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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

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 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
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
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
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.
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
Week 4: Single-cell RNASeq with 'Orchestrating Single Cell Analysis' in 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 4: Single-cell RNASeq with 'Orchestrating Single Cell Analysis' in R / Bioconductor https://tess.elixir-europe.org/materials/week-4-single-cell-rnaseq-with-orchestrating-single-cell-analysis-in-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
Week 1: Using R / Bioconductor in AnVIL

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 1: Using R / Bioconductor in AnVIL https://tess.elixir-europe.org/materials/week-1-using-r-bioconductor-in-anvil 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
Updates to default caching location

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

Updates to default caching location https://tess.elixir-europe.org/materials/updates-to-default-caching-location 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.
Release schedule discussion

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

Release schedule discussion https://tess.elixir-europe.org/materials/release-schedule-discussion 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.
EJP RD MOOC "Diagnosing Rare Diseases: from the Clinic to Research and back"

Discover the role of research, clinical investigation and data sharing in diagnosing rare diseases. This course offers an exploration of key questions around rare disease diagnostic research and issues today, as well as insights into patient experiences.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

EJP RD MOOC "Diagnosing Rare Diseases: from the Clinic to Research and back" https://tess.elixir-europe.org/materials/ejp-rd-mooc-diagnosing-rare-diseases-from-the-clinic-to-research-and-back Discover the role of research, clinical investigation and data sharing in diagnosing rare diseases. This course offers an exploration of key questions around rare disease diagnostic research and issues today, as well as insights into patient experiences. Rare diseases Rare Diseases & Research PhD students postdoctoral researchers Researchers healthcare professionals Patient Advocates rare disease patients representatives
Access Bioinformatics Databases with Biopython

In this 1-hour long project-based course, you will learn how to access, parse, and visualize data from various bioinformatics sequence and structural online databases such as ENTREZ, PDB, KEGG and NCBI using Biopython. You will also interact with various bioinformatics file formats such as FASTA,...

Keywords: data-science, life-sciences, data-analysis, health-informatics

Access Bioinformatics Databases with Biopython https://tess.elixir-europe.org/materials/access-bioinformatics-databases-with-biopython In this 1-hour long project-based course, you will learn how to access, parse, and visualize data from various bioinformatics sequence and structural online databases such as ENTREZ, PDB, KEGG and NCBI using Biopython. You will also interact with various bioinformatics file formats such as FASTA, PDB, GENBANK and XML along with various parsers to read and modify these files using Biopython. Note: This course works best for learners who are based in the North America region. We’re currently working on providing the same experience in other regions. data-science, life-sciences, data-analysis, health-informatics
R7 for 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...

Resource type: Talk

R7 for Bioconductor https://tess.elixir-europe.org/materials/r7-for-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.
Making cohort data FAIR

CINECA webinar about how to make data from cohort studies FAIR

Scientific topics: Data management, Data integration and warehousing

Keywords: FAIR data, Cohort data, Ontologies, Standards

Resource type: Video

Making cohort data FAIR https://tess.elixir-europe.org/materials/making-cohort-data-fair CINECA webinar about how to make data from cohort studies FAIR Data management Data integration and warehousing FAIR data, Cohort data, Ontologies, Standards
Testing R Packages

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

Testing R Packages https://tess.elixir-europe.org/materials/testing-r-packages 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.
Discovering scientific evidence using Europe PMC SciLite annotation

For readers of life sciences journal articles, annotations make it easier to scan an article and get a quick overview, find key concepts, and discover evidence, such as gene disease associations or molecular interactions. This webinar will demonstrate how to use the power of text mining to find...

Keywords: Biomedical Literature, Annotations, Literature search, SciLite, Protein structure viewer, Chemical viewer

Resource type: Life Sciences Literature Database

Discovering scientific evidence using Europe PMC SciLite annotation https://tess.elixir-europe.org/materials/discovering-scientific-evidence-using-europe-pmc-scilite-annotation For readers of life sciences journal articles, annotations make it easier to scan an article and get a quick overview, find key concepts, and discover evidence, such as gene disease associations or molecular interactions. This webinar will demonstrate how to use the power of text mining to find evidence in scientific literature. Who is this course for? This webinar is suitable for scientists, database curators or anyone who wishes to learn more about how to use annotations. Outcomes By the end of the webinar you will be able to: Explore Europe PubMed Central Use text mining for scientific literature searches Aravind Venkatesan Biomedical Literature, Annotations, Literature search, SciLite, Protein structure viewer, Chemical viewer
Finding the data behind research publications with Europe PMC

This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis. Europe PMC is an open biomedical literature database including PubMed indexed articles, preprints,...

