanish

Resource type: PDF, e-learning, slideck/ presentation

Elaboración de un Plan de Gestión de Datos (DMP): teoria y práctica https://tess.elixir-europe.org/materials/elaboracion-de-un-plan-de-gestion-de-datos-dmp-teoria-y-practica PDF with slides of the course in Spanish - Data management definitions - DMP Objectives - DMP Content and structure - Competencies needed - Practical session: DMP content analysis and evaluation FAIR data Data management ELIXIR-CONVERGE, DMP, DMP tools, DMP templates, DMP evaluation, Data managment plan, research data management, FAIR principles, tools, template, competency, evaluation, online, e-learning, Spanish operational manager IT support data manager project manager policy officer
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
Ten simple rules for making training materials FAIR

Sharing, reusing and reproducing data, software and other digital objects are the basis for open science practices, and to ease this the scientific community has developed the Findable, Accessible, Interoperable and Reusable (FAIR) principles. FAIR principles are however not so simple to...

Scientific topics: FAIR data

Operations: Data handling

Keywords: FAIR data, FAIR, ELIXIR-CONVERGE

Resource type: Video

Ten simple rules for making training materials FAIR https://tess.elixir-europe.org/materials/ten-simple-rules-for-making-training-materials-fair Sharing, reusing and reproducing data, software and other digital objects are the basis for open science practices, and to ease this the scientific community has developed the Findable, Accessible, Interoperable and Reusable (FAIR) principles. FAIR principles are however not so simple to understand and adopt, and may be quite convoluted for some. The ELIXIR Training Platform in cooperation with other associated partner ZB MED has put together a Ten Simple Rules for Making Training Materials FAIR which simplify the FAIR principles by breaking them down into very practical steps. This webinar introduced these ten rules and discussed the challenges and ideas to put them into practice. FAIR data FAIR data, FAIR, ELIXIR-CONVERGE PhD students Post Docs Undergraduate students
Research Data Management and Sharing MOOC

This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management...

Scientific topics: Data management

Keywords: Data Life Cycle, Data managment plan

Resource type: online modules

Research Data Management and Sharing MOOC https://tess.elixir-europe.org/materials/research-data-management-and-sharing-mooc This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management plans, and be familiar with best practices for working with data including the organization, documentation, and storage and security of data. Learners will also understand the impetus and importance of archiving and sharing data as well as how to assess the trustworthiness of repositories. Data management Data Life Cycle, Data managment plan Life Science Researchers 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
Data publishing and archival

Slides for the "Data publishing and archival" session of the "Research Data Management and Stewardship Training" held on 14 June 2021 by ELIXIR-Luxembourg.

Scientific topics: FAIR data, Data submission, annotation, and curation

Keywords: Data publishing, data archiving, Data preserving

Resource type: Presentation

Data publishing and archival https://tess.elixir-europe.org/materials/data-publishing-and-archival Slides for the "Data publishing and archival" session of the "Research Data Management and Stewardship Training" held on 14 June 2021 by ELIXIR-Luxembourg. Pinar Alper Roland Krause Nene Barry Vilem Ded FAIR data Data submission, annotation, and curation Data publishing, data archiving, Data preserving Master students data stewards Researchers PhD candidates
Mantra Research Data Management Training

MANTRA is a free, online non-assessed course with guidelines to help you understand and reflect on how to manage the digital data you collect throughout your research. It has been crafted for the use of post-graduate students, early career researchers, and also information professionals. It is...

Mantra Research Data Management Training https://tess.elixir-europe.org/materials/mantra-research-data-management-training MANTRA is a free, online non-assessed course with guidelines to help you understand and reflect on how to manage the digital data you collect throughout your research. It has been crafted for the use of post-graduate students, early career researchers, and also information professionals. It is freely available on the web for anyone to explore on their own. Through a series of interactive online units you will learn about terminology, key concepts, and best practice in research data management.
Introduction to research data management, data management planning and services provided by CSC – IT Center for Science

Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project.

