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In this course you will acquire practical skills in RNA-seq data analysis. You will learn about quality control, alignment, and quantification of gene expression against a reference transcriptome. Additionally, you will learn to conduct downstream analysis in R, exploring techniques like PCA and clustering for exploratory analysis. The course also covers differential expression analysis using the DESeq2 R/Bioconductor package. Furthermore, the course covers how to generate visualisations like heatmaps and performing gene set testing to link differential genes with established biological functions or 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.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to identify binding sites for transcription factors, histone modifications and other DNA-binding proteins across the genome. In this course, we will cover the fundamentals of ChIP-seq data analysis, from raw data to downstream applications.

We will start with an introduction to ChIP-seq methods and cover the bioinformatic steps in processing ChIP-seq data. We will then introduce the use of the graphical program SeqMonk to explore and visualise your data. Finally, you will perform peak calling and perform differential enrichment 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 will cover all aspects of the analysis of DNA methylation using sequencing, including primary analysis, mapping and quality control of BS-Seq data, common pitfalls and complications.

It will also include exploratory analysis of methylation, looking at different methods of quantitation, and a variety of ways of looking more widely at the distribution of methylation over the genome. Finally the course will look at statistical methods to predict differential methylation.

The course comprises of a mixture of theoretical lectures and practicals covering a range of different software packages.

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 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.

• ♿ 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 advanced course will cover high-throughput sequencing data processing, ChIP-seq data analysis (including alignment, peak calling), differences in analyses methods for transcription factors (TF) binding and epigenomic datasets, a range of downstream analysis methods for extracting meaningful biology from ChIP-seq data and will provide an introduction to the analysis of open chromatin with ATAC-seq and long-distance interactions with chromosomal conformation capture based Hi-C datasets.

Materials for this course can be found 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.

This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing (HTS) data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in bam format. We will also describe the various resources available through Bioconductor to annotate and visualize HTS data, which can be applied to any type of sequencing experiment.

The course timetable is available here.

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

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.

SeqMonk is a graphical program for the visualisation and analysis of large mapped sequencing datasets such as ChIP-Seq, RNA-Seq, and BS-Seq.

The program allows you to view your reads against an annotated genome and to quantitate and filter your data to let you identify regions of interest. It is a friendly way to explore and analysis very large datasets.

This course provides an introduction to the main features of SeqMonk and will run through the analysis of a couple of different datasets to show what sort of analysis options it provides.

Further information is 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.

This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq data. We will present a workflow for the analysis RNA-seq data starting from aligned reads in bam format and producing a list of differentially-expressed genes. We will also describe the various resources available through Bioconductor to annotate, visualise and gain biological insight from the differential expression results.

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

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.

• ♿ 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 focuses on methods for the analysis of small non-coding RNA data obtained from high-throughput sequencing (HTS) applications (small RNA-seq). During the course, approaches to the investigation of all classes of small non-coding RNAs will be presented, in all organisms.

Day 1 will focus on the analysis of microRNAs and day 2 will cover the analysis of other types of small RNAs, including Piwi-interacting (piRNA), small interfering (siRNA), small nucleolar (snoRNA) and tRNA-derived (tsRNA).

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

This webinar is an Introduction to Biological Networks, their types, and applications. It will include two of the most commonly used open source Network Visualisation Platforms (R-igraph and Cytoscape) with step-wise protocols for creating and visualising your own data as a network. It will present some of the major layout algorithms, visual styles and tips for effective visualisation, with examples from biology revealing how these can improve analysis and provide insights.

The webinar will be presented in the form of a lecture as well as a tutorial with step-wise screenshots that enable listeners to emulate simple Network creation and analysis. Please note that this is a webinar and not a coding exercise. Links to publicly available resources and hands-on tutorials will be shared with you for further reading and practice.

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.

Through the use of real world examples and the JMP, JMP Pro, and JMP Genomics software, we will cover best practices used in both industry and academia today to visually explore data, plan biological experiments, detect differential expression patterns, find signals in next-generation sequencing data and easily discover statistically appropriate biomarker profiles and patterns.

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 whole genome data unearths a multitude of variants of different classes, which need to be filtered, annotated and validated to arrive at a causative variant for a disease. The current short length sequences, whilst being excellent at identifying single nucleotide variants and short insertions/deletions, struggle to correctly map structural variants (SVs). Long-read sequencing technologies offer improvements in the characterisation of genetic variation and regions that are difficult to assess with short-read sequences.

