All Bioinformatics courses

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim 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 short (0.5 day) intensive course serves to introduce you to the command-line interface in Linux.

It is based upon elements of the Software Carpentries Shell(novice) and Shell(extras) courses. It is recommended for those CI personnel planning on attending the CI High Performance Computing facilities (Cluster) course.

This course is run by the CRUK CI Bioinformatics and IT core.

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.

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.

Galaxy (http://galaxyproject.org/) is an open, web-based platform for data intensive life science research that enables non-bioinformaticians to create, run, tune, and share bioinformatic analyses. The goal of this course is to demonstrate how to use Galaxy to explore RNA-seq data, for expression profiling, and ChIP-seq data, to assess genomic DNA binding sites. You will learn how to perform analysis in Galaxy, and then how to share, repeat, and reproduce your analyses.

The timetable for this event can be found here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book by linking here.

This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:

• an introduction to genetic variation as well as data formats and analysis workflows commonly used in NGS data analysis;
• an overview of available analytical tools and discussion of their limitations; and
• hands-on experience with common computational workflows for analysing genome sequence variation using bioinformatics and computational genomics approaches.

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.

This course provides an introduction to high-throughput sequencing (HTS) data analysis methodologies. Lectures will give insight into how biological knowledge can be generated from RNA-seq, ChIP-seq and DNA-seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq, ChIP-seq and DNA-seq data under the guidance of the lecturers and teaching assistants. It is aimed at researchers who are applying or planning to apply HTS technologies and bioinformatics methods in their research.

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.

The course will cover ANOVA, linear regression and some extensions. It will be a mixture of lectures and hands-on time using RStudio to analyse data.

This event is part of a series of training courses organized in collaboration with the Bioinformatics Core Facility at CRUK Cambridge Institute.

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.

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.

• ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.
• Guidance on visiting Cambridge and finding accommodation is available here.

This workshop will focus on the theory and applications of metagenomics for the analysis of complex microbiomes (microbial communities). We will cover a range of methods from the fastest, simplest and cheapest amplicon-based methods up to Hi-C metagenomics techniques that give highly detailed results on complex microbial communities. In addition to the theory, we will introduce several bioinformatic software packages suited for the analysis of metagenomic data, quality control and downstream analysis and interpretation of the results.

If you do not have a University of Cambridge Raven account please book or register your interest here.

• ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.

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.

• ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.
• Guidance on visiting Cambridge and finding accommodation is available here.

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.

• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.