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.
Bulk RNA-seq analysis
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 expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq.
For additional information and to register your interest, follow this link.
Single-cell RNA-seq analysis
In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq.
For additional information and to register your interest, follow this link.
Working with Bacterial Genomes
This comprehensive course equips you with essential skills and knowledge in bacterial genomics analysis, primarily using Illumina-sequenced samples. You'll gain an understanding of how to select the most appropriate analysis workflow, tailored to the genome diversity of a given bacterial species.
For additional information and to register your interest, follow this link.
Introduction to Mass Spectrometry: Theory and Applications
The aim of this course is to provide a comprehensive overview of mass spectrometry techniques, working principles and applications in STEM. Throughout the course, we will consider different ionization techniques and mass analyzers, hyphenation to chromatography or reaction coils, as well as upstream methodologies suitable for mass spectrometry in general. You will gain an understanding of what kind of data different mass spectrometry techniques provide and how to extract information from this data. This knowledge will enable you to plan and design mass spectrometry experiments for different applications.
For additional information and to register your interest, follow this link.
Analysis of ChIP-seq Data with SeqMonk
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to identify binding sites for transcription factors, histone modifications and other DNA-binding proteins across the genome. In this course, we will cover the fundamentals of ChIP-seq data analysis, from raw data to downstream applications.
For additional information and to register your interest, follow this link.
Analysis of DNA methylation using sequencing
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.
For additional information and to register your interest, follow this link.
Expression proteomics analysis in R
This course will present a set of R/Bioconductor packages to access, manipulate, visualise and analyse mass spectrometry (MS) and quantitative proteomics data.
For additional information and to register your interest, follow this link.
Extracting biological information from gene lists
This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis.
For additional information and to register your interest, follow this link.
Quality Control in Sequencing Experiments
This course covers the potential pitfalls of short-read sequencing studies and provides options for visualisation and quality control (QC) for early detection and diagnosis of issues.
For additional information and to register your interest, follow this link.
Metabolomics data analysis
The aim of this course is to provide an overview of metabolomics and its applications in life sciences, clinical and environmental settings.
For additional information and to register your interest, follow this link.
Metagenomics data analysis
This course will focus on the theory and applications of metagenomics, for the analysis of complex microbiomes (microbial communities).
For additional information and to register your interest, follow this link.
Foundations of Phylogenetic Inference
This course will provide training for bench-based biologists to use molecular data to construct and interpret phylogenies, and test their hypotheses.
For additional information and to register your interest, follow this link
Building Computational Pipelines with Snakemake
This 1-day workshop will cover the principles for building workflows using Snakemake, as well as more advanced strategies to fully customise, automate and scale your analysis.
For additional information and to register your interest, follow this link.
Managing Bioinformatics Software and Pipelines
Setting up a computer for running bioinformatic analysis can be a challenging process. Most bioinformatic applications involve the use of many different software packages, which are often part of long data processing pipelines. In this course we will teach you how to overcome these challenges by using package managers and workflow management software.
For additional information and to register your interest, follow this link.
Protein Structure Modelling
This course covers analytical approaches for the interpretation of biomacromolecular structures.
This two-day course covers how to computationally predict the 3D structure of proteins from their amino acid sequences. We will focus on AlphaFold, a software that has revolutionised this process due to its outstanding (near-experimental) prediction accuracy. Other key aspects will be covered such as retrieving structural information from public databases, evaluating the quality of the predicted models, model visualisation with PyMOL, multimer predictions, prediction of ligand binding sites and docking. After this course you should be able to produce 3D predictions of your proteins, while critically evaluating the output of the methods covered in the course.
For additional information and to register your interest, follow this link.
Prompting for biologists: using AI chatbots for effective data analysis
As the use of AI chatbots continues to rise, it is crucial to understand what they are, how they work, and how to make the most of them. Prompting is the method of interacting with AI, and as AI chatbots become more openly and widely available, a good and effective prompt could make all the difference.
In this course, we will provide background on the history of AI chatbots as well as an understanding of how they work. We will provide hands-on use cases of how to prompt like a bioinformatician/software engineer as well as providing strategies and tactics of prompting to unleash the full potential of AI chatbots in biological data analysis. This course is aimed at researchers with no computational background.
For additional information and to register your interest, follow this link.
Mass Spectrometry for Environmental Samples: from Data to Insights
The aim of this course is to provide a comprehensive overview of FTMS techniques and their areas of application. Throughout the course we will consider various case studies where the full power of FTMS is demonstrated, including its use in biogeochemistry, ecology, environmental and atmospheric chemistry. Additionally, we will discuss how FTMS is used to study whiskey, beer, meteorites and mummies. You will get an understanding of the types of data provided by FTMS, where you can apply it and how to manage the large data it generates. We will also cover how to analyse and visualise FTMS data in various applications.
For additional information and to register your interest, follow this link.
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