Bioinformatics course timetable
December 2022
| Thu 1 |
PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click here. 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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
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PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here. 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. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
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| Fri 2 |
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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Mon 5 |
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 theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Thu 8 |
The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. 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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Fri 9 |
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 how to use the Ensembl REST APIs, including understanding the major endpoints and how to write scripts to call them. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Mon 12 |
Have you heard about High Performance Computing, but are not sure what it is or whether it is relevant for your work? Would you like to use a HPC, but are not sure where to start? Are you using your personal computer to run computationally demanding tasks, which take long and slow down your work? Do you need to use software that runs on Linux, but don't have access to a Linux computer? If any of these questions apply to you, then this course might be for you! Knowing how to work on a High Performance Computing system is an essential skill for applications such as bioinformatics, big-data analysis, image processing, machine learning, parallelising tasks, and other high-throughput applications. In this course we will cover the basics of High Performance Computing, what it is and how you can use it in practice. This is a hands-on workshop, which should be accessible to researchers from a range of backgrounds and offering several opportunities to practice the skills we learn along the way. As an optional session for those interested, we will also introduce the (free) HPC facilities available at Cambridge University (the course is not otherwise Cambridge-specific). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Tue 13 |
Have you heard about High Performance Computing, but are not sure what it is or whether it is relevant for your work? Would you like to use a HPC, but are not sure where to start? Are you using your personal computer to run computationally demanding tasks, which take long and slow down your work? Do you need to use software that runs on Linux, but don't have access to a Linux computer? If any of these questions apply to you, then this course might be for you! Knowing how to work on a High Performance Computing system is an essential skill for applications such as bioinformatics, big-data analysis, image processing, machine learning, parallelising tasks, and other high-throughput applications. In this course we will cover the basics of High Performance Computing, what it is and how you can use it in practice. This is a hands-on workshop, which should be accessible to researchers from a range of backgrounds and offering several opportunities to practice the skills we learn along the way. As an optional session for those interested, we will also introduce the (free) HPC facilities available at Cambridge University (the course is not otherwise Cambridge-specific). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
January 2023
| Tue 10 |
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). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here. |
| Wed 11 |
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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Thu 12 |
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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Wed 18 |
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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Thu 19 |
Day 1 will introduce you to next generation sequencing technologies (NGS) and how they work, providers, common bioinformatics workflows, standardised file types, quality control. This session will include an introduction to Galaxy. 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. Day 2 will be hands-on practicals on using Galaxy to explore sequencing quality control, before and after removal of low quality samples. This forms the core of all NGS analyses and this day will conclude with how this data pipes into gene expression studies, variant calling and genome assemblies. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Fri 20 |
Day 1 will introduce you to next generation sequencing technologies (NGS) and how they work, providers, common bioinformatics workflows, standardised file types, quality control. This session will include an introduction to Galaxy. 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. Day 2 will be hands-on practicals on using Galaxy to explore sequencing quality control, before and after removal of low quality samples. This forms the core of all NGS analyses and this day will conclude with how this data pipes into gene expression studies, variant calling and genome assemblies. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Wed 25 |
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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
February 2023
| Wed 1 |
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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Fri 3 |
R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Fri 10 |
R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Thu 16 |
This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course:
R is an open source programming language so all of the software we will use in the course is free. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Fri 17 |
This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course:
R is an open source programming language so all of the software we will use in the course is free. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Thu 23 |
This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course:
R is an open source programming language so all of the software we will use in the course is free. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Fri 24 |
This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course:
R is an open source programming language so all of the software we will use in the course is free. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
March 2023
| Thu 2 |
This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course:
R is an open source programming language so all of the software we will use in the course is free. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Fri 3 |
This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course:
R is an open source programming language so all of the software we will use in the course is free. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |
| Tue 7 |
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 theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here. |