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Bioinformatics Training

Bioinformatics course timetable

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Tue 7 Apr – Thu 24 Sep

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April 2020

Thu 16
Data Science in Python (ONLINE LIVE TRAINING) (1 of 2) [Full] 09:30 - 16:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

Discount offer of 50% off normal fees applies to this course.

This course covers concepts and strategies for working more effectively with Python with the aim of writing reusable code, using function and libraries. Participants will acquire a working knowledge of key concepts which are prerequisites for advanced programming in Python e.g. writing modules and classes.

Note: this course is the continuation of the Introduction to Solving Biological Problems with Python; participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python.

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
Data Science in Python (ONLINE LIVE TRAINING) (2 of 2) [Full] 09:30 - 16:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

Discount offer of 50% off normal fees applies to this course.

This course covers concepts and strategies for working more effectively with Python with the aim of writing reusable code, using function and libraries. Participants will acquire a working knowledge of key concepts which are prerequisites for advanced programming in Python e.g. writing modules and classes.

Note: this course is the continuation of the Introduction to Solving Biological Problems with Python; participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python.

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
Introduction to R for Biologists (ONLINE LIVE TRAINING) (1 of 2) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

Discount offer of 50% off normal fees applies to this course.

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.

Tue 21
Introduction to R for Biologists (ONLINE LIVE TRAINING) (2 of 2) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

Discount offer of 50% off normal fees applies to this course.

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.

Wed 22
Extracting biological information from gene lists (ONLINE LIVE TRAINING) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online in conjunction with the presenters.

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.

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 29
Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) (1 of 3) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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.

Thu 30
Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) (2 of 3) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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.

May 2020

Fri 1
Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) (3 of 3) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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 6
Introduction to metagenomics (ONLINE LIVE TRAINING) new (1 of 2) [Full] 09:30 - 17:00 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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 methods and will go up to the Hi-C metagenomics methods that give highly detailed results on the complex microbial communities. The practical component will cover bioinformatics analysis of metagenomics.

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 7
Introduction to metagenomics (ONLINE LIVE TRAINING) new (2 of 2) [Full] 09:30 - 16:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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 methods and will go up to the Hi-C metagenomics methods that give highly detailed results on the complex microbial communities. The practical component will cover bioinformatics analysis of metagenomics.

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.

Mon 11
Introduction to R for Biologists (ONLINE LIVE TRAINING) (1 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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.

Tue 12
Introduction to R for Biologists (ONLINE LIVE TRAINING) (2 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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.

Mon 18
Reproducible Research with R new [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team are investigating a workable solution to offer some of the courses on a remote basis and will be in contact with updates as soon as possible.

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.

June 2020

Wed 24
An Introduction to Machine Learning (1 of 3) [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes.

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.

Thu 25
An Introduction to Machine Learning (2 of 3) [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes.

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.

Fri 26
An Introduction to Machine Learning (3 of 3) [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes.

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.

Mon 29
An Introduction to MATLAB for biologists (1 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts.

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 30
An Introduction to MATLAB for biologists (2 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts.

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.

September 2020

Tue 1
Using the Ensembl Genome Browser [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

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.

Wed 2
Ensembl REST API workshop [Places] 09:30 - 15:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

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.

Mon 21
Data Science School: Machine learning applications for life sciences new charged (1 of 4) [Places] 10:00 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This School 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 learning in Python, and related statistics, as well as Gaussian Process models.

Providing practical experience in the implementation of machine learning methods relevant to biomedical applications, including Gaussian processes, we will illustrate best practices that should be adopted in order to enable reproducibility in any data science application.

This event is sponsored by Cambridge Centre for Data-Driven Discovery (C2D3).

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 22
Data Science School: Machine learning applications for life sciences new charged (2 of 4) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This School 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 learning in Python, and related statistics, as well as Gaussian Process models.

Providing practical experience in the implementation of machine learning methods relevant to biomedical applications, including Gaussian processes, we will illustrate best practices that should be adopted in order to enable reproducibility in any data science application.

This event is sponsored by Cambridge Centre for Data-Driven Discovery (C2D3).

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.

Wed 23
Data Science School: Machine learning applications for life sciences new charged (3 of 4) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This School 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 learning in Python, and related statistics, as well as Gaussian Process models.

Providing practical experience in the implementation of machine learning methods relevant to biomedical applications, including Gaussian processes, we will illustrate best practices that should be adopted in order to enable reproducibility in any data science application.

This event is sponsored by Cambridge Centre for Data-Driven Discovery (C2D3).

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.

Thu 24
Data Science School: Machine learning applications for life sciences new charged (4 of 4) [Places] 09:30 - 15:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This School 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 learning in Python, and related statistics, as well as Gaussian Process models.

Providing practical experience in the implementation of machine learning methods relevant to biomedical applications, including Gaussian processes, we will illustrate best practices that should be adopted in order to enable reproducibility in any data science application.

This event is sponsored by Cambridge Centre for Data-Driven Discovery (C2D3).

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.