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1399 materials found

3DAROC18 - 3C-based data analysis and 3D reconstruction of chromatin folding (2018)

Training Material focused in 3C-Data Analysis and 3D Chromatin Folding

Keywords: Hi-C

Resource type: Documentation, Exercise, Handout, Scripts

3DAROC18 - 3C-based data analysis and 3D reconstruction of chromatin folding (2018) http://tess.elixir-uk.org/materials/3daroc18-3c-based-data-analysis-and-3d-reconstruction-of-chromatin-folding-2018 Training Material focused in 3C-Data Analysis and 3D Chromatin Folding Marc A. Martí-Renom François Serra David Castillo Hi-C Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ABSTAT18 - Advanced Biostatistics for Bioinformatics Tool Users using R (2018)

Training Material centred in Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data.

Keywords: Statistics and probability

Resource type: Documentation, Exercise, Handout, Scripts

ABSTAT18 - Advanced Biostatistics for Bioinformatics Tool Users using R (2018) http://tess.elixir-uk.org/materials/abstat18-advanced-biostatistics-for-bioinformatics-tool-users-using-r-2018 Training Material centred in Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Lisete Sousa Carina Silva Statistics and probability Academia/ Research Institution Industry Non-Profit Organisation Healthcare
PGDH18 - Population Genetics and Demographic History: model-based approaches (2018)

Training material for hands-on course with a practical approach in the analysis of genetic and genomic data.

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

PGDH18 - Population Genetics and Demographic History: model-based approaches (2018) http://tess.elixir-uk.org/materials/pgdh18-population-genetics-and-demographic-history-model-based-approaches-2018 Training material for hands-on course with a practical approach in the analysis of genetic and genomic data. Mark Beaumont Lounès Chikhi Willy Rodríguez Armando Arredondo Soto Vitor Sousa Population Genomics, Phylogenetics Academia/ Research Institution Industry Non-Profit Organisation
PSLS20 - Practical Statistics for the Life Sciences (2020)

Training material that covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences.

Keywords: Statistics, General Linear Models

Resource type: Documentation, Exercise, Handout, Scripts

PSLS20 - Practical Statistics for the Life Sciences (2020) http://tess.elixir-uk.org/materials/psls20-practical-statistics-for-the-life-sciences-2020 Training material that covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. Lieven Clement Jeroen Gilis Statistics, General Linear Models Academia/ Research Institution Industry Healthcare Non-Profit Organisation
How to use V-pipe (SARS-CoV-2 data)

How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data)

Scientific topics: Workflows, Genetic variation, Virology

Operations: Read pre-processing, Alignment, Variant calling

Keywords: coronavirus, NGS bioinformatics, Variant-calling

Resource type: Computer Software, workflow

How to use V-pipe (SARS-CoV-2 data) http://tess.elixir-uk.org/materials/how-to-use-v-pipe-sars-cov-2-data How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data) Workflows Genetic variation Virology coronavirus, NGS bioinformatics, Variant-calling bioinformaticians Biologists, Genomicists, Computer Scientists
bio.tools documentation

Documentation for the [bio.tools](https://bio.tools) Bioinformatics Tools and Services Discovery Portal.

Scientific topics: Ontology and terminology, Computational biology, Data submission, annotation, and curation, Bioinformatics

Operations: Data retrieval

Keywords: Tools, Curation, Software, Sofware curation, Tool curation

Resource type: Documentation, API reference

bio.tools documentation http://tess.elixir-uk.org/materials/bio-tools-documentation Documentation for the [bio.tools](https://bio.tools) Bioinformatics Tools and Services Discovery Portal. Ontology and terminology Computational biology Data submission, annotation, and curation Bioinformatics Tools, Curation, Software, Sofware curation, Tool curation Researchers Software providers Developers Curators
Integrated DEsign and AnaLysis of small population group trials (IDeAl)

This series of webinars inform stakeholders about the new IDEAL methodology; the main achievements of each WP of the project and the main outcomes of the whole project.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research, Training material

Resource type: Webinar, e-learning

Integrated DEsign and AnaLysis of small population group trials (IDeAl) http://tess.elixir-uk.org/materials/integrated-design-and-analysis-of-small-population-group-trials-ideal This series of webinars inform stakeholders about the new IDEAL methodology; the main achievements of each WP of the project and the main outcomes of the whole project. Rare diseases Rare Diseases & Research, Training material
Slides from Data Management Planning Workshop

