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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
Plant Phenotyping Data managment Webinar (MIAPPE)

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

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

Operations: Standardisation and normalisation

Resource type: Video, Slides

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

Electronic laboratory notebooks - basic intro in their use and functionality

Resource type: Presentation, hackathon

ELN basics training materials https://tess.elixir-europe.org/materials/eln-basics-training-materials Electronic laboratory notebooks - basic intro in their use and functionality 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://tess.elixir-europe.org/materials/cineca-discovery-service-catalog Description and demonstration of the CINECA service catalog 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://tess.elixir-europe.org/materials/a-common-framework-for-designing-portable-federated-pipelines This video describes a common framework for designing portable federated pipelines 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://tess.elixir-europe.org/materials/fair-software-tools CINECA webinar discussing the importance of the FAIR principles for software tools used in research 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://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
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://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. 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://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 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...

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.
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://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. 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://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) 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://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
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://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). 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://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. 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://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. 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://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 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...

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.
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://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. 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://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 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://tess.elixir-europe.org/materials/data-security-and-encryption 1. Data security 2. Encryption 3. Passwords 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://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
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://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 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://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 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://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