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://www.futurelearn.com/courses/rare-genetic-disease
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://www.coursera.org/learn/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
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
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...
R7 for Bioconductor
https://bioconductor.org2021/BiocDevelForum/20-R7.pdf
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.
Michael Lawrence
ELN basics training materials
Electronic laboratory notebooks - basic intro in their use and functionality
Resource type: Presentation, hackathon
ELN basics training materials
https://zenodo.org/record/4518805#.YFCyPucxlhE
https://tess.elixir-europe.org/materials/eln-basics-training-materials
Electronic laboratory notebooks - basic intro in their use and functionality
Anastasios Papadiamantis, UoB
Martin Himly, PLUS
experimental nanoscientists
CINECA discovery service catalog
Description and demonstration of the CINECA service catalog
Keywords: Cohort data, Standards, federated data analysis, Beacon queries
Resource type: Series of videos
CINECA discovery service catalog
https://www.youtube.com/playlist?list=PLD6bAdANKoMX5ntDRlNHAWKrnPdshLVgT
https://tess.elixir-europe.org/materials/cineca-discovery-service-catalog
Description and demonstration of the CINECA service catalog
Jonathan Dursi
Jordi Rambla
Frédéric Haziza
Cohort data, Standards, federated data analysis, Beacon queries
A common framework for designing portable federated pipelines
This video describes a common framework for designing portable federated pipelines
Scientific topics: Data architecture, analysis and design
Keywords: data access, federated data analysis
Resource type: Video
A common framework for designing portable federated pipelines
https://www.youtube.com/watch?v=oFmgC2upkSU
https://tess.elixir-europe.org/materials/a-common-framework-for-designing-portable-federated-pipelines
This video describes a common framework for designing portable federated pipelines
Kirill Tsukanov
Alvaro Gonzalez
Data architecture, analysis and design
data access, federated data analysis
FAIR software tools
CINECA webinar discussing the importance of the FAIR principles for software tools used in research
Scientific topics: Software engineering
Keywords: FAIR, software tools, Software
Resource type: Video
FAIR software tools
https://www.youtube.com/watch?v=VEvHBrJlE6M
https://tess.elixir-europe.org/materials/fair-software-tools
CINECA webinar discussing the importance of the FAIR principles for software tools used in research
Carlos Martinez Ortiz
Marta Lloret Llinares
Software engineering
FAIR, software tools, Software
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://www.youtube.com/watch?v=NWeffXwRa-U
https://tess.elixir-europe.org/materials/making-cohort-data-fair
CINECA webinar about how to make data from cohort studies FAIR
Will Hsiao
Marta Lloret Llinares
Data management
Data integration and warehousing
FAIR data, Cohort data, Ontologies, Standards
Introduction to FAIR principles - Open science through FAIR health data networks: dream or reality?
CINECA webinar about the basics of FAIR health data.
Scientific topics: Data management
Keywords: FAIR data, Health data, Open science
Resource type: Video
Introduction to FAIR principles - Open science through FAIR health data networks: dream or reality?
https://www.youtube.com/watch?v=Or3AKpERvrw
https://tess.elixir-europe.org/materials/introduction-to-fair-principles-open-science-through-fair-health-data-networks-dream-or-reality
CINECA webinar about the basics of FAIR health data.
Kees van Bochove
Marta Lloret Llinares
Data management
FAIR data, Health data, Open science
Data Gravity in the Life Sciences: Lessons learned from the HCA and other federated data projects
CINECA webinar discussing when to bring compute to the data
Scientific topics: Data architecture, analysis and design
Keywords: Cloud computing, Data analysis, Standards, Translational research
Resource type: Video
Data Gravity in the Life Sciences: Lessons learned from the HCA and other federated data projects
https://www.youtube.com/watch?v=oiEFnWDVjP8
https://tess.elixir-europe.org/materials/data-gravity-in-the-life-sciences-lessons-learned-from-the-hca-and-other-federated-data-projects
CINECA webinar discussing when to bring compute to the data
Tony Burdett
Marta Lloret Llinares
Data architecture, analysis and design
Cloud computing, Data analysis, Standards, Translational research
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...
Testing R Packages
https://bioconductor.org2021/BiocDevelForum/19-testing.pdf
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.
Dirk Eddelbuettel
Introduction à la programmation Python pour la biologie
Cours de Python pour des biologistes par Patrick Fuchs et Pierre Poulain.
Keywords: Python, Programming, Python for Biologists
Introduction à la programmation Python pour la biologie
https://python.sdv.univ-paris-diderot.fr/
https://tess.elixir-europe.org/materials/introduction-a-la-programmation-python-pour-la-biologie
Cours de Python pour des biologistes par Patrick Fuchs et Pierre Poulain.
