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Difficulty level: Beginner 

Groovy Cheminformatics with the Chemistry Development Kit

Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language.

Scientific topics: Cheminformatics, Chemistry

Resource type: Book

Groovy Cheminformatics with the Chemistry Development Kit https://tess.elixir-europe.org/materials/groovy-cheminformatics-with-the-chemistry-development-kit Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language. Cheminformatics Chemistry PhD candidates Master students Chemists Biologists
A network biology workflow to study transcriptomics data of the diabetic liver

Description of a network biology workflow for pathway and network analysis methods to study the rewiring of the diabetic liver.

Keywords: Biological networks, Network Visualization

A network biology workflow to study transcriptomics data of the diabetic liver https://tess.elixir-europe.org/materials/a-network-biology-workflow-to-study-transcriptomics-data-of-the-diabetic-liver Description of a network biology workflow for pathway and network analysis methods to study the rewiring of the diabetic liver. Susan Coort Martina Kutmon Chris Evelo Biological networks, Network Visualization
FAIRsharing Educational Material

Whether you are a researcher, standard/database developer, funder, journal editor, librarian or data manager, FAIRsharing can help you understand which standards are mature and appropriate to your use case. By mapping the relationships between standards and the databases that implement them, or...

Keywords: Databases, Standards, Data Policies, FAIR

Resource type: Metadata Registry

FAIRsharing Educational Material https://tess.elixir-europe.org/materials/fairsharing-educational-material Whether you are a researcher, standard/database developer, funder, journal editor, librarian or data manager, FAIRsharing can help you understand which standards are mature and appropriate to your use case. By mapping the relationships between standards and the databases that implement them, or the policies that recommend them, FAIRsharing enables you to make an informed decision as to which standard or database to use or endorse. In this training, educational material, we describe the FAIRsharing resource and explain how you can use it to find the appropriate resource for your work. Databases, Standards, Data Policies, FAIR Researchers data managers data stewards Policy makers database managers biocurators standard developers
Adding schema.org to a GitHub Pages site

This guide will show you how to do add schema.org to GitHub Pages.

Scientific topics: Computer science

Keywords: Mark-up, Bioschemas, Interoperability

Resource type: Training materials

Adding schema.org to a GitHub Pages site https://tess.elixir-europe.org/materials/adding-schema-org-to-a-github-pages-site This guide will show you how to do add schema.org to GitHub Pages. Raniere Silva Computer science Mark-up, Bioschemas, Interoperability web developers System administrators
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 https://tess.elixir-europe.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
Single cell RNA-seq data analysis with Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials, Video

Single cell RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-with-chipster-6cc8f0fb-1c92-444b-ab19-b04fe6454430 This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also learn how to compare two samples and detect conserved cluster markers and differentially expressed genes in them. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq Biologists bioinformaticians
Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R

An overview of Unix and R for bioinformatics

Keywords: Unix, R-programming

Resource type: Training materials

Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R https://tess.elixir-europe.org/materials/summer-school-2018-trainmalta-epigenomics-introduction-to-unix-and-r An overview of Unix and R for bioinformatics Luigi Grassi Unix, R-programming PhD students Life Science Researchers
Programming in the Life Sciences

This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API.

Scientific topics: Pharmacology, Drug discovery

Programming in the Life Sciences https://tess.elixir-europe.org/materials/programming-in-the-life-sciences This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API. Pharmacology Drug discovery bioinformaticians
Data Carpentry in R

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover Data organization in spreadsheets, data...

Keywords: Data analysis, Data carpentry, SoftwareCarpentry

Resource type: course materials

Data Carpentry in R https://tess.elixir-europe.org/materials/data-carpentry-in-r Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover Data organization in spreadsheets, data cleaning with OpenRefine, and learn how to use the statistical program R. If time allows we will also talk about Interacting with databases from R. Participants will be encouraged to help one another and to apply what they have learned to their own research problems Data analysis, Data carpentry, SoftwareCarpentry Anyone
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 https://tess.elixir-europe.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 R

This course provides a short beginners introduction to the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to input, explore, plot and output data in R. Everybody is welcome, if you would like to follow along...

