Register training material
22 materials found

Licence: Other (Not Open) 


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

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

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

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

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

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

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: Statistics and probability, Software engineering

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

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

Keywords: John Innes Centre, JIC