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Machine Learning & BioStatistics Hackathon 2020

Materials created at the Machine Learning and BioStatistics hackathon organised by ELIXIR-GR (CERTH) in October and November 2020.

Scientific topics: Computer science, Statistics and probability, Machine learning

Keywords: machine learning, biostatistics, eLearning, EeLP

Resource type: Training materials

Machine Learning & BioStatistics Hackathon 2020 http://tess.elixir-uk.org/materials/machine-learning-biostatistics-hackathon-2020 Materials created at the Machine Learning and BioStatistics hackathon organised by ELIXIR-GR (CERTH) in October and November 2020. Computer science Statistics and probability Machine learning machine learning, biostatistics, eLearning, EeLP Life Science Researchers statisticians Training Designers Training instructors Trainers
HPC Hackathon Materials

Materials developed at the HPC hackathon hosted by ELIXIR-SI (UL) in May and June 2021.

Scientific topics: Computer science

Keywords: HPC, high-performance computing, eLearning, EeLP

Resource type: Training materials

HPC Hackathon Materials http://tess.elixir-uk.org/materials/hpc-hackathon-materials Materials developed at the HPC hackathon hosted by ELIXIR-SI (UL) in May and June 2021. Computer science HPC, high-performance computing, eLearning, EeLP Life Science Researchers Training Designers Training instructors Trainers
Containers and Workflows training materials hackathon

Materials developed at the Containers and Workflows hackathon organised by ELIXIR-BE (VIB) in February and April 2021.

Scientific topics: Computer science

Keywords: Containers, Workflows, eLearning, EeLP

Resource type: Training materials

Containers and Workflows training materials hackathon http://tess.elixir-uk.org/materials/containers-and-workflows-training-materials-hackathon Materials developed at the Containers and Workflows hackathon organised by ELIXIR-BE (VIB) in February and April 2021. Computer science Containers, Workflows, eLearning, EeLP Life Science Researchers Training Designers Training instructors Trainers
DSW Workshop for Finnish Data Support Personnel

Presentation from DSW Workshop to explain what is the purpose of smart data management plans as living documents, core ideas behind [Data Stewardship Wizard](https://ds-wizard.org), and how to use it in practice. It also briefly explains the versability of DSW, possibilities of integrations with...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

DSW Workshop for Finnish Data Support Personnel http://tess.elixir-uk.org/materials/dsw-workshop-for-finnish-data-support-personnel Presentation from DSW Workshop to explain what is the purpose of smart data management plans as living documents, core ideas behind [Data Stewardship Wizard](https://ds-wizard.org), and how to use it in practice. It also briefly explains the versability of DSW, possibilities of integrations with other systems in institutions, and other customizations. Data management DMP, DMP tools, data stewardship, FAIR, FAIR data Researchers data stewards
Helis Academy course FAIR data stewardship 2021, Day 6, Metadata

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: FAIR, Data management planning, Metadata

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 6, Metadata http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-6-metadata This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021 Data management FAIR data FAIR, Data management planning, Metadata PhD candidates
DSW Template Development Kit: The Tutorial

[Data Stewardship Wizard](ds-wizard.org) is a flexible questionnaire-based tool that uses Jinja2 templates to produce documents. It allows creating documents in practically any textual format. Such documents can be intended for both humans (HTML, Markdown, reStructuredText, etc.) and machines...

Scientific topics: Data management

Keywords: data stewardship, data management plan, FAIR, data management, software tools, DMP templates, template development

Resource type: Video, Slides, Webinar

DSW Template Development Kit: The Tutorial http://tess.elixir-uk.org/materials/dsw-template-development-kit-the-tutorial [Data Stewardship Wizard](ds-wizard.org) is a flexible questionnaire-based tool that uses Jinja2 templates to produce documents. It allows creating documents in practically any textual format. Such documents can be intended for both humans (HTML, Markdown, reStructuredText, etc.) and machines (e.g. RDF, YAML, or JSON). Our Template Development Kit (DSW TDK) is a command-line tool to make the work on templates efficient. Data management data stewardship, data management plan, FAIR, data management, software tools, DMP templates, template development data stewards data managers
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) http://tess.elixir-uk.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
runBioSimulations tutorial and help

runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA),...