Keywords: Biomedical Literature, Data links, databases, External links

Resource type: Life Sciences Literature Database

Finding the data behind research publications with Europe PMC https://tess.elixir-europe.org/materials/finding-the-data-behind-research-publications-with-europe-pmc This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis. Europe PMC is an open biomedical literature database including PubMed indexed articles, preprints, micropublications and more. Who is this course for? This webinar is aimed at scientists with an interest in learning more about the data-rich literature search tools provided by Europe PMC. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful. Michael Parkin Biomedical Literature, Data links, databases, External links
Using Europe PMC for effective literature research

This webinar will explain how to find and access relevant scientific literature and show how you can follow the latest developments in your scientific field. It will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex...

Keywords: Literature search, peer reviewed articles, Europe PMC, Preprints, Data links, Annotations, Europe PMC, ORCID

Resource type: Life Science Literature Database, Life Sciences Literature Database

Using Europe PMC for effective literature research https://tess.elixir-europe.org/materials/using-europe-pmc-for-effective-literature-research This webinar will explain how to find and access relevant scientific literature and show how you can follow the latest developments in your scientific field. It will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex queries. Europe PMC (https://europepmc.org/) is an open biomedical literature database including PubMed indexed articles, preprints, micropublications and more. This webinar is aimed at scientists who want to optimise their literature searches. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful. Michael Parkin Literature search, peer reviewed articles, Europe PMC, Preprints, Data links, Annotations, Europe PMC, ORCID
Searching and browsing scientific publications with the new Europe PMC

Literature search is an essential and routine task in scientific research. Following the release of the new Europe PMC website, this webinar will show you the new full-text searching and browsing features built to optimise the literature research. Learn how to find the most recent, most relevant...

Keywords: Literature search, Data links, preprints

Resource type: Life Sciences Literature Database

Searching and browsing scientific publications with the new Europe PMC https://tess.elixir-europe.org/materials/searching-and-browsing-scientific-publications-with-the-new-europe-pmc Literature search is an essential and routine task in scientific research. Following the release of the new Europe PMC website, this webinar will show you the new full-text searching and browsing features built to optimise the literature research. Learn how to find the most recent, most relevant and most cited articles in a topic of interest. Also, learn how to find and explore the enhanced content available in Europe PMC. This webinar is aimed at life science scientists who are interested in optimising their literature search skills. No prior knowledge of bioinformatics is required. Michael Parkin Literature search, Data links, preprints
Say Hello to ALTREP

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

Say Hello to ALTREP https://tess.elixir-europe.org/materials/say-hello-to-altrep 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.
Valorisation and intellectual properties in research data management

### Valorisation and IP * Basics of Tech Transfer and IPR from an academic perspective * Insights as to: * Why is it important when handling and managing research data? * How do IP rights fit in FAIR data principles * When to safeguard data for proprietary protection? * Where/how...

Scientific topics: Data management

Keywords: intellectual property protection

Resource type: Presentation

Valorisation and intellectual properties in research data management https://tess.elixir-europe.org/materials/valorisation-and-interlectual-properties-in-research-data-management ### Valorisation and IP * Basics of Tech Transfer and IPR from an academic perspective * Insights as to: * Why is it important when handling and managing research data? * How do IP rights fit in FAIR data principles * When to safeguard data for proprietary protection? * Where/how share and publish data if valorisation is in scope? Data management intellectual property protection life scientists
Alternate Representations of R Objects or ALTREP

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

Alternate Representations of R Objects or ALTREP https://tess.elixir-europe.org/materials/alternate-representations-of-r-objects-or-altrep 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.
Presentation on sparseMatrixStats

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

Presentation on sparseMatrixStats https://tess.elixir-europe.org/materials/presentation-on-sparsematrixstats 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.
Bacterial Bioinformatics

This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses PATRIC, the PathoSystems Resource Integration Center, as the platform for analysis. PATRIC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center,...

Keywords: life-sciences, health-informatics, research

Bacterial Bioinformatics https://tess.elixir-europe.org/materials/bacterial-bioinformatics This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses PATRIC, the PathoSystems Resource Integration Center, as the platform for analysis. PATRIC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center, providing comprehensive bacterial genomic data with integrated analysis tools and visualizations. PATRIC also provides a private workspace where users can upload and analyze their own data. Course participants will gain skills needed to do comparative analysis of bacterial genomes, starting with raw sequence data.The lessons in the first module cover genome assembly, annotation, phylogenetic tree construction, and protein family / proteome comparisons. Each lesson builds on the previous, creating a complete baseline analysis workflow. life-sciences, health-informatics, research