The aim of this course is to familiarise participants with long read sequencing technologies, their applications and the bioinformatics tools used to assemble this kind of data. Lectures will introduce this technology and provide insight into methods for the analysis of genomic data, while the hands-on sessions will allow participants to run analysis pipelines, focusing on data generated by the Oxford Nanopore Technologies (ONT) platform.

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.

THIS COURSE IS NOT RETURNING IN ITS CURRENT FORM. PLEASE CHECK OUR WEBSITE FOR MORE INFORMATION.

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.

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 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.

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 aim of this course is to introduce participants to the basics of statistical analysis and the open source statistical software R, a free software environment for statistical computing and graphics.

Participants will actively use R throughout the course, during which they will be introduced to principles of statistical thinking and interpretation by example, exercises and discussion about a range of problems. The examples will be used to present a variety of statistical concepts and techniques, with no focus on any specific discipline.

Important information: We have 12 configured laptops for use at the workshop. After these laptops have been allocated, participants will either need to share, or bring their own. These laptops will be allocated to the first individuals to express an interest in using them. When booking, please indicate under "Special requirements" if you wish to use one of the 12 laptops or bring your own. Participants bringing their own laptop will be given instructions on what software to install.

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.

This course is aimed at those new to programming and provides an introduction to programming using Perl.

During this course you will learn the basics of the Perl programming language, including how to store data in Perl’s standard data structures such as arrays and hashes, and how to process data using loops, functions, and many of Perl’s built in operators. You will learn how to write and run your own Perl scripts and how to pass options and files to them. The course also covers sorting, regular expressions, references and multi-dimensional data structures.

The course will be taught using the online Learning Perl materials created by Sofia Robb of the University of California Riverside.

The course website providing links to the course materials is 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 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.

Please note that this course has been discontinued and has been replaced by the Introduction to R for biologists.

R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research.

In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided.

The course website providing links to the course materials is here.

Please note that although we will demonstrate how to perform statistical analysis in R, we will not cover the theory of statistical analysis in this course. Those seeking an in-depth explanation of how to perform and interpret statistical tests are advised to see the list of Related courses. Moreover, those with some programming experience in other languages (e.g. Python, Perl) might wish to attend the follow-on Data Analysis and Visualisation in R course.

This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1).

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.

THIS EVENT IS NOW FULLY BOOKED!

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 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).

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 workshop will cover the basics of de novo genome assembly using a small genome example. This includes project planning steps, selecting fragment sizes, initial assembly of reads into fully covered contigs, and then assembling those contigs into larger scaffolds that may include gaps. The end result will be a set of contigs and scaffolds with sufficient average length to perform further analysis on, including genome annotation (link to that nomination). This workshop will use tools and methods targeted at small genomes. The basics of assembly and scaffolding presented here will be useful for building larger genomes, but the specific tools and much of the project planning will be different.

This workshop will also introduce genome annotation in the context of small genomes. We’ll begin with genome annotation concepts, and then introduce resources and tools for automatically annotating small genomes. The workshop will finish with a review of options for further automatic and manual tuning of the annotation, and for maintaining it as new assemblies or information becomes available.

This session will include an introduction to the Galaxy platform.

This event is co-organized with EMBL-ABR and the Genomics Virtual Lab. Course materials 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 three day course is intended to open doors to applying statistics - whether directly increasing skills and personally undertaking analyses, or by expanding knowledge towards identifying collaborators. The end goal is to drive confident engagement with data analysis and further training - increasing the quality and reliability of interpretation, and putting that interpretation and subsequent presentation into the hands of the researcher. Each day of the course will deliver a mixture of lectures, workshops and hands-on practicals – and will focus on the following specific elements.

Day 1 focuses on basic approaches and the computer skills required to do downstream analysis. Covering: Basic skills for data manipulation in R. How to prepare your data effectively. Principles of experimental design and how this influences analysis.

On day 2, participants will explore the core concepts of statistics – so that they can begin to see how they can be applied to their own work, and to also help with better critical evaluation of the work of others. Covering: Basic statistics concepts and practice: power, variability, false discovery, t-test, effect size, simulations to understand what a p-value means.

On day 3 we will continue to explore core concepts of statistics, focusing on linear regression and multiple testing correction.

Course materials are available here.

This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1).

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

Recent advances in genomics, proteomics, imaging and other technologies, have resulted in data being generated at a faster rate than they can be meaningfully analysed. In this course we will show you how cloud computing can be used to meet the challenges of storage, management and analysis of big data. The first half of the course will introduce cloud infrastructure technologies. The second half will cover tools for collaborative working, resource management, and creation of workflows. The instructors will demonstrate how they are using cloud computing in their own research.