Keywords: R-programming

Resource type: course materials

Introduction to R https://tess.elixir-europe.org/materials/introduction-to-r-327a9c78-9b0c-4133-adfc-180c02c93023 This course provides a short beginners introduction to the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to input, explore, plot and output data in R. 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 https://tess.elixir-europe.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 https://tess.elixir-europe.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
InterMine user tutorial

A tutorial for end users of InterMine

Keywords: Data querying, Data analysis, Data download, FAIR

Resource type: Tutorial

InterMine user tutorial https://tess.elixir-europe.org/materials/intermine-user-tutorial A tutorial for end users of InterMine Data querying, Data analysis, Data download, FAIR Life Science Researchers Bioinformaticians
InterMine user manual

Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine.

Keywords: Data querying, data visualization, Data download, FAIR

Resource type: Documentation

InterMine user manual https://tess.elixir-europe.org/materials/intermine-user-manual Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine. Data querying, data visualization, Data download, FAIR Life Science Researchers Bioinformaticians
#metawinterschool contribution by BiGCaT

Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis.

Scientific topics: Metabolomics

Keywords: Metabolomics, Identifiers

Resource type: Tutorial

#metawinterschool contribution by BiGCaT https://tess.elixir-europe.org/materials/metawinterschool-contribution-by-bigcat Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis. Metabolomics Metabolomics, Identifiers Biologists
BridgeDbR Tutorial

Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites.

Resource type: Tutorial, Vignette

BridgeDbR Tutorial https://tess.elixir-europe.org/materials/bridgedbr-tutorial Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites. Biologists Chemists
Introductory image processing on biological images using python.

A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples.

Resource type: Jupyter notebook, PDF

Introductory image processing on biological images using python. https://tess.elixir-europe.org/materials/introductory-image-processing-on-biological-images-using-python A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples. Anatole Chessel Volker Baecker Bioimage Analysts Image Analysts Computer Vision scientists bioinformaticians computational scientists Biophysicists Biologists Microscopists Python for Biologists PhD students
Browsing the eNanoMapper ontology with BioPortal, AberOWL and Protégé

This tutorial explains how the eNanoMapper ontology can be browsed with three tools, of which two are online.

Keywords: nanotoxicology, Ontologies, BioPortal, AberOWL, Protégé

Resource type: Tutorial

Browsing the eNanoMapper ontology with BioPortal, AberOWL and Protégé https://tess.elixir-europe.org/materials/browsing-the-enanomapper-ontology-with-bioportal-aberowl-and-protege This tutorial explains how the eNanoMapper ontology can be browsed with three tools, of which two are online. nanotoxicology, Ontologies, BioPortal, AberOWL, Protégé PhD students post-docs
Community analysis of amplicon sequencing data (16S rRNA)

This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the...

Resource type: course materials, Video

Community analysis of amplicon sequencing data (16S rRNA) https://tess.elixir-europe.org/materials/community-analysis-of-amplicon-sequencing-data-16s-rrna This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody.
Virus detection using small RNA-seq

This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences....

Scientific topics: RNA-Seq

Resource type: course materials, Video

Virus detection using small RNA-seq https://tess.elixir-europe.org/materials/virus-detection-using-small-rna-seq This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
RNA-seq data analysis

This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises,...

Scientific topics: RNA-Seq

Resource type: course materials, Video

RNA-seq data analysis https://tess.elixir-europe.org/materials/rna-seq-data-analysis-with-chipster This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
Metagenomics data analysis

This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of...

Scientific topics: Metagenomics

Resource type: Video, course materials

Metagenomics data analysis https://tess.elixir-europe.org/materials/metagenomics-data-analysis This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of amplicon sequencing data (16S rRNA). Finally, international databases and standards for storing the data are introduced. The course material includes slides, exercises and lecture videos. The workshop is organized in collaboration with the ELIXIR EXCELERATE project and PRACE, and it is part of the PRACE Advanced Training Centre activity. Eija Korpelainen Metagenomics
STRING exercises

Hands-on exercises using the STRING, STITCH, and DISEASES databases through their respective web interfaces.

