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Bioinformatics Training

Bioinformatics course timetable

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Fri 10 Mar – Thu 18 May

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March 2023

Fri 10
An Introduction to Machine Learning (ONLINE LIVE TRAINING) (4 of 6) [Full] 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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.

Mon 13
An Introduction to Machine Learning (ONLINE LIVE TRAINING) (5 of 6) [Full] 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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.

Tue 14
An Introduction to Machine Learning (ONLINE LIVE TRAINING) (6 of 6) [Full] 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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.

Wed 15
Introduction to working with UNIX and bash (ONLINE LIVE TRAINING) (1 of 2) [Places] 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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).

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.

Thu 16
Introduction to working with UNIX and bash (ONLINE LIVE TRAINING) (2 of 2) [Places] 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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).

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.

Fri 17
Analysis of bulk RNA-seq data (IN PERSON) (1 of 3) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here.

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.

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.

Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) (1 of 3) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click here.

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 20
Analysis of bulk RNA-seq data (IN PERSON) (2 of 3) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here.

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.

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.

Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) (2 of 3) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click here.

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.

Tue 21
Analysis of bulk RNA-seq data (IN PERSON) (3 of 3) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here.

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.

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.

Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) (3 of 3) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click here.

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.

Wed 22
High Performance Computing: An Introduction (ONLINE LIVE TRAINING) (1 of 3) [Places] 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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).

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
High Performance Computing: An Introduction (ONLINE LIVE TRAINING) (2 of 3) [Places] 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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).

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
High Performance Computing: An Introduction (ONLINE LIVE TRAINING) (3 of 3) [Places] 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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).

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.

April 2023

Tue 18
Introduction to Python for Biologists (ONLINE LIVE TRAINING) (1 of 4) [Full] 09:30 - 12:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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.

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.

Variant Discovery with GATK4 (IN PERSON) (1 of 4) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will focus on the core steps involved in calling variants from Illumina next generation sequencing data using the Genome Analysis Toolkit (GATK). You will learn about best practices in calling somatic variants: single nucleotide variants (SNVs), short insertion/deletions (indels) and copy number variants (CNVs). We will also cover considerations to take when calling variants on the mitochondrial genome, as well as variant calling from bulk and single-cell RNA-seq data. We will also cover how the data structures provided by GATK can help you process large datasets in parallel and at scale. Although this workshop focuses on human data, the majority of the concepts and approaches apply to non-human data, and we will cover some adaptations needed in those situations.

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 19
Introduction to Python for Biologists (ONLINE LIVE TRAINING) (2 of 4) [Full] 09:30 - 12:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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.

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.

Variant Discovery with GATK4 (IN PERSON) (2 of 4) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will focus on the core steps involved in calling variants from Illumina next generation sequencing data using the Genome Analysis Toolkit (GATK). You will learn about best practices in calling somatic variants: single nucleotide variants (SNVs), short insertion/deletions (indels) and copy number variants (CNVs). We will also cover considerations to take when calling variants on the mitochondrial genome, as well as variant calling from bulk and single-cell RNA-seq data. We will also cover how the data structures provided by GATK can help you process large datasets in parallel and at scale. Although this workshop focuses on human data, the majority of the concepts and approaches apply to non-human data, and we will cover some adaptations needed in those situations.

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.

Thu 20
Variant Discovery with GATK4 (IN PERSON) (3 of 4) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will focus on the core steps involved in calling variants from Illumina next generation sequencing data using the Genome Analysis Toolkit (GATK). You will learn about best practices in calling somatic variants: single nucleotide variants (SNVs), short insertion/deletions (indels) and copy number variants (CNVs). We will also cover considerations to take when calling variants on the mitochondrial genome, as well as variant calling from bulk and single-cell RNA-seq data. We will also cover how the data structures provided by GATK can help you process large datasets in parallel and at scale. Although this workshop focuses on human data, the majority of the concepts and approaches apply to non-human data, and we will cover some adaptations needed in those situations.

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.

Fri 21
Variant Discovery with GATK4 (IN PERSON) (4 of 4) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will focus on the core steps involved in calling variants from Illumina next generation sequencing data using the Genome Analysis Toolkit (GATK). You will learn about best practices in calling somatic variants: single nucleotide variants (SNVs), short insertion/deletions (indels) and copy number variants (CNVs). We will also cover considerations to take when calling variants on the mitochondrial genome, as well as variant calling from bulk and single-cell RNA-seq data. We will also cover how the data structures provided by GATK can help you process large datasets in parallel and at scale. Although this workshop focuses on human data, the majority of the concepts and approaches apply to non-human data, and we will cover some adaptations needed in those situations.

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.

Tue 25
Introduction to Python for Biologists (ONLINE LIVE TRAINING) (3 of 4) [Full] 09:30 - 12:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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.

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 26
Introduction to Python for Biologists (ONLINE LIVE TRAINING) (4 of 4) [Full] 09:30 - 12:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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.

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.

May 2023

Thu 4
Reproducible Research with R (ONLINE LIVE TRAINING) (1 of 2) Not bookable 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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.

Fri 5
Reproducible Research with R (ONLINE LIVE TRAINING) (2 of 2) Not bookable 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

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.

Thu 18
Analysis of single cell RNA-seq data (IN PERSON) (1 of 3) Not bookable 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

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.