Patrick Fuchs
Pierre Poulain
Python, Programming, Python for Biologists
Introduction to Nextflow workshop
workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available...
Scientific topics: Workflows
Keywords: Nextflow, DSL2
Resource type: Presentation, course materials
Introduction to Nextflow workshop
https://github.com/vibbits/nextflow-jnj
https://tess.elixir-europe.org/materials/introduction-to-nextflow-workshop
workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available [here](https://github.com/vibbits/nextflow-jnj/blob/master/presentation/slidedeck.pdf)
Tuur Muyldermans
Workflows
Nextflow, DSL2
bioinformaticians
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://trainingcontent.embl.org/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
Dayane Araujo
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://www.ebi.ac.uk/training-beta/events/finding-data-behind-research-articles-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.
Dayane Araujo
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://www.ebi.ac.uk/training-beta/events/using-europe-pmc-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.
Dayane Araujo
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://www.ebi.ac.uk/training-beta/events/searching-and-browsing-scientific-publications-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.
Dayane Araujo
Michael Parkin
Literature search, Data links, preprints
Annotating data using next generation biobanking ontology (NGBO)
This video explains why we need data standardization and how to annotate data using next generation biobanking ontology (NGBO).
Scientific topics: Ontology and terminology, Data integration and warehousing
Keywords: Standards, Ontologies, Data Integration, data harmonization, Standardised vocabulary
Resource type: Video
Annotating data using next generation biobanking ontology (NGBO)
https://www.youtube.com/watch?v=jGatQTTp-Dg
https://tess.elixir-europe.org/materials/annotating-data-using-next-generation-biobanking-ontology-ngbo
This video explains why we need data standardization and how to annotate data using next generation biobanking ontology (NGBO).
Dalia Alghamdi
Ontology and terminology
Data integration and warehousing
Standards, Ontologies, Data Integration, data harmonization, Standardised vocabulary
Applying data standards to the harmonization of COVID-19 datasets from different sources
This video describes how public health genomics has played a key role in international responses to the COVID-19 pandemic, and how data standards are being used to harmonize data across jurisdictions for Canadian COVID-19 surveillance and outbreak investigations.
Scientific topics: Data integration and warehousing
Keywords: Data integration, Standards, Standardised vocabulary, data harmonization, Ontologies
Resource type: Video
Applying data standards to the harmonization of COVID-19 datasets from different sources
https://www.youtube.com/watch?v=Z20ZOrtQ7Cs
https://tess.elixir-europe.org/materials/applying-data-standards-to-the-harmonization-of-covid-19-datasets-from-different-sources
This video describes how public health genomics has played a key role in international responses to the COVID-19 pandemic, and how data standards are being used to harmonize data across jurisdictions for Canadian COVID-19 surveillance and outbreak investigations.
Emma Griffiths
Data integration and warehousing
Data integration, Standards, Standardised vocabulary, data harmonization, Ontologies
Anyone interested in data standardization and/or the ontology approach (i.e. public, end users).
Useful ontologies for harmonizing cohort data
This video describes a community of practice for interoperable ontology building called the OBO Foundry, and highlights a number of well curated and maintained ontologies that are useful for annotating cohort data.
Scientific topics: Ontology and terminology, Data management, Data integration and warehousing
Keywords: Ontologies, Cohort data, data annotation
Resource type: Video
Useful ontologies for harmonizing cohort data
https://www.youtube.com/watch?v=7m6xtJEh1WE
https://tess.elixir-europe.org/materials/useful-ontologies-for-harmonizing-cohort-data
This video describes a community of practice for interoperable ontology building called the OBO Foundry, and highlights a number of well curated and maintained ontologies that are useful for annotating cohort data.
Emma Griffiths
Ontology and terminology
Data management
Data integration and warehousing
Ontologies, Cohort data, data annotation
Anyone interested in data standardization and/or the ontology approach (i.e. public, end users).
Slides from Data Management Planning Workshop
Slides from Data Management Planning online workshop for Life Science Projects for researchers at UiO 2020-12-11
Scientific topics: Data management
Operations: Deposition, Data retrieval, Data handling
Keywords: Data management plan, data management
Resource type: Slides
Slides from Data Management Planning Workshop
https://doi.org/10.5281/zenodo.4317590
https://tess.elixir-europe.org/materials/slides-from-data-management-planning-workshop-96479971-67e0-47d6-a5de-b2b8f4dbea62
Slides from Data Management Planning online workshop for Life Science Projects for researchers at UiO 2020-12-11
Korbinian Bösl
Elin Stangeland
Lars Soligard
Federico Bianchini
Data management
Data management plan, data management
PhD students
Professors
Professors
All postgraduates
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...