Scientific topics: FAIR data, Data management

Keywords: DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE

Resource type: Series of videos, Video, youtube video

Introduction to research data management, data management planning and services provided by CSC – IT Center for Science https://tess.elixir-europe.org/materials/introduction-to-research-data-management-data-management-planning-and-services-provided-by-csc-it-center-for-science Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project. Maria Lehtivaara FAIR data Data management DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE Researchers Life Science Researchers Undergraduate students Master students PhD candidates postdoctoral researchers Senior Researchers, Lab Managers, Postdocs and PhD Students with basic knowledge of DMPs. Participants in the "Introduction to Data Management Plans" workshop.
Slides DMP writing workshop for Researchers in Bergen online 21.04. - 22.04.2021

Slides DMP writing workshop for Researchers in Bergen online 21.04. - 22.04.2021

Scientific topics: Data management

Operations: Deposition, Data handling, Data retrieval

Keywords: Data management plan, data management

Resource type: Slides

Slides DMP writing workshop for Researchers in Bergen online 21.04. - 22.04.2021 https://tess.elixir-europe.org/materials/slides-dmp-writing-workshop-for-researchers-in-bergen-online-21-04-22-04-2021 Slides DMP writing workshop for Researchers in Bergen online 21.04. - 22.04.2021 Data management Data management plan, data management All postgraduates
Slides from DMP writing workshop, for Researchers in Aas, online 09.03.- 10.03.2021

Slides from DMP writing workshop, for Researchers in Aas, online 09.03.- 10.03.2021

Scientific topics: Data management

Operations: Data retrieval, Data handling, Deposition

Keywords: Data management plan, data management

Resource type: Slides

Slides from DMP writing workshop, for Researchers in Aas, online 09.03.- 10.03.2021 https://tess.elixir-europe.org/materials/slides-from-dmp-writing-workshop-for-researchers-in-aas-online-09-03-10-03-2021 Slides from DMP writing workshop, for Researchers in Aas, online 09.03.- 10.03.2021 Data management Data management plan, data management All postgraduates
WEBINAR: Making sense of phosphoproteomics data with Phosphomatics

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021.

Scientific topics: Protein modifications, Proteomics

Keywords: Phosphoproteomics

WEBINAR: Making sense of phosphoproteomics data with Phosphomatics https://tess.elixir-europe.org/materials/webinar-making-sense-of-phosphoproteomics-data-with-phosphomatics This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021. Protein modifications Proteomics Phosphoproteomics
WEBINAR: Getting started with deep learning

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Getting started with deep learning’. This webinar took place on 21 July 2021.

Scientific topics: Machine learning

Keywords: Deep learning

WEBINAR: Getting started with deep learning https://tess.elixir-europe.org/materials/webinar-getting-started-with-deep-learning This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Getting started with deep learning’. This webinar took place on 21 July 2021. Machine learning Deep learning
WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021.

Scientific topics: Phylogeny, Phylogenetics

WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset https://tess.elixir-europe.org/materials/webinar-detection-of-and-phasing-of-hybrid-accessions-in-a-target-capture-dataset This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021. Phylogeny Phylogenetics
WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021.

Scientific topics: Phylogenetics

WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation https://tess.elixir-europe.org/materials/webinar-conflict-in-multi-gene-datasets-why-it-happens-and-what-to-do-about-it-deep-coalescence-paralogy-and-reticulation This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021. Phylogenetics
WORKSHOP: Variant calling in humans, animals and plants with Galaxy

This Zenodo record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.

Scientific topics: Genetic variation

Keywords: Variant calling

WORKSHOP: Variant calling in humans, animals and plants with Galaxy https://tess.elixir-europe.org/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy This Zenodo record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021. Genetic variation Variant calling
WEBINAR: Getting started with command line bioinformatics

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Getting started with command line bioinformatics’. This webinar took place on 22 June 2021.

Scientific topics: Computational biology

Keywords: Command line

WEBINAR: Getting started with command line bioinformatics https://tess.elixir-europe.org/materials/webinar-getting-started-with-command-line-bioinformatics This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Getting started with command line bioinformatics’. This webinar took place on 22 June 2021. Carolyn Hogg Computational biology Command line
GA4GH Passports and ELIXIR AAI

The target group of the training is developers and administrators of services that want to make use of GA4GH Passports to authenticate a user and authorise them to call an API.

Keywords: AAI , GA4GH, Passports, Auhtorisation

Resource type: Training materials, Video

GA4GH Passports and ELIXIR AAI https://tess.elixir-europe.org/materials/ga4gh-passports-and-elixir-aai The target group of the training is developers and administrators of services that want to make use of GA4GH Passports to authenticate a user and authorise them to call an API. Stefan Negru Teemu Kataja AAI , GA4GH, Passports, Auhtorisation software developers, bioinformaticians
Practicalities of data handling

Slides for the "Practicalities of data handling" session of the "Research Data Management and Stewardship Training" held regularly by ELIXIR-Luxembourg.

