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Content provider: Bioinformatics and Biomathe... 

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Difficulty level: Beginner 


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

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

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 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

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

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

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

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

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 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

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