Bioinformatics and Biomathematics Training Hub

The Bioinformatics and Biomathematics Training Hub (BBTH) is a BBSRC-funded collaborative project to coordinate the development and sharing of training materials and expertise across the UK’s National Institutes of Bioscience (NIB — http://www.nib.ac.uk/) for the increasingly important areas of bioinformatics and biomathematics.

Guided by our NIB partners, researcher surveys, and interactions with interested bodies such as Elixir-UK, we will work to ensure that best use is made of existing assets and capabilities, that best practice is shared across the NIB, and that redundant effort is minimised going forwards.

Bioinformatics and Biomathematics Training Hub http://tess.elixir-uk.org/content_providers/bioinformatics-and-biomathematics-training-hub The Bioinformatics and Biomathematics Training Hub (BBTH) is a BBSRC-funded collaborative project to coordinate the development and sharing of training materials and expertise across the UK’s National Institutes of Bioscience (NIB — http://www.nib.ac.uk/) for the increasingly important areas of bioinformatics and biomathematics. Guided by our NIB partners, researcher surveys, and interactions with interested bodies such as Elixir-UK, we will work to ensure that best use is made of existing assets and capabilities, that best practice is shared across the NIB, and that redundant effort is minimised going forwards. /system/content_providers/images/000/000/061/original/BBTH_logo.png?1480508618
Showing 62 materials out of 62. View all results.
Train the trainer

Five PowerPoint presentations and an Excel worksheet for a Train the Trainer course developed by Chris Taylor while at the Earlham Institute working for the National Institutes of Science's Bioinformatics and Biomathematics Training hub. The five slide decks cover pedagogical theory, trainer...

Scientific topics: Bioinformatics, Computational biology

Keywords: training, pedagogy

Introduction to R: A software environment for statistical computing

Overview

R is a programming language and associated environment developed for statistical computing and data analysis. It provides many powerful tools for statistics, data visualisation and bioinformatics.

Learning outcomes

  • What R is suitable for.
  • How to use R...

Scientific topics: Software engineering, Statistics and probability

Keywords: John Innes Centre, JIC

Introduction to RNA-Seq Using Galaxy: Studying the transcriptome

Audience

The intended audience includes any student, postdoc or RA who has an interest in bioinformatics and who intends to conduct RNA-Seq analysis on a Galaxy platform.

Overview

RNA-Seq is an immensely powerful technique that allows us to examine the presence and...

Scientific topics: RNA, RNA-Seq

Keywords: John Innes Centre, JIC

Introduction to Perl: Programming for bioinformatics

Overview

Perl is a programming language for getting your job done. It is designed to make the easy jobs easy, without making the hard jobs impossible. Perl is also well known for BioPerl, a collection of modules which greatly simplify complicated bioinformatics tasks.
Learning...

Scientific topics: Software engineering

Keywords: perl, John Innes Centre, JIC

Introduction to Linux: The operating system for bioinformatics

Overview

The Linux operating system underlies the HPC cluster at the NBI, and other clusters throughout the world. Unlike Windows and OS X, we usually interact with these systems through the command line. The course will teach the basics of Linux use.

Learning...

Keywords: John Innes Centre, JIC

R for Genomics

R is an open source programming/scripting language.

  • Inspired by the programming language S.
  • Useful for statistics and data science.
  • Superior like commercial alternatives (over 7,000 user contributed packages at this time).
  • Widely used both in academia and industry.
  • Available on...

Scientific topics: Genomics

Keywords: IBERS, Institute of Biological, Environmental and Rural Sciences

Unix and Perl primers for biologists

UNIX is the most commonly used operating system in bioinformatics. Increasingly, the raw output of biological research exists as in silico data, usually in the form of large text files. Unix is particularly suited to work with such files and has several powerful (and flexible) commands that...

Keywords: IBERS, Institute of Biological, Environmental and Rural Sciences

Mapping reads on Galaxy server

Introduction to Galaxy

  • Introduction to Reads Mapping
  • Hands-on experience:
  • Upload data on Galaxy repository
  • Perform bioinformatics analysis with Galaxy
  • Save data
  • Visualize the results

Keywords: Galaxy, IBERS, Institute of Biological, Environmental and Rural Sciences

QC or not QC Data is the question

Sequence processing Issues

General sequence quality

  • 5’ base bias
  • 3’ quality decline

Library diversity

  • Low complexity sequence
  • Over-amplification

Contamination

  • Intrinsic to sample?
  • Cross contamination? *...