Slides from Data Management Planning workshop for Life Science Projects in Ås 11 March 2020

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 http://tess.elixir-uk.org/materials/slides-from-data-management-planning-workshop-1bb3798d-4e70-423c-87b6-82ac7e5e5c54 Slides from Data Management Planning workshop for Life Science Projects in Ås 11 March 2020 Data management Data management plan, data management PhD students Post Docs Professors
Slides from Data Management Planning Workshop

Slides from Data Management Planning workshop for Life Science Projects in Bergen 04 March 2020

Scientific topics: Data management

Operations: Data handling, Data retrieval, Deposition

Keywords: Data management plan, data management

Resource type: Slides

Slides from Data Management Planning Workshop http://tess.elixir-uk.org/materials/slides-from-data-management-planning-workshop Slides from Data Management Planning workshop for Life Science Projects in Bergen 04 March 2020 Data management Data management plan, data management PhD students Post Docs Professors
Rare Disease Pathway and Network Analysis

The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis.

Keywords: Pathway analysis, Biological networks, Network analysis, Pathways

Resource type: Tutorial

Rare Disease Pathway and Network Analysis http://tess.elixir-uk.org/materials/rare-disease-pathway-and-network-analysis The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis. Pathway analysis, Biological networks, Network analysis, Pathways Life Science Researchers
WheatIS DataDiscovery webinar

The [WheatIS project](http://www.wheatis.org/) aims at building an International Wheat Information System to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools. The project is...

Scientific topics: Data management

Keywords: wheat, information system, data discovery

Resource type: Webinar, Slides, Video

WheatIS DataDiscovery webinar http://tess.elixir-uk.org/materials/wheatis-datadiscovery-webinar The [WheatIS project](http://www.wheatis.org/) aims at building an International Wheat Information System to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools. The project is endorsed by the [Wheat Initiative](https://www.wheatinitiative.org/). The [WheatIS DataDiscovery tool](https://urgi.versailles.inrae.fr/wheatis/) allows to search data in all the wheat resources around the world. This Webinar described how to use the tool, what data are available, how to join, etc. The replay is available on [Youtube](https://youtu.be/FoVXBhO8arY). Taner Sen Data management wheat, information system, data discovery Researchers Scientists
Data Stewardship Wizard Workshop (Feb 2020)

[Data Stewardship Wizard](ds-wizard.org) brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data management, Data governance

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides

Data Stewardship Wizard Workshop (Feb 2020) http://tess.elixir-uk.org/materials/data-stewardship-wizard-workshop-feb-2020 [Data Stewardship Wizard](ds-wizard.org) brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into per-project questionnaires to be filled by researchers. This workshop explains the core functionality of the Data Stewardship Wizard. Video recording from the workshop is available **[here](https://www.youtube.com/watch?v=aGpr6JFMuiE)**. Data management Data governance Data management plan, data stewardship, FAIR, data management, software tools Researchers data stewards
How to use Common Workflow Language

**This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).**

Scientific topics: Workflows

Keywords: commonwl, common workflow language, CWL, Workflows, eLearning, EeLP

Resource type: Installation instructions, Manual

How to use Common Workflow Language http://tess.elixir-uk.org/materials/how-to-use-common-workflow-language **This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).** Rob Finn Michael Crusoe Workflows commonwl, common workflow language, CWL, Workflows, eLearning, EeLP bioinformaticians life scientists programmers
The Turing Way

The Turing Way is a lightly opinionated guide to reproducible data science. Our goal is to provide all the information that researchers need at the start of their projects to ensure that they are easy to reproduce at the end. This also means making sure PhD students, postdocs, PIs, and...

Keywords: Data Science, Reproducibility, Version control, Reproducible Environment, Continuous integration

Resource type: e-learning

The Turing Way http://tess.elixir-uk.org/materials/the-turing-way The Turing Way is a lightly opinionated guide to reproducible data science. Our goal is to provide all the information that researchers need at the start of their projects to ensure that they are easy to reproduce at the end. This also means making sure PhD students, postdocs, PIs, and funding teams know which parts of the “responsibility of reproducibility” they can affect, and what they should do to nudge data science to being more efficient, effective, and understandable. Data Science, Reproducibility, Version control, Reproducible Environment, Continuous integration
Introduction to GitHub

The aim for today is to learn the basics of GitHub so that you can use it for your own projects. - Background - What is version control? What is Git? What is GitHub? - How can you use GitHub? How can it be useful for your work? - Practical session: working with GitHub