Scientific topics: Data management, Data acquisition, Data security

Operations: Data handling

Keywords: data encryption, data protection, setup, checksums

Resource type: Presentation

Practicalities of data handling https://tess.elixir-europe.org/materials/practicalities-of-data-handling Slides for the "Practicalities of data handling" session of the "Research Data Management and Stewardship Training" held regularly by ELIXIR-Luxembourg. Pinar Alper Roland Krause Nene Barry Data management Data acquisition Data security data encryption, data protection, setup, checksums Researchers PhD Master students
Reproducible analysis

Slides for the "Reproducible analysis" session of the "Best practices in research data management and stewardship" held regularly by ELIXIR-Luxembourg.

Scientific topics: Data architecture, analysis and design

Keywords: Workflows, Literate programming, Reproducible Science, Data analysis

Resource type: Presentation

Reproducible analysis https://tess.elixir-europe.org/materials/reproducible-analysis Slides for the "Reproducible analysis" session of the "Best practices in research data management and stewardship" held regularly by ELIXIR-Luxembourg. Pinar Alper Vilem Ded Data architecture, analysis and design Workflows, Literate programming, Reproducible Science, Data analysis PhD candidates Researchers
HCA / Bioconductor Seed Network Symposium

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

HCA / Bioconductor Seed Network Symposium https://tess.elixir-europe.org/materials/hca-bioconductor-seed-network-symposium Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Translating R package documentation

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Translating R package documentation https://tess.elixir-europe.org/materials/translating-r-package-documentation Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Data Management Planning workshop for new Life Science Projects

Slides from Data Management Planning online workshop for Life Science Projects for researchers

Scientific topics: Data management

Operations: Data retrieval, Data handling, Deposition

Keywords: data management plan, NeLS, TSD, metadata, sensitive, data publication, data protection, storage, identifiers, DMP, licensing, Compliance, data life cycle - collect, data life cycle - reuse, data life cycle - analyse, data life cycle - process, data life cycle - preserve, data life cycle - share, data life cycle - plan

Resource type: Slides

Data Management Planning workshop for new Life Science Projects https://tess.elixir-europe.org/materials/data-management-planning-workshop-for-new-life-science-projects Slides from Data Management Planning online workshop for Life Science Projects for researchers Nazeefa Fatima Espen Åberg Eivind Coward Federico Bianchini Data management data management plan, NeLS, TSD, metadata, sensitive, data publication, data protection, storage, identifiers, DMP, licensing, Compliance, data life cycle - collect, data life cycle - reuse, data life cycle - analyse, data life cycle - process, data life cycle - preserve, data life cycle - share, data life cycle - plan Professor PhD candidate Postdoctoral researcher Researcher data steward / data manager data manager Senior scientist/ Principal investigator Life sciences
Multi-omics data visualization with PathVisio

With this tutorial you can follow a step-by-step guide for visualizing multi-omics data with the pathway drawing software PathVisio

Keywords: biological pathways, Pathways, Pathway analysis

Resource type: Tutorial

Multi-omics data visualization with PathVisio https://tess.elixir-europe.org/materials/multi-omics-data-visualization-with-pathvisio With this tutorial you can follow a step-by-step guide for visualizing multi-omics data with the pathway drawing software PathVisio biological pathways, Pathways, Pathway analysis
Biological network data tutorial

In this skills session, you will learn: how to upload a biological network from STRING how to extend a network using CyTargetLinker how to load a pathway diagram from WikiPathways how to upload a network shared via NDEx how to visualize data in a network how to create a sub network how to...

Keywords: Biological networks, Network Visualization

Resource type: Tutorial

Biological network data tutorial https://tess.elixir-europe.org/materials/biological-network-data-tutorial In this skills session, you will learn: how to upload a biological network from STRING how to extend a network using CyTargetLinker how to load a pathway diagram from WikiPathways how to upload a network shared via NDEx how to visualize data in a network how to create a sub network how to extend a network via R Biological networks, Network Visualization Life Science Researchers PhD students, computer scientists, bioinformaticians and developers who need to maintain/extend existing tools or develop new tools for Galaxy.
Week 7: Participant stories

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Week 7: Participant stories https://tess.elixir-europe.org/materials/week-7-participant-stories Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Workshop
Week 6: Reproducible research with AnVILPublish

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Week 6: Reproducible research with AnVILPublish https://tess.elixir-europe.org/materials/week-6-reproducible-research-with-anvilpublish Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Workshop
Week 5: Using AnVIL for teaching R / Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Week 5: Using AnVIL for teaching R / Bioconductor https://tess.elixir-europe.org/materials/week-5-using-anvil-for-teaching-r-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Workshop