66 materials found
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://egonw.github.io/cdkbook/
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.
Egon Willighagen
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://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-971
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://www.fairsharing.org/educational
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.
Peter McQuilton
Susanna-Assunta Sansone
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://bioschemas.gitbook.io/training-portal/how-to/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.
Niall Beard
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://elixir.mf.uni-lj.si/course/view.php?id=42
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
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://chipster.csc.fi/manual/courses.html#single-cell
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
Maria Lehtivaara
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://github.com/semacu/20180726_TrainMalta_Unix_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
Sergio Martínez Cuesta
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://egonw.github.io/pils/
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.
Egon Willighagen
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://tavareshugo.github.io/2018-06-28-cambridge/
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
Sandra Cortijo
Hugo Tavares
Sergio Martínez Cuesta
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://github.com/semacu/20180531_DataVisualisationRggplot2_Wolfson_Cambridge/
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.
Sergio Martínez Cuesta
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://github.com/semacu/20180315_IntroductionToR_Wolfson_Cambridge/blob/master/README.Rmd
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.
Sergio Martínez Cuesta
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://github.com/semacu/20171024_GitHub_Chemistry_Cambridge/blob/master/README.md
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
Sergio Martínez Cuesta
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://github.com/semacu/20180223_ORCID_Chemistry_Cambridge/blob/master/README.md
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
Sergio Martínez Cuesta
Clair Castle
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://figshare.com/articles/InterMine_training_slides/4737313
https://tess.elixir-europe.org/materials/intermine-user-tutorial
A tutorial for end users of InterMine
Rachel Lyne
Yo Yehudi
Julie Sullivan
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
http://flymine.readthedocs.io/en/latest
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.
Rachel Lyne
Julie Sullivan
Gos Micklem
Sergio Contrino
Yo Yehudi
Daniela Butano
Justin Clark-Casey
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://egonw.github.io/metawinterschool-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.
Egon Willighagen
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://bioconductor.org/packages/release/bioc/vignettes/BridgeDbR/inst/doc/tutorial.html
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.
Egon Willighagen
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://github.com/dwaithe/model-training/
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.
Dominic Waithe
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://enanomapper.github.io/tutorials/BrowseOntology/Tutorial%20browsing%20eNM%20ontology.html
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.
Egon Willighagen
Friederike Ehrhart
Linda Rieswijk
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://chipster.csc.fi/manual/courses.html#16S
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.
Eija Korpelainen
Maria Lehtivaara
Jarno Tuimala
Anu Mikkonen
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://chipster.csc.fi/manual/courses.html#virusdetect
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
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://chipster.csc.fi/manual/courses.html#rna
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
Maria Lehtivaara
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://www.csc.fi/web/training/-/metagenomics
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
Nils Peder Willassen
Espen Mikal Robertsen
Erik Hjerde
Rob Finn
Anu Mikkonen
Jenni Hultman
Petri Auvinen
Kimmo Mattila
Maria Lehtivaara
Jarno Tuimala
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
http://jensenlab.org/training/string/
https://tess.elixir-europe.org/materials/string-exercises
Hands-on exercises using the STRING, STITCH, and DISEASES databases through their respective web interfaces.
Lars Juhl Jensen
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
http://mygoblet.org/training-portal/materials/train-trainer-course-materials
https://tess.elixir-europe.org/materials/train-the-trainer
Train the Trainer course materials
Chris Taylor
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
http://moodle.ifr.ac.uk/moodle/course/view.php?id=5
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.
Mark Fernandes
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://hub.docker.com/r/foodresearch/ifr_rnaseq_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.
Mark Fernandes
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://hub.docker.com/r/foodresearch/ngs_intro/
https://tess.elixir-europe.org/materials/docker-version-of-welsh-gene-park-ngs-course
Docker version of Welsh Gene Park NGS course
Mark Fernandes
Welsh Gene Park
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://hub.docker.com/r/foodresearch/bppc/
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
Mark Fernandes
Welsh Gene Park
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://www.ebi.ac.uk/training/online/course/phenomenal-accessing-metabolomics-workflows-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.
Namrata Kale
Sijin He
Pablo Moreno
Chemical biology
Metabolomics
Galaxy
Beginners