Scientific topics: Simulation experiment, Computational biology, Systems biology

Operations: Modelling and simulation

Keywords: biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL

Resource type: Tutorial, Documentation

runBioSimulations tutorial and help http://tess.elixir-uk.org/materials/runbiosimulations-tutorial-and-help runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BNGL, SBML). runBioSimulations also provides a REST API for programmatic access to the same simulation capabilities. The runBioSimulations tutorial and help describes how to use this web application and web service to execute simulations and visualize their results. This includes instructions on how to create COMBINE/OMEX archives of modeling projects. Ion Moraru Bilal Shaikh Gnaneswara Marupilla Simulation experiment Computational biology Systems biology biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL modelers
BioSimulators tutorial and help

BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms,...

Scientific topics: Simulation experiment, Computational biology, Systems biology

Operations: Modelling and simulation

Keywords: Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL

Resource type: Tutorial, Documentation

BioSimulators tutorial and help http://tess.elixir-uk.org/materials/biosimulators-help BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects. The BioSimulators help describes how to use this registry: - How to find a containerized simulation tools that are capable of executing a modeling study. - How to use containerized simulation tools to execute modeling studies. - How to containerize a simulation tool and submit it to the BioSimulators registry. Ion Moraru Bilal Shaikh Simulation experiment Computational biology Systems biology Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL modelers Computational biologists software developers, bioinformaticians
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
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
An introduction to the role of experimental data in Intellectual Property

data ownership the role of experimental data in acquiring a patent the role of data in establishing a prior use right trade secrets

Keywords: patents

Resource type: PDF

An introduction to the role of experimental data in Intellectual Property http://tess.elixir-uk.org/materials/an-introduction-to-the-role-of-experimental-data-in-intellectual-property data ownership the role of experimental data in acquiring a patent the role of data in establishing a prior use right trade secrets patents
How to install and deploy Beacon

**This is an OPEN-ACCESS online tutorial where you can learn how to install and deploy Beacon.**

Scientific topics: Genomics

Keywords: genomics, open access, eLearning, EeLP

Resource type: Video, Manual, Slides, Installation instructions

How to install and deploy Beacon http://tess.elixir-uk.org/materials/how-to-install-and-deploy-beacon **This is an OPEN-ACCESS online tutorial where you can learn how to install and deploy Beacon.** Juha Tornroos Sabela de la Torre Jordi Rambla Genomics genomics, open access, eLearning, EeLP life scientists Researchers
Galaxy Proteomics workshop Prague 2018

Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic

Scientific topics: Proteomics

Keywords: Galaxy, training, proteomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Galaxy Proteomics workshop Prague 2018 http://tess.elixir-uk.org/materials/galaxy-proteomics-workshop-prague-2018 Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic Andrea Argentini Frederik Coppens Pavel Dvorak Matthias Fahrner Melanie Foell Björn Grüning Martin Hubalek Hana Pergl Sustkova Marek Vrbacky Proteomics Galaxy, training, proteomics, eLearning, EeLP life scientists Researchers PhD Students
How to get the most out of your microarray experiment. A Webinar

Materials from the ELIXIR webinar "How to get the most out of your microarray experiment", Feb 14, 2017

Scientific topics: Microarray experiment

Keywords: life sciences, microarrays, eLearning, EeLP

Resource type: course materials, Training materials, Slides

How to get the most out of your microarray experiment. A Webinar http://tess.elixir-uk.org/materials/how-to-get-the-most-out-of-your-microarray-experiment-a-webinar Materials from the ELIXIR webinar "How to get the most out of your microarray experiment", Feb 14, 2017 Eva Freyhult Jessica Lindvall Mihaela Martis Microarray experiment life sciences, microarrays, eLearning, EeLP Researchers
ELIXIR eLearning definitions

Materials from the asynchronous learning course "ELIXIR eLearning definitions"

Keywords: eLearning, training, EeLP

Resource type: course materials, Training materials, Documentation

ELIXIR eLearning definitions http://tess.elixir-uk.org/materials/elixir-elearning-definitions Materials from the asynchronous learning course "ELIXIR eLearning definitions" Brane Leskosek Jure Dimec Eija Korpelainen Teresa Attwood Sarah Morgan Nicola Mulder Celia van Gelder Patricia Palagi eLearning, training, EeLP Researchers teachers Trainers
RNA-seq data analysis using Chipster

Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017

Scientific topics: Transcriptomics, Genomics

Keywords: transcriptomics, RNA-Seq, eLearning, EeLP

Resource type: course materials, Training materials, Slides, Video

RNA-seq data analysis using Chipster http://tess.elixir-uk.org/materials/rna-seq-data-analysis-using-chipster Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017 Eija Korpelainen Maria Lehtivaara Transcriptomics Genomics transcriptomics, RNA-Seq, eLearning, EeLP Researchers
ELIXIR TtR course: Basic genomics using advanced analysis tools

Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia

Scientific topics: Genomics

Keywords: Galaxy, training, Genomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

ELIXIR TtR course: Basic genomics using advanced analysis tools http://tess.elixir-uk.org/materials/elixir-ttr-course-basic-genomics-using-advanced-analysis-tools Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia Christophe Antoniewski Olivier Inizan Genomics Galaxy, training, Genomics, eLearning, EeLP life scientists beginner bioinformaticians Postgraduate students
Hands-on workshop in Marine Metagenomics

Materials from the ELIXIR workshop “Hands-on workshop in Marine Metagenomics”, Nov 26-30 2018 at the Arctic University of Norway, Tromso, Norway

Scientific topics: Marine biology, Metagenomics, Genomics

Keywords: Marine Metagenomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Hands-on workshop in Marine Metagenomics http://tess.elixir-uk.org/materials/hands-on-workshop-in-marine-metagenomics Materials from the ELIXIR workshop “Hands-on workshop in Marine Metagenomics”, Nov 26-30 2018 at the Arctic University of Norway, Tromso, Norway Erik Hjerde Nils Peder Willassen Espen Aberg Espen Mikal Robertsen Marine biology Metagenomics Genomics Marine Metagenomics, eLearning, EeLP Researchers Master students PhD students
Implementation of Data Management Plans & Data Stewardship in practice

Materials from the ELIXIR workshop “Implementation of Data Management Plans & Data Stewardship in practice”, Sept 11, 2018 at ECCB2018, Athens, Greece.

Scientific topics: Data submission, annotation, and curation, Data management

Keywords: data management, data stewardship, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Implementation of Data Management Plans & Data Stewardship in practice http://tess.elixir-uk.org/materials/implementation-of-data-management-plans-data-stewardship-in-practice Materials from the ELIXIR workshop “Implementation of Data Management Plans & Data Stewardship in practice”, Sept 11, 2018 at ECCB2018, Athens, Greece. Celia van Gelder Roland Krause Mateusz Kuzak Brane Leskosek Marko Vidak Robert Pergl Marek Suchanek Jan Slifka Vojtech Knaisl Data submission, annotation, and curation Data management data management, data stewardship, eLearning, EeLP bioinformaticians data stewards
Data visualisation with R and ggplot2

This course provides a short beginners introduction to data visualisation using the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to import data, perform different types of plots and export graphics using R...

Keywords: R-programming

Resource type: course materials

Data visualisation with R and ggplot2 http://tess.elixir-uk.org/materials/data-visualisation-with-r-and-ggplot2 This course provides a short beginners introduction to data visualisation using the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to import data, perform different types of plots and export graphics using R standard functions and the library ggplot2. Everybody is welcome; if you would like to follow along with your laptop, please bring R and RStudio downloaded and installed before the session. R-programming PhD students Researchers
Introduction to GitHub for chemists

Are you interested in learning Git and GitHub to manage your code, manuscripts or research data? This introductory workshop will be covering the following: - Background and motivation - What is Git? What is version control? What is GitHub? - How can Git and GitHub be useful for you? -...

Keywords: Git, GitHub

Resource type: course materials

Introduction to GitHub for chemists http://tess.elixir-uk.org/materials/introduction-to-github-for-chemists Are you interested in learning Git and GitHub to manage your code, manuscripts or research data? This introductory workshop will be covering the following: - Background and motivation - What is Git? What is version control? What is GitHub? - How can Git and GitHub be useful for you? - Practical session: working with Git and GitHub Clair Castle Git, GitHub Researchers PhD students Staff
Make your academic life easy with ORCID: an introduction

Many funders and publishers now require you to get an Open Researcher and Contributor ID (ORCID): an identifier that is unique to you and which comes with you wherever you go. It eliminates ambiguity about your name so you can get full credit for your work. Do you have an ORCID id? Are you sure...

Keywords: ORCID

Resource type: Tutorial

Make your academic life easy with ORCID: an introduction http://tess.elixir-uk.org/materials/make-your-academic-life-easy-with-orcid-an-introduction Many funders and publishers now require you to get an Open Researcher and Contributor ID (ORCID): an identifier that is unique to you and which comes with you wherever you go. It eliminates ambiguity about your name so you can get full credit for your work. Do you have an ORCID id? Are you sure how best to use it? Bring your own device to this practical session and register for an ORCID id, explore its features and find out more ORCID Researchers PhD students Staff