N.B. If you sign up for this course, you will be automatically registered for an AWS educate account, which will provide you with sufficient AWS credits to complete the course exercises. If you decide to continue using cloud computing after the course, you will need to either purchase more credits or apply for a grant from programs like: AWS Cloud Credits for Research, Microsoft Azure for Research or Google Cloud Platform Education Grants.

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

In this course we will introduce web-based, open source tools to analyse and interpret high-throughput biological data.

The main focus will be g:Profiler - a toolset for finding most significant functional groups for a given gene or protein list; MEM - a query engine allowing to mine hundreds of public gene expression datasets to find most co-expressed genes based on a query gene; and ClustVis - a web tool for visualizing clustering of multivariate data using Principal Component Analysis (PCA) plot and heatmap.

MEM and g:Profiler are ELIXIR-Estonia node services.

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

This 1-week course provides an introduction to data exploration of biological data. It provides a learning journey starting with learning about how we can automate processes that can be reproduced to analyse our biological data.

The course will begin with discussing what opportunities and challenges are associated with aspects of bioinformatics analyses. We will address a subset of them in greater detail in the central part of the course and provide time for participants to practise using some of the associated bioinformatics tools.

Focusing on solutions around handling biological data, we will cover programming in R, version control, statistical analyses, and data exploration. The R component of the course will cover from the foundations of programming in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming is required. At the end of the course we will address issues relating to reusability and reproducibility.

More information about the course can be found 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.

The aim of this workshop is to provide principal investigators with an introduction to the challenges of working with biological data and to the best practices, and tools, needed to perform bioinformatics research effectively and reproducibly.

On day 1, we will cover the importance of experimental design, discuss the challenges associated with (i) the analysis of high-throughput sequencing data (utilising RNA-seq as a working example) and (ii) the application of machine learning algorithms, as well as issues relating to reusability and reproducibility.

On day 2, we will put into practice concepts from day 1, running a RNA-seq data analysis pipeline, going from raw reads through differential expression analysis and the interpretation of downstream analysis results. Challenges encountered at each step of the analytical pipeline will be discussed. Please note that day 2 is optional.

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.

This workshop will introduce students to EMBL-EBI, the databases and services it offers, and basic concepts in bioinformatics that will be of use to their disease related research work.

It will explain the role of the EMBL-EBI in curating and sharing biological data with scientists around the world, and introduce concepts for locating relevant data and information of interest.

Sessions with trainers from Ensembl, ArrayExpress and the GWAS catalog will introduce practical skills in browsing genes and variation in a genomic context, in exploring SNP-trait associations and will show how further understanding can be gained on the location and level of gene expression across the body.

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.

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. 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.

InterMine is a freely available open-source data warehouse built specifically for the integration and analysis of complex biological data sets.

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants (over 87 plant genomes), nematodes, fly, zebrafish, Hymenoptera, Planaria, and more recently human.

Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression. InterMine provides sophisticated query and visualisation tools both through a web interface and a powerful web service API, with multiple language bindings including Python and R.

This course will focus on programmatic access to InterMine through the API and InterMine searches will be done using Python and R scripts. The exercises will mainly use the fly, human and mouse databases, but the course is applicable to anyone working with data for which an InterMine database is available (a comprehensive list of InterMine databases is available here.

This event is organised alongside a half day course on Biological data analysis using the InterMine User Interface. More information on this event 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 Interest by linking here.

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. 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.

InterMine is a freely available open-source data warehouse built specifically for the integration and analysis of complex biological data.

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants (over 87 plant genomes), nematodes, fly, zebrafishHymenoptera, Planaria, and more recently human.

Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression. InterMine provides sophisticated query and visualisation tools both through a web interface and a powerful web service API, with multiple language bindings including Python and R.

This course will focus on the InterMine web interface and will introduce participants to all aspects of the user interface, starting with some simple exercises and building up to more complex analysis encompassing several analysis tools and comparative analysis across organisms. The exercises will mainly use the fly, human and mouse databases, but the course is applicable to anyone working with data for which an InterMine database is available (a comprehensive list of InterMine databases is available here.)

This event is organised alongside a half day course on Biological data analysis using the InterMine API. More information on this event is available here.

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 Open Microscopy Environment (OME) is an open-source software project that develops tools that enable access, analysis, visualization, sharing and publication of biological image data.

OME has three components:

• OME-TIFF, standardised file format and data model;
• Bio-Formats, a software library for reading proprietary image file formats; and
• OMERO, a software platform for image data management and analysis.

In this one day course, we will present the OMERO platform, and show how Facility Managers can use it to manage users, groups, and their microscopy, HCS and digital pathology data.

