Specialized Training Courses

These courses aim to familiarise the participants with advanced data analysis methodologies and provide hands-on training on the latest analytical approaches for specific types of biological data.

The analysis of high-throughput sequencing data is the most popular topic, as reflected by the wide range of courses covering this subject (e.g. RNA-seq, ChIP-seq, variation, DNA methylation, whole exome sequencing analysis) but the spectrum of training courses on offer is much wider.

An Introduction to Data Exploration, Experimental Design, and Biomarker Expression Analysis using JMP Software Tools

Description Through the use of real world examples and the JMP, JMP Pro, and JMP Genomics software , we will cover best practices used in both industry and academia today to visually explore data, plan biological experiments, detect differential expression patterns, find signals in next-generation...

Analysis of bulk RNA-seq data

Description The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data . This course starts with a brief introduction to RNA-seq and discusses quality control issues . Next, we will present the alignment step, quantification of expression and differential...

Analysis of DNA methylation using sequencing

Description This course will cover all aspects of the analysis of DNA methylation using sequencing , including primary analysis, mapping and quality control of BS-Seq ( Bisulfite-Sequencing ) data, common pitfalls and complications. It will also include exploratory analysis of methylation data...

Analysis of single-cell RNA-seq data

Description Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is...

Bioimage analysis with Python

Description The aim of this 5 days course is to develop motivated participants toward becoming independent BioImage Analysts in an imaging facility or research role. Participants will be taught theory and algorithms relating to bioimage analysis using Python as the primary coding language. Lectures...

Bioinformatics for Biologists: An introduction to Data Exploration, Statistics, and Reproducibility

Description This 1-week course aims to provide an introduction to the best practices and tools needed to perform bioinformatics research effectively and reproducibly. Focusing on solutions around handling biological data, we will cover introductory lessons in data manipulation and visualisation in...

Bioinformatics for Principal Investigators

Description The aim of this workshop is to provide principal investigators with an introduction to the challenges of working with biological data and to the best practices , and tools , needed to perform bioinformatics research effectively and reproducibly . Prerequisites Principal Investigators...

Biological Network Series

Description The Biological Network Series c onsists of three webinars, each presented in the form of a 2-hour lecture as well as a tutorial with step-wise screenshots that enable listeners to emulate the subject at hand. Please note that these are webinars and not a coding exercises . LECTURE 1: An...

ChIP-seq and ATAC-seq analysis

Description The primary aim of this course is to familiarise participants with the analysis of ChIP-seq and ATAC-seq data and provide hands-on training on the latest analytical approaches. The course starts with an introduction to ChIP-seq experiments for the detection of genome-wide DNA binding...

Data Science: Machine learning applications for life sciences

Description This course aims to familiarise biomedical students and researchers with principles of Data Science . Focusing on utilising machine learning algorithms to handle biomedical data , it will cover: effects of experimental design , data readiness , pipeline implementations , machine...

Ensembl REST API workshop

Description The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers using the REST API , including...

Experimental Design

Description Modern technologies are able to deliver an unprecedented amount of data rapidly. However, without due care and attention early in the experimental process, such data are meaningless if they cannot adequately answer the intended research question. This course is aimed at those planning...

Exploring, visualising and analysing proteomics data in R

Description This course will present a set of R/Bioconductor packages to access, manipulate, visualise and analyse mass spectrometry (MS) and quantitative proteomics data. Prerequisites The course is targeted to either proteomics practitioners or data analysts/bioinformaticians that would like to...

Extracting biological information from gene lists

Description 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...

Image analysis for biologists (3-day)

Description This course will focus on computational methods for analysing cellular images and extracting quantitative data from them . The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative...

Introduction to Machine Learning

Description Machine learning gives computers the ability to learn without being explicitly programmed. It encompasses a broad range of approaches to data analysis with applicability across the biological sciences. Lectures will introduce commonly used algorithms and provide insight into their...

Introduction to metabolomics and its application in life-sciences

Description The goal of metabolomics is to identify and quantify the complete biochemical composition of a biological sample. With the increase in genomic, transcriptomic and proteomic information there is a growing need to understand the metabolic phenotype that these genes and proteins ultimately...

Introduction to metagenomics

Description This two days course will focus on the theory and applications of metagenomics, for the analysis of complex microbiomes (microbial communities). The course will include theoretical (~40%) and practical (~60%) training. We will start with the fastest, simplest and cheapest amplicon based...

Introduction to scientific figure design

Description 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...

KNIME: Practical introduction to KNIME Analytics platform and its application in bioinformatics

Description This event introduces participants to the KNIME Analytics Platform, an open source data science platform with a visual workflow editor, that can be used by users without prior programming experience or integrated with existing scripts written in R or Python. These sessions are aimed...

Molecular phylogenetics

Description This course will provide training for bench-based biologists to use molecular data to construct and interpret phylogenies , and test their hypotheses . Delegates will gain hands-on practice of using a variety of programs freely-available online and commonly used in molecular studies...

Ontologies and ontology-based data analysis

Description Ontologies have long provided a core foundation in the organization of biomedical entities , their attributes , and their relationships . With over 500 biomedical ontologies currently available there are a number of new and exciting opportunities emerging in using ontologies for large...

Protein Structure Analysis

Description This course covers analytical approaches for the interpretation of biomacromolecular structures including how to find information about the structure and function of your protein sequence using CATH , principles of modern state-of-the-art protein modelling with Phyre2 and methods for...

R object-oriented programming and package development

Description The course will teach intermediate R object-oriented programming and how to build a fully functional R package . Relevant teaching materials are available here and the sequences example package used as template in the course can be found here . Prerequisites A good knowledge of R and...

Snakemake workshop

Description Data analyses usually entail the application of many command line tools or scripts to transform, filter, aggregate or plot data and results. With ever increasing amounts of data being collected in science, reproducible and scalable automatic workflow management becomes increasingly...

Transcriptome Analysis for Non-Model Organisms

Description RNA-Seq technology has been transformative in our ability to explore gene content and gene expression in all realms of biology, and de novo transcriptome assembly has enabled opportunities to expand transcriptome analysis to non-model organisms. This course provides an overview of...

Using CellProfiler and CellProfiler Analyst to analyse biological images

Description Microscopy experiments have proven to be a powerful means of generating information-rich data for biological applications. From small-scale microscopy experiments to time-lapse movies and high-throughput screens, automatic image analysis is more objective and quantitative and less...

Variant Discovery with GATK4

Description This workshop will focus on the core steps involved in calling germline short variants, somatic short variants, and copy number alterations with the Broad’s Genome Analysis Toolkit (GATK) , using “Best Practices” developed by the GATK methods development team. A team of methods...

Analysis of high-throughput sequencing data with Bioconductor

Description This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in 'bam' format. We will also...

Introduction to Galaxy: data manipulation and visualisation

Description Galaxy is an open, web-based platform for data intensive life science research that enables non-bioinformaticians to create, run, tune and share their own bioinformatic analyses. This introductory course will cover Galaxy's basic functionality, simple data manipulation and visualization...

Analysis of gene regulatory sequencing data: ChIP-seq, ATAC-seq and Hi-C

Description This advanced course will cover high-throughput sequencing data processing , ChIP-seq data analysis (including alignment, peak calling), differences in analyses methods for transcription factors (TF) binding and epigenomic datasets , a range of downstream analysis methods for extracting...