Scientific topics: Quality affairs

Keywords: IBERS, Institute of Biological, Environmental and Rural Sciences

Introduction to Mixed Models

  1. Introduction

  2. What Are Mixed Models?

  3. Potential Advantages of Mixed Models

  4. Historical Perspective

  5. Example 1: Biological & Technical Replicates

  6. Example 2: Rabbit Inspiration Time – Sources of Variation

  7. Non-Normal Data

  8. Example 3: Non-normal data

9....

Keywords: Mixed models, Roslin Institute

Introduction to Sample Size Calculation

  1. Introduction

  2. Sample Size Calculation – Basic Formula

  3. Example 1

  4. Calculating In Terms of ‘Difference to Detect’ & Power From Sample Size

  5. Example 2

  6. Different Numbers Per Group

  7. Different Variances for Groups

  8. Binary Data

  9. Allowing for...

Keywords: Sample size, Roslin Institute

Summarising Data

  1. Introduction

  2. Introduction to Data Summary & Types of data

  3. Continuous Data – Measures of Location

  4. Continuous Data – Measures of Spread & Accuracy

  5. Continuous Data with Skewed or Odd Distributions – Measures of Spread

  6. Choosing Appropriate Summary Statistics...

Keywords: Summarising data, Roslin Institute

A Brief Introduction to R

  1. A Brief Introduction to R

  2. Very Basic Functions

  3. Demo Data - Rivers

  4. Demo Data - Rivers (Cont.)

  5. Demo Data - Orange

  6. Demo Data - Orange (Cont.)

  7. Demo data - Anderson's Iris Data

  8. Demo Data - US Judge Rating

  9. Summary

Keywords: R language, Roslin Institute

Introduction to Experimental Design

  1. Introduction

  2. Achieving Statistical Significance

  3. Achieving Generalisable Results

  4. Avoiding Bias

  5. Questions to Address When Planning

  6. Examples of Experimental Designs

  7. Randomised Block Design

  8. Crossover & Repeated Measures Designs

  9. Pilot & Proof...

Keywords: Experimental design, Roslin Institute

Graphical & Computational Modelling of Biological Pathways

  1. Introduction

  2. Many Views of A Pathway(Lecture)

  3. Pathway Models & Pathway Types (Lecture)

  4. Sources of ‘Pathway Data’ (Lecture)

  5. Issues (Lecture)

  6. SBGN (Lecture)

  7. mEPN (Lecture)

  8. Practical Session: Pathway to Pathway Construction - yED(1)

  9. Practical...

Keywords: Graphical modelling, Computational modelling, Roslin Institute

Introduction to R

R is a popular language and environment that allows powerful and fast manipulation of data, offering many statistical and graphical options. This course aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. It will focus...

Scientific topics: Software engineering

Keywords: R programming, Babraham Institute

SAS Introduction

1.Introduction

  1. Data summary

  2. Demo – Data Summary

  3. Demo – Data Summary cont.

  4. Data summary using PROC TABULATE and PROC GPLOT

  5. Statistical analysis

  6. Example analysis

  7. Example analysis cont.1

  8. Example analysis cont.2

  9. Reading and manipulating...

Keywords: SAS, Roslin 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

Phylogenetics & Phylogeography Practical (Advanced Analytical Methods)

  1. Phylogenetics & Phylogeography Practical - Overview

  2. Phylogenetics & Phylogeography Practical 1

  3. Phylogenetics & Phylogeography Practical 2 - Part 1

  4. Phylogenetics & Phylogeography Practical 2 - Part 2

  5. Phylogenetics & Phylogeography Practical 3

6....

Keywords: Phylogenetics, Phylogeography, Roslin Institute

Plotting complex figures with R

This course is a comprehensive guide to the use of the built in R plotting functionality to construct everything from customised simple plots to complex multi-layered figures. It follows on from the material in our introductory R course and participants are expected to have a basic understanding...

Keywords: Graph plotting, R Programming, 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.

**Course...

Keywords: ggPlot, 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.

Course Content

*...

Keywords: 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

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.

Course Content

*...