Keywords: GitHub, Reproducibility

Resource type: Training materials

Introduction to GitHub http://tess.elixir-uk.org/materials/introduction-to-github The aim for today is to learn the basics of GitHub so that you can use it for your own projects. - Background - What is version control? What is Git? What is GitHub? - How can you use GitHub? How can it be useful for your work? - Practical session: working with GitHub Gabriella Rustici GitHub, Reproducibility Senior Managers
Beginners introduction to Git and GitHub

__Morning session__ (Sergio and Mark) https://tinyurl.com/git-intro-zoology: - Background and motivation - What is version control? What is Git? What is GitHub? - How can you use Git and GitHub? How can they be useful for you? - Practical session: working with Git and GitHub __Afternoon...

Keywords: Git, GitHub, control version, Reproducibility

Resource type: Training materials

Beginners introduction to Git and GitHub http://tess.elixir-uk.org/materials/beginners-introduction-to-git-and-github __Morning session__ (Sergio and Mark) https://tinyurl.com/git-intro-zoology: - Background and motivation - What is version control? What is Git? What is GitHub? - How can you use Git and GitHub? How can they be useful for you? - Practical session: working with Git and GitHub __Afternoon session__ (Mark and Anne) https://tinyurl.com/git-course: markdown, pages and wikis; creating good README files; issue tracking; sofware licenses Mark Fernandes pajanne Git, GitHub, control version, Reproducibility Researchers
Constraint-based reconstruction and analysis toolbox tutorials

A suite of >50 tutorials to enable beginners, as well as intermediate and advanced users to practice a wide variety of COBRA methods.

Keywords: Biomodelling

Resource type: Tutorial

Constraint-based reconstruction and analysis toolbox tutorials http://tess.elixir-uk.org/materials/constraint-based-reconstruction-and-analysis-toolbox-tutorials A suite of >50 tutorials to enable beginners, as well as intermediate and advanced users to practice a wide variety of COBRA methods. Biomodelling Biologists, Genomicists, Computer Scientists
BridgeDbR Tutorial

This tutorial describes how to use the BridgeDbR package for identifier mapping.

Keywords: ELIXIR RIR, BridgeDb

BridgeDbR Tutorial http://tess.elixir-uk.org/materials/bridgedbr-tutorial-ce581787-b018-4a34-b161-5ed1b9cc8902 This tutorial describes how to use the BridgeDbR package for identifier mapping. ELIXIR RIR, BridgeDb
Liftr & sbgr

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: Workflows

Liftr & sbgr http://tess.elixir-uk.org/materials/detecting-differential-binding-in-chip-seq-data-with-csaw-7a3a67bf-a44b-4bcb-a54f-02412e71104c 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. Workflows
Data Management Planning

Slides for the Data Management Plannning session of the "Research Data Manegement and Stewardship Training" held regularly by ELIXIR-Luxembourg

Keywords: Data management plan

Resource type: Presentation

Data Management Planning http://tess.elixir-uk.org/materials/data-management-planning Slides for the Data Management Plannning session of the "Research Data Manegement and Stewardship Training" held regularly by ELIXIR-Luxembourg Data management plan Researchers data steward / data manager PhD candidates Master students
Introduction to FAIR principles

Slides for the "Introduction to FAIR Principles" session of the "Research Data Manegement and Stewardship Training" held regularly by ELIXIR-Luxembourg.

Keywords: FAIR data

Resource type: Presentation

Introduction to FAIR principles http://tess.elixir-uk.org/materials/introduction-to-fair-principles Slides for the "Introduction to FAIR Principles" session of the "Research Data Manegement and Stewardship Training" held regularly by ELIXIR-Luxembourg. Roland Krause FAIR data Researchers data steward / data manager PhD candidates Master students
Implementing GDPR in a Biomedical Research Institute

Slides for the "Data protection, working with sensitive human data in research." session of the "Research Data Management and Stewardship Training" held regularly by ELIXIR-Luxembourg.

