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
Basic Statistical Tests
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: Statistical tests, Roslin Institute
Basic Statistical Tests
https://www.youtube.com/playlist?list=PLbyRmcun-giu-881XGH-F5baTmqiKrv-z
https://tess.elixir-europe.org/materials/basic-statistical-tests
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
Statistical tests, Roslin Institute
Introduction to Experimental Design
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, January 2016.
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: Experimental design, Roslin Institute
Introduction to Experimental Design
https://www.youtube.com/playlist?list=PLbyRmcun-gis3nonV8IeVFRYjlpvpCufm
https://tess.elixir-europe.org/materials/introduction-to-experimental-design
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, January 2016.
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
Experimental design, Roslin Institute
Introduction to Sample Size Calculation
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, January 2016.
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.
A spreadsheet...
Keywords: Sample size, Roslin Institute
Introduction to Sample Size Calculation
https://www.youtube.com/playlist?list=PLbyRmcun-givegZIS4FAA6ZHDuMYnUNJl
https://tess.elixir-europe.org/materials/introduction-to-sample-size-calculation
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, January 2016.
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.
A spreadsheet to carry out the calculations described in the presentation may be copied here: http://datashare.is.ed.ac.uk/handle/10283/1996
Helen Brown
Sample size, Roslin Institute
Introduction to Statistical Modelling
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: Statistical modelling, Roslin Institute
Introduction to Statistical Modelling
https://www.youtube.com/playlist?list=PLbyRmcun-givlS2DuKFcgWA3kcweQALuj
https://tess.elixir-europe.org/materials/introduction-to-statistical-modelling
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
Statistical modelling, Roslin Institute
Introduction to Mixed Models
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016.
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: Mixed models, Roslin Institute
Introduction to Mixed Models
https://www.youtube.com/playlist?list=PLbyRmcun-giuz5hW11nD64zeiJZSDV4aD
https://tess.elixir-europe.org/materials/introduction-to-mixed-models
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016.
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
Mixed models, Roslin Institute
Introduction to Analysing Repeated Measures Data
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016.
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: Data analysis, Repeated measures, Roslin Institute
Introduction to Analysing Repeated Measures Data
https://www.youtube.com/playlist?list=PLbyRmcun-gitPRwGoNRC4exkkQyR-8qjj
https://tess.elixir-europe.org/materials/introduction-to-analysing-repeated-measures-data
Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016.
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
Data analysis, Repeated measures, Roslin Institute
Quality Control in Sequencing Experiments
This course looks at the different ways in which sequencing based studies can fail and the options for visualisation and QC which allow you to identify and diagnose these failures at an early stage. It is designed to be of use to anyone who is using sequencing as part of their research, not just...
Scientific topics: Quality affairs
Keywords: Babraham Institute
Quality Control in Sequencing Experiments
http://www.bioinformatics.babraham.ac.uk/training.html#sequenceqc
https://tess.elixir-europe.org/materials/quality-control-in-sequencing-experiments
This course looks at the different ways in which sequencing based studies can fail and the options for visualisation and QC which allow you to identify and diagnose these failures at an early stage. It is designed to be of use to anyone who is using sequencing as part of their research, not just those who are running sequencing facilities.
Simon Andrews
Laura Biggins
Boo Virk
Quality affairs
Babraham Institute
Extracting biological information from gene lists
Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting...
Keywords: Functional analysis, Gene lists, Babraham Institute
Extracting biological information from gene lists
http://www.bioinformatics.babraham.ac.uk/training.html#fagl
https://tess.elixir-europe.org/materials/extracting-biological-information-from-gene-lists
Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists.
This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication.
Simon Andrews
Laura Biggins
Functional analysis, Gene lists, Babraham Institute
Sample size estimation
Power analysis is a method to estimate the samples sizes needed to detect statistical effects with high probability. This course provides an introduction to the basic principles of power analysis and goes through the variables for power calculation. It also addresses the issues associated with...