Help pages on 'Using OMERO for Facility Managers' can be found here.

This course is organized alongside a one day course on Biological Imaging Data Management for Life Scientists. More information on this event are available here.

This course will be delivered by members of the OMERO team. The OME project is supported by BBSRC and Wellcome Trust.

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 Open Microscopy Environment (OME) is an open-source software project that develops tools that enable access, analysis, visualization, sharing and publication of biological image data.

OME has three components:

• OME-TIFF, standardised file format and data model;
• Bio-Formats, a software library for reading proprietary image file formats; and
• OMERO, a software platform for image data management and analysis.

In this one day course, we will present the OMERO platform, and show how to import, organise, view, search, annotate and publish imaging data. Additionally, we will briefly introduce how to use a variety of processing tools with OMERO.

This course is organized alongside a one day course on Biological Imaging Data Processing for Data Scientists. More information on this event are available here.

This course will be delivered by members of the OMERO team. The OME project is supported by BBSRC and Wellcome Trust.

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 Open Microscopy Environment (OME) is an open-source software project that develops tools that enable access, analysis, visualization, sharing and publication of biological image data.

OME has three components:

• OME-TIFF, standardised file format and data model;
• Bio-Formats, a software library for reading proprietary image file formats; and
• OMERO, a software platform for image data management and analysis.

In this one day course, we will present the OMERO platform, and show how to transition from manual data processing to automated processing workflows. We will introduce how to write applications against the OMERO API, how to integrate a variety of processing tools with OMERO and how to automatically generate output ready for publication.

This course is organized alongside a one day course on Biological Imaging Data Management for Life Scientists. More information on this event are available here.

This course will be delivered by members of the OMERO team. The OME project is supported by BBSRC and Wellcome Trust.

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.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to identify binding sites for transcription factors, histone modifications and other DNA-binding proteins across the genome. In this course, we will cover the fundamentals of ChIP-seq data analysis, from raw data to downstream applications.

We will start with an introduction to ChIP-seq methods, including important considerations when designing your experiments. We will cover the bioinformatic steps in a standard ChIP-seq analysis workflow, covering raw data quality control, trimming/filtering, mapping, duplicate removal, post-mapping quality control, peak calling and peak annotation. We will discuss metrics used for quality assessment of the called peaks when multiple replicates are available, as well as the analysis of differential binding across sample groups. Throughout the course we will also cover tools and packages that can be used for visualising and exploring your results.

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.

PLEASE NOTE The Bioinformatics Team are presently teaching many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room.

Complex natural systems permeate many aspects of everyday life—including human intelligence, social media, biomedicine, agriculture, economics, even our personal and professional relationships. The past decade has seen intensification of research into structural and dynamical properties of complex networks. This course will introduce the basic principles of network theory, and hands-on DIY Network analysis using Cytoscape, one of the most widely used global platforms for construction and analysis of biomolecular networks such as gene regulatory interactions, protein complexes, hydrogen-bonding meshwork in active sites and neuronal networks. The aim is to conceptualize your own textual, tabular or genomic datasets as networks, and to understand how simple topological features can help to decipher complex properties of systems and processes.

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.

PLEASE NOTE that this course will be taught live online, with demonstrators available to help you throughout if have any questions. All lecture components will be recorded and uploaded to the course Moodle page so that you will be able to access that information even if technical or time zone restrictions means that you aren't able to join us for the live sessions.

This virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R or Python software environments. 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:

1. Use R or Python confidently for statistics and data analysis
2. Be able to analyse datasets using standard statistical techniques
3. Know which tests are and are not appropriate

Both R and Python are free software environments that are suitable for statistical and data analysis.

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 or Python and moreover know when, and when not, to apply these techniques.

The Bioinformatics Team are presently teaching this course live online, with tutors available to help you throughout if have any questions. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching in our training room.

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:

1. Use R confidently for statistics and data analysis
2. Be able to analyse datasets using standard statistical techniques
3. Know which tests are and are not appropriate

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.

This award winning 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:

1. Use R confidently for statistics and data analysis
2. Be able to analyse datasets using standard statistical techniques
3. Know which tests are and are not appropriate

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.

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.

COSMIC, the Catalogue of Somatic Mutations in Cancer, is the world’s largest and most comprehensive expert manually curated resource for exploring the impact of somatic mutations in human cancer. Based at the Wellcome Sanger Institute and available publicly at https://cancer.sanger.ac.uk/cosmic, the latest release includes almost 6 million coding mutations across 1.4 million samples from over 26,000 papers. COSMIC captures the full spectrum of genomic data relating to somatic mutations, so in addition to coding mutations, gene fusions, non-coding mutations, copy-number variants, methylation and drug resistance mutations are included.