Scientific topics: Data management, Data governance

Keywords: GDPR, data protection, sensitive data

Implementing GDPR in a Biomedical Research Institute http://tess.elixir-uk.org/materials/implementing-gdpr-in-a-biomedical-research-institute Slides for the "Data protection, working with sensitive human data in research." session of the "Research Data Management and Stewardship Training" held regularly by ELIXIR-Luxembourg. Regina Becker Vilem Ded Data management Data governance GDPR, data protection, sensitive data Researchers data stewards data managers
Querying SIB resources with SPARQL



Querying SIB resources with SPARQL http://tess.elixir-uk.org/materials/sparql 
NBIS Reproducible research course

The material available on these pages is produced and maintained for a course on how to make your data analyses reproducible. In particular, it covers: Data management Conda Snakemake Git Jupyter R Markdown Docker

Keywords: data management, Reproducibility, Data analysis

Resource type: Training materials

NBIS Reproducible research course http://tess.elixir-uk.org/materials/nbis-reproducible-research-course The material available on these pages is produced and maintained for a course on how to make your data analyses reproducible. In particular, it covers: Data management Conda Snakemake Git Jupyter R Markdown Docker Leif Wigge Rasmus Ågren John Sundh data management, Reproducibility, Data analysis bioinformaticians
Helis Academy - FAIRify your data

FAIRify your data: FAIRification & Data modelling using linked data

Keywords: linked data, Wikidata, data management

Resource type: Slides

Helis Academy - FAIRify your data http://tess.elixir-uk.org/materials/helis-academy-fairify-your-data FAIRify your data: FAIRification & Data modelling using linked data linked data, Wikidata, data management bioinformaticians software developers, bioinformaticians Life Science Researchers
Online course 'Learn to write your Data Management Plan'

Writing a Data Management Plan can be new to you. ‘Learn to write your Data Management Plan’, an online self-study course, can help you decide how to take good care of your valuable research data. During the course you are writing your DMP step by step. As a result you have written a DMP for...

Keywords: Data management plan, data management

Resource type: e-learning

Online course 'Learn to write your Data Management Plan' http://tess.elixir-uk.org/materials/online-course-learn-to-write-your-data-management-plan Writing a Data Management Plan can be new to you. ‘Learn to write your Data Management Plan’, an online self-study course, can help you decide how to take good care of your valuable research data. During the course you are writing your DMP step by step. As a result you have written a DMP for you research project. While you are training, you can write your DMP in DMPonline. You can do the whole course or just parts of it. That is all up to you. Data management plan, data management Life Science Researchers
Ready For BioData Management?

"Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences.

Scientific topics: Data management

Keywords: Data managment plan

Resource type: course materials

Ready For BioData Management? http://tess.elixir-uk.org/materials/ready-for-biodata-management "Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences. Marta Silva Data management Data managment plan Life Science Researchers PhD students Master students Technicians
OpenRiskNet: Ontology Walkthrough and Workshop

Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.

Scientific topics: Ontology and terminology, Toxicology

Resource type: Tutorial

OpenRiskNet: Ontology Walkthrough and Workshop http://tess.elixir-uk.org/materials/openrisknet-ontology-walkthrough-and-workshop Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology. Ontology and terminology Toxicology Biologists bioinformaticians Chemists
Discussion: Guidelines for submitting data to ExperimentHub

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

Discussion: Guidelines for submitting data to ExperimentHub http://tess.elixir-uk.org/materials/discussion-guidelines-for-submitting-data-to-experimenthub 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.
ELIXIR Webinar: Requirements in data protection law and the upcoming General Data Protection Regulation (GDPR) implementation

Regina Becker (ELIXIR Luxembourg) will give an introduction into the upcoming General Data Protection Legislation (GDPR) that will come into force on 25 May 2018. The new regulation has considerable consequences for managing and storing personal data, imposing more responsibility on the data...

Keywords: GDPR

Resource type: Webinar

ELIXIR Webinar: Requirements in data protection law and the upcoming General Data Protection Regulation (GDPR) implementation http://tess.elixir-uk.org/materials/elixir-webinar-requirements-in-data-protection-law-and-the-upcoming-general-data-protection-regulation-gdpr-implementation Regina Becker (ELIXIR Luxembourg) will give an introduction into the upcoming General Data Protection Legislation (GDPR) that will come into force on 25 May 2018. The new regulation has considerable consequences for managing and storing personal data, imposing more responsibility on the data controllers and data processors. During the webinar, relevant parts of the legislation for research and data sharing will be highlighted. Practical consequences for research institutions and in particular ELIXIR Nodes will be explained, and measures outlined that should be implemented for compliance. In addition, challenges and open questions will be addressed and suggestions made on how to jointly tackle these challenges in ELIXIR. This webinar is of interest for data stewards, Technical Coordinators, and everyone interested in the requirements for processing data for research under the GDPR. GDPR