Keywords: Power analysis, Sample size, Babraham Institute
Sample size estimation
http://www.bioinformatics.babraham.ac.uk/training.html#power
https://tess.elixir-europe.org/materials/sample-size-estimation
Power analysis is a method to estimate the samples sizes needed to detect statistical effects with high probability. This course provides an introduction to the basic principles of power analysis and goes through the variables for power calculation. It also addresses the issues associated with technical and biological replicates. The program is intended for people who have no prior knowledge of power. Basic statistical knowledge is extremely useful but prior attendance on a statistics course is not compulsary.
Anne Segonds-Pichon
Power analysis, Sample size, Babraham Institute
Statistical Analysis using SPSS
Statistics are an important part of most modern studies and being able to effectively use a statistics package can help you to understand your results. This course provides an introduction to statistics illustrated though the use of the friendly SPSS package.
Scientific topics: Statistics and probability
Keywords: Babraham Institute
Statistical Analysis using SPSS
http://www.bioinformatics.babraham.ac.uk/training.html#spss
https://tess.elixir-europe.org/materials/statistical-analysis-using-spss
Statistics are an important part of most modern studies and being able to effectively use a statistics package can help you to understand your results. This course provides an introduction to statistics illustrated though the use of the friendly SPSS package.
Anne Segonds-Pichon
Statistics and probability
Babraham Institute
Statistical Analysis using GraphPad Prism
GraphPad Prism is a powerful and friendly package which allows you to plot and analyse your data. This course acts not only as an introduction to Prism, but also goes through the basic statistical knowledge which should allow you to make the most of your data.
Keywords: GraphPad Prism, Babraham Institute
Statistical Analysis using GraphPad Prism
http://www.bioinformatics.babraham.ac.uk/training.html#prism
https://tess.elixir-europe.org/materials/statistical-analysis-using-graphpad-prism
GraphPad Prism is a powerful and friendly package which allows you to plot and analyse your data. This course acts not only as an introduction to Prism, but also goes through the basic statistical knowledge which should allow you to make the most of your data.
Anne Segonds-Pichon
GraphPad Prism, Babraham Institute
Scientific Figure Design
This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and...
Scientific topics: Data visualisation
Keywords: Figure design, Babraham Institute
Scientific Figure Design
http://www.bioinformatics.babraham.ac.uk/training.html#figuredesign
https://tess.elixir-europe.org/materials/scientific-figure-design
This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures.
The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools.
Simon Andrews
Anne Segonds-Pichon
Boo Virk
Data visualisation
Figure design, Babraham Institute
An Introduction to Unix
Increasing amounts of bioinformatics work is done in a command line unix environment. Most large scale processing applications are written for unix and most large scale compute environments are also based on this.
This course provides an introduction to the concepts of unix and provides a...
Keywords: Unix, Babraham Institute
An Introduction to Unix
http://www.bioinformatics.babraham.ac.uk/training.html#unix
https://tess.elixir-europe.org/materials/an-introduction-to-unix
Increasing amounts of bioinformatics work is done in a command line unix environment. Most large scale processing applications are written for unix and most large scale compute environments are also based on this.
This course provides an introduction to the concepts of unix and provides a practical introduction to working in this environment. Internally we link this course to a more specific course illustrating the use of our internal cluster environment and this part of the course could be adapted for other sites with different compute infrastructure.
Simon Andrews
Unix, Babraham Institute
An Introduction to ggplot
Ggplot is the most popular plotting extension to R and replicates many of the graph types found in the core plotting libraries. This course provides an introduction to the ggplot2 libraries and gives a practical guide for how to use these to create different types of graphs.
Keywords: ggPlot, Babraham Institute
An Introduction to ggplot
http://www.bioinformatics.babraham.ac.uk/training.html#ggplot
https://tess.elixir-europe.org/materials/an-introduction-to-ggplot
Ggplot is the most popular plotting extension to R and replicates many of the graph types found in the core plotting libraries. This course provides an introduction to the ggplot2 libraries and gives a practical guide for how to use these to create different types of graphs.
Anne Segonds-Pichon
ggPlot, Babraham Institute