Bioinformatics course timetable
November 2023
| Tue 21 |
The Ensembl Project provides an interface and an infrastructure for accessing genomic information, including genes, variants, comparative genomics and gene regulation data, covering over 300 vertebrate species. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Wed 22 |
The Ensembl project provides an interface and an infrastructure for accessing genomic information, including genes, variants, comparative genomics and gene regulation data, covering over 300 vertebrate species. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write scripts to call them.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Thu 23 |
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 biological themes which turn up in the lists. This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication. Course materials are available here.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Fri 24 |
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 expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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This course introduces concepts about reproducibility that can be used when you are programming in R. We will explore how to create notebooks - a way to integrate your R analyses into reports using Rmarkdown. The course also introduces the concept of version control. We will learn how to create a repository on GitHub and how to work together on the same project collaboratively without creating conflicting versions of files.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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December 2023
| Fri 1 |
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 expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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This course will teach you how to use molecular data to construct and interpret phylogenies. We will start by introducing basic concepts in phylogenetic analysis, what trees represent and how to interpret them. We will then cover how to produce a multiple sequence alignment from DNA and protein sequences, and the pros and cons of different alignment algorithms. You will then learn about different methods of phylogenetic inference, with a particular focus on maximum likelihood and how to assess confidence in your tree using bootstrap resampling. Finally, we will introduce how Bayesian methods can help to estimate the uncertainty in the inferred tree parameters as well as incorporate information for more advanced/bespoke phylogenetic analysis.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Tue 5 |
This workshop focuses on expression proteomics, which aims to characterise the protein diversity and abundance in a particular system. You will learn about the bioinformatic analysis steps involved when working with these kind of data, in particular several dedicated proteomics Bioconductor packages, part of the R programming language. We will use real-world datasets obtained from label free quantitation (LFQ) as well as tandem mass tag (TMT) mass spectrometry. We cover the basic data structures used to store and manipulate protein abundance data, how to do quality control and filtering of the data, as well as several visualisations. Finally, we include statistical analysis of differential abundance across sample groups (e.g. control vs. treated) and further evaluation and biological interpretation of the results via gene ontology analysis. By the end of this workshop you should have the skills to make sense of expression proteomics data, from start to finish.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Wed 6 |
This workshop focuses on expression proteomics, which aims to characterise the protein diversity and abundance in a particular system. You will learn about the bioinformatic analysis steps involved when working with these kind of data, in particular several dedicated proteomics Bioconductor packages, part of the R programming language. We will use real-world datasets obtained from label free quantitation (LFQ) as well as tandem mass tag (TMT) mass spectrometry. We cover the basic data structures used to store and manipulate protein abundance data, how to do quality control and filtering of the data, as well as several visualisations. Finally, we include statistical analysis of differential abundance across sample groups (e.g. control vs. treated) and further evaluation and biological interpretation of the results via gene ontology analysis. By the end of this workshop you should have the skills to make sense of expression proteomics data, from start to finish.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Thu 7 |
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 control. The aim of this course is to provide an introductory overview of metabolomics and its applications in life sciences and environmental settings. We will introduce different techniques used to extract metabolites and analyse samples to collect metabolomic data (such as HPLC or GC-based MS and NMR), present how to analyse such data, how to identify metabolites using online databases and how to map the metabolomic data to metabolic pathways.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core concepts of Python including Python syntax, data structures and reading/writing files. These are illustrated by a series of example programs. Upon completion of the course, participants will be able to write simple Python programs.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Fri 8 |
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 control. The aim of this course is to provide an introductory overview of metabolomics and its applications in life sciences and environmental settings. We will introduce different techniques used to extract metabolites and analyse samples to collect metabolomic data (such as HPLC or GC-based MS and NMR), present how to analyse such data, how to identify metabolites using online databases and how to map the metabolomic data to metabolic pathways.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core concepts of Python including Python syntax, data structures and reading/writing files. These are illustrated by a series of example programs. Upon completion of the course, participants will be able to write simple Python programs.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Mon 11 |
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. Through hands-on training, you'll apply both de novo assembly and reference-based mapping approaches to obtain bacterial genomes for your isolates. You will apply standardised workflows for genome assembly and annotation, including quality assessment criteria to ensure the reliability of your results. Furthermore, you'll learn how to construct phylogenetic trees using whole genome and core genome alignments, enabling you to explore the evolutionary relationships among bacterial isolates. Lastly, you'll apply methods to detect antimicrobial resistance genes. As examples we will use Mycobacterium tuberculosis, Staphylococcus aureus and Streptococcus pneumoniae, allowing you to become well-equipped to conduct bacterial genomics analyses on a range of species.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Tue 12 |
