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
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
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
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
InterMine operator manual
Documentation on how to install, configure and operate an InterMine instance.
Keywords: Data integration, Data analysis, Data publishing, FAIR
Resource type: Documentation
InterMine operator manual
http://intermine.readthedocs.io/en/latest
https://tess.elixir-europe.org/materials/intermine-operator-manual
Documentation on how to install, configure and operate an InterMine instance.
Julie Sullivan
Gos Micklem
Yo Yehudi
Sergio Contrino
Rachel Lyne
Daniela Butano
Justin Clark-Casey
Data integration, Data analysis, Data publishing, FAIR
Bioinformaticians
software engineers
MouseMine at MGI
MouseMine at MGI - M. musculus InterMine intro
MouseMine at MGI
https://www.youtube.com/watch?v=FtlsoM8TGGs&t=139s
https://tess.elixir-europe.org/materials/mousemine-at-mgi
MouseMine at MGI - M. musculus InterMine intro
MouseMine
YeastMine videos
YeastMine videos - SGD has quite a broad range of tutorials based on S. Cerevisiae data.
YeastMine videos
https://www.youtube.com/watch?v=fnWv6qRl_DA&list=PL0VHJdmmIuj-b00aNRfqwMe9TvkfWWcyZ
https://tess.elixir-europe.org/materials/yeastmine-videos
YeastMine videos - SGD has quite a broad range of tutorials based on S. Cerevisiae data.
YeastMine
Thalemine tutorials
Thalemine tutorials - A. thaliana-based tutorials.
Thalemine tutorials
https://www.araport.org/tutorials
https://tess.elixir-europe.org/materials/thalemine-tutorials
Thalemine tutorials - A. thaliana-based tutorials.
Thalemine
TargetMine tutorials Tutorials for an InterMine designed to help identify drug targets.
TargetMine tutorials Tutorials for an InterMine designed to help identify drug targets.
TargetMine tutorials Tutorials for an InterMine designed to help identify drug targets.
http://targetmine.mizuguchilab.org/tutorials
https://tess.elixir-europe.org/materials/targetmine-tutorials-tutorials-for-an-intermine-designed-to-help-identify-drug-targets
TargetMine tutorials Tutorials for an InterMine designed to help identify drug targets.
TargetMine
FlyMine intro videos
FlyMine intro videos - for the Drosophila-minded among us.
FlyMine intro videos
http://intermine.readthedocs.io/en/latest/help/
https://tess.elixir-europe.org/materials/flymine-intro-videos
FlyMine intro videos - for the Drosophila-minded among us.
FlyMine
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
Accessing Expert‐Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY
The IUPHAR/BPS Guide to PHARMACOLOGY is an expert‐curated, open‐access database of information on drug targets and the substances that act on them. This unit describes the procedures for searching and downloading ligand‐target binding data and for finding detailed annotations and the most...
Scientific topics: Immunology, Pharmacology
Resource type: PDF
Accessing Expert‐Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY
https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpbi.46
https://tess.elixir-europe.org/materials/accessing-expert-curated-pharmacological-data-in-the-iuphar-bps-guide-to-pharmacology
The IUPHAR/BPS Guide to PHARMACOLOGY is an expert‐curated, open‐access database of information on drug targets and the substances that act on them. This unit describes the procedures for searching and downloading ligand‐target binding data and for finding detailed annotations and the most relevant literature. The database includes concise overviews of the properties of 1,700 data‐supported human drug targets and related proteins, divided into families, and 9,000 small molecule and peptide experimental ligands and approved drugs that bind to those targets. More detailed descriptions of pharmacology, function, and pathophysiology are provided for a subset of important targets. The information is reviewed regularly by expert subcommittees of the IUPHAR Committee on Receptor Nomenclature and Drug Classification. A new immunopharmacology portal has recently been added, drawing together data on immunological targets, ligands, cell types, processes and diseases. The data are available for download and can be accessed computationally via Web services. © 2018 by John Wiley & Sons, Inc.
Joanna L. Sharman
Simon D. Harding
Christopher Southan
Elena Faccenda
Adam J. Pawson
Jamie A. Davies
Immunology
Pharmacology
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
LXDE RStudio with support for bioconductor tools
An LXDE Rstudio with pre-loaded Bioconductor tools for rna-seq DE analysis & visualisation
Keywords: RNA-Seq, IFR, Institute of Food Research, Quadram Institute
LXDE RStudio with support for bioconductor tools
https://hub.docker.com/r/foodresearch/ifr_rstudio_bioc/
https://tess.elixir-europe.org/materials/lxde-rstudio-with-support-for-bioconductor-tools
An LXDE Rstudio with pre-loaded Bioconductor tools for rna-seq DE analysis & visualisation
Mark Fernandes
RNA-Seq, IFR, Institute of Food Research, Quadram Institute
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
Phylogenetics & Phylogeography (Advanced Analytical Methods)
Phylogenetics and Phylogeography(Advanced Analytical Methods)
Lecture by Dr Sam Lycett, filmed at The Roslin Institute, March 2015.
Keywords: Phylogenetics, Roslin Institute
Phylogenetics & Phylogeography (Advanced Analytical Methods)
https://www.youtube.com/playlist?list=PLbyRmcun-givl8ofEKQjrPn6cBKU6HiPu
https://tess.elixir-europe.org/materials/phylogenetics-phylogeography-advanced-analytical-methods
Phylogenetics and Phylogeography(Advanced Analytical Methods)
Lecture by Dr Sam Lycett, filmed at The Roslin Institute, March 2015.
Sam Lycett
Phylogenetics, Roslin Institute
Molecular epidemiology practical
Practical session with Dr. Emily Richardson, filmed at The Roslin Institute, March 2015.