Say Hello to ALTREP
https://bioconductor.org2020/BiocDevelForum/17-ALTREP2.pdf
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.
Jiefei Wang
Introduction to Protein Structure Analysis
This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure....
Operations: Visualisation
Keywords: Protein structure visualisation
Resource type: e-learning
Introduction to Protein Structure Analysis
https://elearning.bits.vib.be/courses/protein-structure-analysis/
https://tess.elixir-europe.org/materials/introduction-to-protein-structure-analysis
This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure. Different hands-on exercises will allow you to compare the structure of homologues, to predict a structural model of proteins (without any structure information) and to find homologous structures. We will use online tools to quantify various interactions in the structures.
## Objectives
* Get to know the data generated from protein structure determination experiments (high-resolution NMR spectroscopy, X-ray crystallography, electron microscopy, ...) and where to get it.
* Display protein structure data and compare structures, through the use of Yasara.
* Create high-quality graphical representations of the structures.
* Calculate the effect of mutations on the stability of your protein.
Alexander Botzki
Joost Van Durme
Janick Mathys
Protein structure visualisation
Life Science Researchers
Reproducible data analysis with RStudio, github and Rmarkdown
Best practices for writing reproducible data-analysis
Creating a reproducible and re-usable data-analysis environment with Rstudio
Input: https://github.com/vibbits/RDM-LS
Output: https://github.com/vibbits/RDM-LS-solution
Scientific topics: Data management, Data architecture, analysis and design
Resource type: Presentation
Reproducible data analysis with RStudio, github and Rmarkdown
https://osf.io/qrt95/
https://tess.elixir-europe.org/materials/reproducible-data-analysis-with-rstudio-github-and-rmarkdown
Best practices for writing reproducible data-analysis
Creating a reproducible and re-usable data-analysis environment with Rstudio
Input: https://github.com/vibbits/RDM-LS
Output: https://github.com/vibbits/RDM-LS-solution
Tuur Muyldermans
Data management
Data architecture, analysis and design
life scientists
Data security and encryption
1. Data security
2. Encryption
3. Passwords
Scientific topics: Data management, Data security
Keywords: data encryption
Resource type: Presentation
Data security and encryption
https://osf.io/k263z/
https://tess.elixir-europe.org/materials/data-security-and-encryption
1. Data security
2. Encryption
3. Passwords
Jan Lammertyn
Data management
Data security
data encryption
life scientists
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://osf.io/dht3z/
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?
Griet Den Herder
Data management
intellectual property protection
life scientists
Preserve, publish and share your data
- why preserve data
- what data should be preserved
- how share data
- where to deposit your data
- Fairsharing, re3data
- ELIXIR Core Resources
- Data Formats
- Generic archives
Scientific topics: Data management, Data submission, annotation and curation
Keywords: data formats, ELIXIR Core resources, FAIR data submission
Resource type: Presentation
Preserve, publish and share your data
https://osf.io/whj7t/
https://tess.elixir-europe.org/materials/preserve-publish-and-share-your-data
- why preserve data
- what data should be preserved
- how share data
- where to deposit your data
- Fairsharing, re3data
- ELIXIR Core Resources
- Data Formats
- Generic archives
Alexander Botzki
Data management
Data submission, annotation and curation
data formats, ELIXIR Core resources, FAIR data submission
life scientists
Reusing existing data
- how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub)
- licenses
- datasets as first-class research products
- research software as first-class research products
- data citations
Scientific topics: Data management
Keywords: data licenses, software licenses, data journal
Resource type: Presentation
Reusing existing data
https://osf.io/syx4m/
https://tess.elixir-europe.org/materials/reusing-existing-data
- how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub)
- licenses
- datasets as first-class research products
- research software as first-class research products
- data citations
Alexander Botzki
Data management
data licenses, software licenses, data journal
life scientists
Organising your data: structure and versioning
how to store and organize data safe, easy and efficient - practical recommendation for folder structures and file naming schemes
Scientific topics: Data management
Keywords: data stewardship, data collection
Resource type: Presentation
Organising your data: structure and versioning
https://osf.io/fpvgy/
https://tess.elixir-europe.org/materials/organising-your-data-structure-and-versioning
how to store and organize data safe, easy and efficient - practical recommendation for folder structures and file naming schemes
Nele Pauwels
Data management
data stewardship, data collection