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. Through hands-on training, you'll apply both de novo assembly and reference-based mapping approaches to obtain bacterial genomes for your isolates. You will apply standardised workflows for genome assembly and annotation, including quality assessment criteria to ensure the reliability of your results. Furthermore, you'll learn how to construct phylogenetic trees using whole genome and core genome alignments, enabling you to explore the evolutionary relationships among bacterial isolates. Lastly, you'll apply methods to detect antimicrobial resistance genes. As examples we will use Mycobacterium tuberculosis, Staphylococcus aureus and Streptococcus pneumoniae, allowing you to become well-equipped to conduct bacterial genomics analyses on a range of species.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Wed 13 |
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. Through hands-on training, you'll apply both de novo assembly and reference-based mapping approaches to obtain bacterial genomes for your isolates. You will apply standardised workflows for genome assembly and annotation, including quality assessment criteria to ensure the reliability of your results. Furthermore, you'll learn how to construct phylogenetic trees using whole genome and core genome alignments, enabling you to explore the evolutionary relationships among bacterial isolates. Lastly, you'll apply methods to detect antimicrobial resistance genes. As examples we will use Mycobacterium tuberculosis, Staphylococcus aureus and Streptococcus pneumoniae, allowing you to become well-equipped to conduct bacterial genomics analyses on a range of species.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Thu 14 |
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. Through hands-on training, you'll apply both de novo assembly and reference-based mapping approaches to obtain bacterial genomes for your isolates. You will apply standardised workflows for genome assembly and annotation, including quality assessment criteria to ensure the reliability of your results. Furthermore, you'll learn how to construct phylogenetic trees using whole genome and core genome alignments, enabling you to explore the evolutionary relationships among bacterial isolates. Lastly, you'll apply methods to detect antimicrobial resistance genes. As examples we will use Mycobacterium tuberculosis, Staphylococcus aureus and Streptococcus pneumoniae, allowing you to become well-equipped to conduct bacterial genomics analyses on a range of species.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Fri 15 |
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. Through hands-on training, you'll apply both de novo assembly and reference-based mapping approaches to obtain bacterial genomes for your isolates. You will apply standardised workflows for genome assembly and annotation, including quality assessment criteria to ensure the reliability of your results. Furthermore, you'll learn how to construct phylogenetic trees using whole genome and core genome alignments, enabling you to explore the evolutionary relationships among bacterial isolates. Lastly, you'll apply methods to detect antimicrobial resistance genes. As examples we will use Mycobacterium tuberculosis, Staphylococcus aureus and Streptococcus pneumoniae, allowing you to become well-equipped to conduct bacterial genomics analyses on a range of species.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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January 2024
| Mon 8 |
This one-day course is primarily aimed at life science researchers, but covers many topics that are applicable to other fields. It combines key theoretical knowledge with practical application, which will aid researchers in designing effective experiments. The focus throughout the course is to link experimental design to a clear analysis strategy. This ensures that the collected data will be suitable for statistical analysis. During this course, we cover:
Topics included in the course include: crafting a good research question, operationalising variables effectively, identifying and dealing with confounding variables and pseudoreplication, and practical tips for power analysis and piloting. The course is delivered via a mix of lectures, group discussion and worked examples.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Tue 9 |
The Unix shell (command line) is a powerful and essential tool for modern researchers, in particular those working in computational disciplines such as bioinformatics and large-scale data analysis. In this course we will explore the basic structure of the Unix operating system and how we can interact with it using a basic set of commands. You will learn how to navigate the filesystem, manipulate text-based data and combine multiple commands to quickly extract information from large data files. You will also learn how to write scripts, use programmatic techniques to automate task repetition, and communicate with remote servers (such as High Performance Computing servers).
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Fri 19 |
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 also more challenging. 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.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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This is a first course on machine learning. It aims to provide a foundation for future work with machine learning. This course will get you to the point where you can confidently engage with literature referencing machine learning, but it is not designed to get you to the point where you can actively use modern machine learning methods in your own research. It will however signpost for you which of our other courses will be relevant if you want to get to that stage.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Tue 23 |
This course provides an introduction to the basic theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to overlay large-scale data such as that obtained through RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of one of the most commonly used open source Network Visualisation Platforms, Cytoscape. The course will also access and analyse the data through Cytoscape apps, including IntAct app.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Wed 24 |
This course provides an introduction to the basic theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to overlay large-scale data such as that obtained through RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of one of the most commonly used open source Network Visualisation Platforms, Cytoscape. The course will also access and analyse the data through Cytoscape apps, including IntAct app.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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| Fri 26 |
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 also more challenging. 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.
If you do not have a University of Cambridge Raven account please book or register your interest here. Additional information
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