This course will use the live COSMIC website and tools to show you how to access and explore this information, seeking to identify genetic causes and targets in all human cancers.

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.

Fiji/ImageJ is a popular open-source image analysis software application. This course will build on top of the Fiji basic course, to continue explore advanced image processing: segmentation, tracking, and with a specific focus on scripting/programming using Fiji scripting environment. We will use python programming language, and aim to give a tutorial on both image processing and python programming.

This course is run by the CRUK CI Light microscopy core facility.

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.

Although microarrays have been superseded by high-throughput sequencing technologies for gene expression profiling, years of experience gained from analysing microarray data has led to a variety of analysis techniques and datasets that can be exploited in other contexts. In this course, we will focus on retrieving and exploring microarray data from public repositories such as Gene Expression Omnibus (GEO).

Course materials can be found here.

This event is part of a series of training courses organized in collaboration with Dr. Mark Dunning at CRUK Cambridge Institute.

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 offers an introduction to working with Linux. We will describe the Linux environment so that participants can start to utilize command-line tools and feel comfortable using a text-based way of interacting with a computer. We will take a problem-solving approach, drawing on types of tasks commonly encountered by Linux users when processing text 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.

Version control is the management of changes to documents, computer programs, and other collections of information. Changes are usually identified by a number named the "revision number". Each revision is associated with a timestamp and the person making the change. Revisions can be compared, restored, and with some types of files, merged.

Version control systems like subversion (svn) and git are frequently used for groups writing software and code, but can be used for any kind of files or projects. Many people share their git repositories on GitHub.

This course will provide an introduction to git and how you can use github to share your projects, or for your own private use if you wish.

Course materials can be found here.

This event is part of a series of training courses organized in collaboration with Dr. Mark Dunning 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.

This course will provide participants with an introduction to EMBL-EBI and its data tools and resources, which cover the whole spectrum of biological / life sciences.

Sessions with trainers from ArrayExpress, Expression Atlas and the GWAS catalog will explore SNP-trait associations and show how further understanding can be gained on the location and level of gene expression across the body.

This event is part of a series of training courses organized in collaboration with Dr. Mark Dunning 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.

Modern technologies are able to deliver an unprecedented amount of data rapidly. However, without due care and attention early in the experimental process, such data are meaningless if they cannot adequately answer the intended research question. This course is aimed at those planning high-throughput experiments and highlights the kinds of questions they should be asking themselves. The course consists of a lecture and small-group discussions led by a member of the Genomics or Bioinformatics Cores.

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 your interest by linking here.

CellProfiler is a free, open-source image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

This course will introduce you the basic usage, and several application examples to help you understand and build up image processing and analysis workflows within CellProfiler. It will also cover a brief introduction to the usage of its companion package CellProfiler Analyst, which allows interactive exploration and analysis of image data. Some related theoretical topics in image processing will also be covered.

This course is run by the CRUK CI Light microscopy core facility.

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.

Fiji/ImageJ is a popular open-source image analysis software application. This course will briefly cover introductory aspects of image processing and analysis theory, but will focus on practical sessions where participants will gain hands on experience with Fiji.

This course is run by the CRUK CI Light microscopy core facility.

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.

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.

Using the Cambridge Institute's High Performance Computing Facilities, this brief (0.5 day) course will give you three things:

• A refresher on Unix and an introduction to cluster computing, i.e. what High Performance Computing facilities re available to you at CI.
• Basic instruction on using our scheduler (The scheduler allots slots of processing time to the jobs submitted by the multiplicity of users on the cluster).
• Some performance hints for efficient use of the HPC

It won't make you an expert on parallel computing and H.P.C, but will let you get to work.

Note that a pre-requisite for this course is either existing familiarity with the Unix/Linux command-line or attendance of our Linux course CRUK: Introduction to Linux Command Line.

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.

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.

A Galaxy introduction course covering basic functions, simple data manipulation using use cases and examples and visualisation mostly targeted at first time users.

Further information is available from the course website.

This event is part of a series of training courses organised in collaboration with Dr. Mark Dunning at CRUK Cambridge Institute.

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 a refresher on the foundations of statistical analysis. The emphasis is on interpreting the results of a statistical test, and being able to determine the correct test to apply.

Practicals are conducted using a series of online apps, and we will not teach a particular statistical analysis package, such as R. For courses that teach R, please see the links under "Related courses" .

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.