Scientific topics: Statistics and probability

Keywords: 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

Phylogenetic analysis of pathogens: Staphylococcus aureus, host switching and antibiotic resistance

  1. Phylogenetic analysis of pathogens (lecture - part1)

  2. Phylogenetic analysis of pathogens (lecture - part2)

  3. Phylogenetic analysis of pathogens (lecture - part3)

  4. Phylogenetic analysis of pathogens (lecture - part4)

  5. Phylogenetic analysis of pathogens (lecture - part5)

6....

Keywords: Phylogenetic analysis, Roslin Institute

Phylogenetics & Phylogeography (Advanced Analytical Methods)

  1. Phylogenetics & Phylogeography (lecture-part 1)

  2. Phylogenetics & Phylogeography (lecture-part 2)

  3. Phylogenetics & Phylogeography (lecture-part 3)

  4. Phylogenetics & Phylogeography (lecture-part 4)

  5. Phylogenetics & Phylogeography (lecture-part 5)

6....

Keywords: Phylogenetics, Roslin Institute

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

Welcome to the IFR Dockerised version of the Welsh Genepark's
Introduction to Command-line NGS Analysis course!
The original materials belong to Welsh Genepark and the original
materials and software can be found here.

This...

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

Docker version of Welsh Gene Park NGS course

Welcome to the IFR Dockerised version of the Welsh Genepark's
Introduction to Command-line NGS Analysis course!
The original materials belong to Wesh Genepark and the original
materials and software can be found here.

This...

Keywords: NGS, 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

Advanced R

This course follows on from the introductory course. It goes into more detail on practical guides to filtering and combining complex data sets. It also looks at other core R concepts such as looping with apply statements and using packages. Finally it looks at how to document your R analyses and...

Keywords: R programming, Babraham Institute

Analysing Mapped Sequence Data with SeqMonk

SeqMonk is a program which can analyse large data sets of mapped genomic positions. It is most commonly used to work with data coming from high-throughput sequencing pipelines.

The program allows you to view your reads against an...

Scientific topics: Sequence alignment

Keywords: Babraham Institute

Basic Statistical Tests

  1. Introduction

  2. Hypothesis Testing

  3. Choosing Between Parametric & Non-Parametric Tests

  4. T-Test for Comparing Two Groups

  5. T-Test – Interpreting Software Output

  6. Paired T-Test

  7. Mann-Whitney U-Test to Compare Two Groups When Data Are Not Normally Distributed

8....

Keywords: Statistical tests, Roslin Institute

Computational Bioimaging: From images to data

Overview

We make extensive use of both light and electron microscopy in our research. The aquisition of images by a microscope is only the beginning of the process of extracting meaningful and useful information from those images. As well as extracting information, it's...

Scientific topics: Imaging, Bioimaging

Keywords: John Innes Centre, JIC

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

Bioinformatics and Virtual Machines

Introduction: What are Virtual Machines?

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

Why use a Virtual machine and what is it?

  • Fetching and installing the VM software

  • Getting Virtualbox Book

*...

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

Graphical & Computational Modelling of Biological Pathways

  1. Introduction

  2. Many Views of A Pathway(Lecture)

  3. Pathway Models & Pathway Types (Lecture)

  4. Sources of ‘Pathway Data’ (Lecture)

  5. Issues (Lecture)

  6. SBGN (Lecture)

  7. mEPN (Lecture)

  8. Practical Session: Pathway to Pathway Construction - yED(1)

  9. Practical...

Keywords: Graphical modelling, Roslin Institute

Galaxy for NGS analysis: A web-based platform for data intensive biological research

Overview

Galaxy is an open, web-based platform for data intensive biomedical research. It offers an accessible, reproducible and transparent computational workbench for the biologist. This workbench is very useful in automating repeated analysis steps in the form of workflows. The...