Scientific topics: Protein interactions, Molecular interactions, pathways and networks, Bioinformatics

STRING exercises https://tess.elixir-europe.org/materials/string-exercises Hands-on exercises using the STRING, STITCH, and DISEASES databases through their respective web interfaces. Protein interactions Molecular interactions, pathways and networks Bioinformatics Bioinformaticians Biologists
Train the trainer

Train the Trainer course materials

Scientific topics: Bioinformatics, Computational biology

Keywords: training, pedagogy

Train the trainer https://tess.elixir-europe.org/materials/train-the-trainer Train the Trainer course materials Emily Angiolini Jamie Edwards Paul Yorke Bioinformatics Computational biology training, pedagogy Trainers
Bioinformatics and Virtual Machines

We introduce the concept of the virtual machine, what they can be used for and the advantages and disadvantages of using them.

Keywords: VM, IFR, Institute of Food Research, Quadram Institute, Bioinformatics

Bioinformatics and Virtual Machines https://tess.elixir-europe.org/materials/bioinformatics-and-virtual-machines We introduce the concept of the virtual machine, what they can be used for and the advantages and disadvantages of using them. VM, IFR, Institute of Food Research, Quadram Institute, Bioinformatics
IFR Dockerised version of the EBI's Introduction to RNA-seq course

This is basically the EBI RNA-seq course bundled up in a Docker container using LXDE via TightVNC to provide a graphical environment. The material has been repackaged to use an Ipython Notebook as the learning environment which can be annotated by the learner.

Keywords: RNA-Seq, IFR, Institute of Food Research, Quadram Institute

IFR Dockerised version of the EBI's Introduction to RNA-seq course https://tess.elixir-europe.org/materials/ifr-dockerised-version-of-the-ebi-s-introduction-to-rna-seq-course This is basically the EBI RNA-seq course bundled up in a Docker container using LXDE via TightVNC to provide a graphical environment. The material has been repackaged to use an Ipython Notebook as the learning environment which can be annotated by the learner. RNA-Seq, IFR, Institute of Food Research, Quadram Institute
Docker version of Welsh Gene Park NGS course

Docker version of Welsh Gene Park NGS course

Keywords: NGS, IFR, Institute of Food Research, Quadram Institute

Docker version of Welsh Gene Park NGS course https://tess.elixir-europe.org/materials/docker-version-of-welsh-gene-park-ngs-course Docker version of Welsh Gene Park NGS course NGS, IFR, Institute of Food Research, Quadram Institute
IFR Dockerised version of the Welsh Genepark's Introduction to Command-line NGS Analysis

The IFR Dockerised version of the Welsh Genepark's Introduction to Command-line NGS Analysis course

Keywords: NGS, Command line, IFR, Institute of Food Research, Quadram Institute

IFR Dockerised version of the Welsh Genepark's Introduction to Command-line NGS Analysis https://tess.elixir-europe.org/materials/ifr-dockerised-version-of-the-welsh-genepark-s-introduction-to-command-line-ngs-analysis The IFR Dockerised version of the Welsh Genepark's Introduction to Command-line NGS Analysis course NGS, Command line, IFR, Institute of Food Research, Quadram Institute
PhenoMeNal: accessing metabolomics workflows in Galaxy

A description of PhenoMeNal and when to use it, the creation of a cloud research environment and how to access Galaxy workflows via PhenoMeNal.

Scientific topics: Chemical biology, Metabolomics

Keywords: Galaxy

PhenoMeNal: accessing metabolomics workflows in Galaxy https://tess.elixir-europe.org/materials/phenomenal-accessing-metabolomics-workflows-in-galaxy A description of PhenoMeNal and when to use it, the creation of a cloud research environment and how to access Galaxy workflows via PhenoMeNal. Chemical biology Metabolomics Galaxy Beginners