Keywords: Molecular epidemiology, Roslin Institute
Molecular epidemiology practical
https://www.youtube.com/playlist?list=PLbyRmcun-git-cAT-fSotFeP2Qg53SS_u
https://tess.elixir-europe.org/materials/molecular-epidemiology-practical
Practical session with Dr. Emily Richardson, filmed at The Roslin Institute, March 2015.
Emily Richardson
Molecular epidemiology, Roslin Institute
Phylogenetic analysis of pathogens: Staphylococcus aureus, host switching and antibiotic resistance
Lecture by professor Ross Fitzgerald, filmed at The Roslin Institute, March 2015.
Keywords: Phylogenetic analysis, Roslin Institute
Phylogenetic analysis of pathogens: Staphylococcus aureus, host switching and antibiotic resistance
https://www.youtube.com/playlist?list=PLbyRmcun-giuxxB-h2-7u5j5s0sC7tlSd
https://tess.elixir-europe.org/materials/phylogenetic-analysis-of-pathogens-staphylococcus-aureus-host-switching-and-antibiotic-resistance
Lecture by professor Ross Fitzgerald, filmed at The Roslin Institute, March 2015.
Ross Fitzgerald
Phylogenetic analysis, Roslin Institute
Graphical & Computational Modelling of Biological Pathways
Lecture by professor Tom Freeman.
Filmed at The Roslin Institute, The University of Edinburgh, March 2015
Keywords: Graphical modelling, Roslin Institute
Graphical & Computational Modelling of Biological Pathways
https://www.youtube.com/playlist?list=PLbyRmcun-giukxMjd7H9BcUZz6SPZ2XCH
https://tess.elixir-europe.org/materials/graphical-computational-modelling-of-biological-pathways-d0b38ce1-0e2e-4ba9-9e0c-39c6af558782
Lecture by professor Tom Freeman.
Filmed at The Roslin Institute, The University of Edinburgh, March 2015
Tom Freeman
Graphical modelling, Roslin Institute
An Introduction to BioLayout Express3D
Lecture by professor Tom Freeman.
Filmed during a half-day training course held at The Roslin Institute, January 2015, aimed at training biologists with little or no experience of gene expression analysis the basics. Features 15 short films covering the background to data generation through to...
Keywords: Gene expression analysis, Roslin Institute
An Introduction to BioLayout Express3D
https://www.youtube.com/playlist?list=PLbyRmcun-givYQ9_dul96W98tC3y6_2st
https://tess.elixir-europe.org/materials/an-introduction-to-biolayout-express3d
Lecture by professor Tom Freeman.
Filmed during a half-day training course held at The Roslin Institute, January 2015, aimed at training biologists with little or no experience of gene expression analysis the basics. Features 15 short films covering the background to data generation through to deriving meaning using network analysis.
- Course aims: the basics of expression data analysis introduction to graph-based analysis introduction to BioLayout Express3D data import navigation of graphs clustering graph analysis data export
Tom Freeman
Gene expression analysis, Roslin Institute
Phylogenetics & Phylogeography Practical (Advanced Analytical Methods)
Practical session with Dr Sam Lycett, filmed at The Roslin Institute, March 2015.
Keywords: Phylogenetics, Phylogeography, Roslin Institute
Phylogenetics & Phylogeography Practical (Advanced Analytical Methods)
https://www.youtube.com/playlist?list=PLbyRmcun-giv7ntsR0wu17DQi_01jDsSs
https://tess.elixir-europe.org/materials/phylogenetics-phylogeography-practical-advanced-analytical-methods
Practical session with Dr Sam Lycett, filmed at The Roslin Institute, March 2015.
Sam Lycett
Phylogenetics, Phylogeography, Roslin Institute
Graphical & Computational Modelling of Biological Pathways
Lecture by professor Tom Freeman.
Filmed at The Roslin Institute, The University of Edinburgh, March 2015
Keywords: Graphical modelling, Computational modelling, Roslin Institute
Graphical & Computational Modelling of Biological Pathways
https://www.youtube.com/playlist?list=PLbyRmcun-giukxMjd7H9BcUZz6SPZ2XCH
https://tess.elixir-europe.org/materials/graphical-computational-modelling-of-biological-pathways
Lecture by professor Tom Freeman.
Filmed at The Roslin Institute, The University of Edinburgh, March 2015
Tom Freeman
Graphical modelling, Computational modelling, Roslin Institute
SAS Introduction
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, April 2015.
These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.
Keywords: SAS, Roslin Institute
SAS Introduction
https://www.youtube.com/playlist?list=PLbyRmcun-giszUmMQLCMIZoHCV1fuCdph
https://tess.elixir-europe.org/materials/sas-introduction
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, April 2015.
These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.
Helen Brown
SAS, Roslin Institute
A Brief Introduction to R
A short training session with Dr. Ian Handel at The Roslin Institute, April 2015
Keywords: R language, Roslin Institute
A Brief Introduction to R
https://www.youtube.com/playlist?list=PLbyRmcun-giskWiTTqWxXnZ27K-W3_PqH
https://tess.elixir-europe.org/materials/a-brief-introduction-to-r
A short training session with Dr. Ian Handel at The Roslin Institute, April 2015
Ian Handel
R language, Roslin Institute
Summarising Data
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, December 2015.
These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.
Keywords: Summarising data, Roslin Institute
Summarising Data
https://www.youtube.com/playlist?list=PLbyRmcun-gittCJyqswN_8gSPc9XkVLge
https://tess.elixir-europe.org/materials/summarising-data
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, December 2015.
These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.
Helen Brown
Summarising data, Roslin Institute