Scientific topics: Workflows, High-throughput sequencing, Nucleic acid sequence analysis, Bioinformatics

Keywords: John Innes Centre, JIC

Introduction to Analysing Repeated Measures Data

  1. Introduction

  2. Potential Analysis Approaches

  3. Mixed Model Analysis

  4. Covariance Pattern Model

  5. Example – Covariance Pattern Model

  6. Significance Testing for Fixed Effects

  7. Model Checking

  8. Random Coefficients (Slopes) Models

  9. Example – Random Coefficients...

Keywords: Data analysis, Repeated measures, Roslin Institute

An Introduction to BioLayout Express3D

1.Introduction to data analysis - course overview (lecture)

2.Introduction to networks (lecture)

  1. BioLayout Express3D - background and benefits (lecture)

  2. BioLayout Express3D – getting started 1 (Practical Session)

  3. BioLayout Express3D – getting started 2 (Practical...

Keywords: Gene expression analysis, Roslin Institute

Introduction to ChIP-Seq Using Galaxy: Analysing protein interactions with DNA

Overview

Chromatin Immunoprecipiation (ChIP) allows us to identify DNA sequences bound by particular proteins. This provides a powerful way to investigate chromatin-associated proteins such as transcription factors. Recent advances in high throughput sequencing allow ChIP data...

Scientific topics: ChIP-seq

Keywords: Roslin Institute

An Introduction to High Performance Computing

What is HPC

  • Our HPC(s)
  • Submitting a job to the HPC
  • Monitoring your running job
  • When your job has finished
  • Checking how the resources on the HPC are being used
  • Submitting multiple jobs
  • Best practice

Keywords: IBERS, Institute of Biological, Environmental and Rural Sciences

Introduction to Statistical Modelling

  1. Introduction

  2. One-Way Analysis of Variance (ANOVA) Recap

  3. Two-Way ANOVA - Assessing Two Effects in Same Model

  4. Two-Way ANOVA - Allowing for Structure in The Data

  5. Paired T-Test Using Two-Way ANOVA & ANOVA With More Effects

  6. Regression Recap

  7. General Linear...

Keywords: Statistical modelling, Roslin Institute

Learning to Program with Perl

For a long time Perl has been a popular language among those programming for the first time. Although it is a powerful language many of its features mean make it especially suited to first time programmers as it reduces the complexity found in many other languages. Perl is also one of the world's...

Keywords: perl, Babraham Institute

Molecular epidemiology practical

  1. Molecular epidemiology - practical 1

  2. Molecular epidemiology - practical 1 review

  3. Molecular epidemiology - practical 2 part 1

  4. Molecular epidemiology - practical 2 part 2

  5. Molecular epidemiology - practical 2 review

  6. Molecular epidemiology - practical 3 part 1

7....

Keywords: Molecular epidemiology, Roslin Institute

Python for Biologists: Programming for Scientific Computing

Overview

Python is a flexible programming language that is becoming increasingly popular for scientific computing. The course is is split into 12 modules and runs over two half days. At the end of each module there a number of exercises to help solidify the learning. By the end of...

Scientific topics: Software engineering

Keywords: Python for Biologists, John Innes Centre, JIC

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

Python

Complete course materials from the 2015 Python course.

Keywords: Earlham Institute

Data QC and preparation

Course materials from the data QC and preparation course.

Keywords: Earlham Institute

A simple genome assembly

Course materials from the 2015 De Novo course.

Keywords: Earlham Institute

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

Browsing plant and pathogen genomes with Ensembl Genomes

Complete course materials from the Ensembl Genomes course.

Keywords: Earlham Institute

Pathways to networks – from in vivo to in silico and backwards

Complete course materials from the 2014 pathways to networks course.

Scientific topics: Molecular interactions, pathways and networks

Keywords: Earlham Institute

Genotyping by sequencing 2014

Complete course materials from the 2014 GBS course.

Scientific topics: Genotype and phenotype

Keywords: Earlham Institute

Summer School 2014

Complete course materials from the 2014 Summer School.

Keywords: Earlham Institute

Genotyping by sequencing 2015

Complete course materials from the 2015 GBS course.

Keywords: Earlham Institute

SeqAhead: NGS current challenges and data analysis for plant researchers

Complete course materials from the 2014 NGS course.

Keywords: next generation sequencing, Earlham Institute

Python for Life Scientists 2013

Complete course materials from the 2013 Python course.

Keywords: Python, Earlham Institute

Sequencing Technologies

Course materials from the 2015 de novo course.

Scientific topics: Sequencing

Keywords: De Novo, Earlham Institute

First pass assembly and QC

Course materials from the 2015 De Novo course.

Keywords: Earlham Institute

Genome assembly and validation

Course materials from the 2015 de novo course.

Keywords: Earlham Institute

Software Carpentry 2014

Complete course materials from the 2014 SWC course.

Keywords: Earlham Institute

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