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Analysis of bulk RNA-seq data Wed 25 Mar 2020   09:30 [Full]

The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data.

This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Analysis of DNA Methylation using Sequencing Wed 20 Nov 2019   09:30 [Full]

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 will be comprised of a mixture of theoretical lectures and practicals covering a range of different software packages.

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 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.

Analysis of mapped NGS data with SeqMonk Wed 3 Feb 2016   09:30 Finished

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 by linking here.

Analysis of RNA-seq data with Bioconductor Wed 28 Mar 2018   09:30 Finished

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.

Analysis of single cell RNA-seq data Mon 16 Dec 2019   09:30 [Full]

Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging.

In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq.

The course website providing links to the course materials can be found here.

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 small RNA-seq data new Tue 2 May 2017   09:30 Finished

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.

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.

An Introduction to Machine Learning Wed 19 Feb 2020   09:30 [Full]

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.

An Introduction to MATLAB for biologists Mon 17 Jun 2019   09:30 Finished

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.

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 overview of metabolomics and its applications in life sciences, clinical and environmental settings. Over 2 days 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.

The course content will predominantly be based on analysing samples from model plant species such as Arabidopsis thaliana but the procedures are transferable to all other organisms, including clinical and environmental settings.

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.

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 aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs.

Course materials are available here.

Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Concepts and strategies for working more effectively with Python are now the focus of a new 2-days course, Data Science in Python.

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.

An Introduction to Solving Biological Problems with R Tue 11 Jun 2019   09:30 Finished

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!

This Autumn 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 Big Data.

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.

Bacterial Genome Assembly and Annotation in Galaxy new Thu 8 Jun 2017   09:30 Finished

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.

Basic statistics and data handling Wed 28 Feb 2018   09:30 Finished

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.

Big Data and Cloud Computing new Fri 1 Jun 2018   09:30 Finished

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.

Bioinformatics for Principal Investigators Mon 16 Sep 2019   09:30 Finished

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.

InterMine is a freely available data integration and analysis system that has been used to create a suite of databases for the analysis of large and complex biological data sets.

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants, nematodes, fly, zebrafish and more recently human. See here for a comprehensive list of InterMine databases.

The InterMine web interface offers sophisticated query and visualisation tools, as well as comprehensive web services for bioinformaticians. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression.

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.

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

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.

Biological data analysis using the InterMine API new Wed 19 Jun 2019   13:30 Finished

InterMine is a freely available data integration and analysis system that has been used to create a suite of databases for the analysis of large and complex biological data sets.

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants, nematodes, fly, zebrafish and more recently human. See here for a comprehensive list of InterMine databases. 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 an extensive API; this course will focus on programmatic access to InterMine through its API and on running InterMine searches using Python, Perl 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.

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.

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.

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.

ChIP-seq and ATAC-seq analysis Wed 23 Oct 2019   09:30 Finished

The primary aim of this course is to familiarise participants with the analysis of ChIP-seq and ATAC-seq data and provide hands-on training on the latest analytical approaches.

The course starts with an introduction to ChIP-seq experiments for the detection of genome-wide DNA binding sites of transcription factors and other proteins. We first show data quality control and basic analytical steps such as alignment, peak calling and motif analysis, followed by practical examples on how to work with biological replicates and fundamental quality metrics for ChIP-seq datasets. On the second day, we then focus on the analysis of differential binding, comparing between different samples. We will also give an introduction to ATAC-seq data analysis for the detection of regions of open chromatin.

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.

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.

CRUK: Analysis of publicly available microarray data Mon 20 Feb 2017   09:30 Finished

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.

CRUK: Beginners guide to version control with git Wed 2 Nov 2016   13:30 Finished

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.

CRUK: Experimental Design Mon 28 Oct 2019   10:00 Finished

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.

CRUK: Image Analysis with Cellprofiler new Mon 2 Jul 2018   12:30 Finished

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.

CRUK: Image Analysis with Fiji Fri 26 Jul 2019   12:30 Finished

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.

CRUK: Introduction to Command Line Linux Mon 11 Nov 2019   09:30 Finished

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.

CRUK: Introduction to Linear Modelling with R Tue 5 Mar 2019   09:45 Finished

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.

CRUK: Introduction to Statistical Analysis Tue 26 Nov 2019   09:30 [Places]

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.

This course provides a refresher on the foundations of statistical analysis. Practicals are conducted using the R commander package, which provides an accessible interface to the R statistical language.

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

Modern genomics technologies are able to produce large volumes of data that often leave researchers feeling overwhelmed and unsure of how to begin the process of biological interpretation.

In this course, we explain the common file formats generated by sequencing technologies and how they can be manipulated and explored by non-bioinformaticians. The tool that we will use is the Integrative Genomics Viewer (IGV).

If time allows, there will be time at the end of the session for you to explore your own datasets with the assistance of the instructors.

This event is part of a series of training courses organized in collaboration with Dr. Mark Dunning at CRUK Cambridge Institute. The materials for the course were developed in collaboration with Dr. Thomas Carroll from the MRC CSC.

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

CRUK: Managing your Research Data Tue 26 Feb 2019   12:30 Finished

How much data would you lose if your laptop was stolen? Have you ever emailed your colleague a file named 'final_final_versionEDITED'? Have you ever struggled to import your spreadsheets into R? Would you be able to write a Data Management Plan as part of a grant proposal?

As a researcher, you will encounter research data in many forms, ranging from measurements, numbers and images to documents and publications. Whether you create, receive or collect data, you will certainly need to organise it at some stage of your project. This workshop will provide an overview of some basic principles on how we can work with data more effectively. We will discuss the best practices for research data management and organisation so that our research is auditable and reproducible by ourselves, and others, in the future.

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.

This course has the following objectives:

  • To provide an overview on the importance of microscopy image analysis and tools in Arivis Vision4D software for the quantification of various biological problems: cell analysis, time-lapse, colocalization, stitching, handle large images etc
  • Practical session with computers during which participants will be introduced to image analysis and visualization using Vision4D
  • Demonstration on how virtual reality can help with image visualization and quantification

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.

CRUK Summer School Mon 24 Jul 2017   09:30 Finished

CRUK Summer School

Event posted for Administration purposes only

CRUK: Using the Ensembl Genome Browser Mon 18 Apr 2016   09:30 Finished

The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This one-day 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.

There may be some tools and topics that do not apply to non-vertebrates; if you have any questions about this, please email the Ensembl Outreach Project Leader, Emily Perry.

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.

Data Carpentry in R Mon 1 Apr 2019   09:30 Finished

In many domains of research the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analysing and sharing data.

Data Carpentry workshops are designed to teach basic concepts, skills and tools for working more effectively with data, using a combination of tools with a main focus in R. The workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of programming, shell scripting, or command line tools.

Course materials are available here.

This course is organised in collaboration with ElixirUK and the Software Sustainability Institute.

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.

Data Manipulation and Visualisation in R Mon 10 Jun 2019   09:30 Finished

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

This course introduces some relatively new additions to the R programming language: dplyr and ggplot2. In combination these R packages provide a powerful toolkit to make the process of manipulating and visualising data easy and intuitive.

Materials for this course can be found here.

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 by linking here.

Data Science in Python Tue 11 Feb 2020   09:30 [Full]

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.

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 three day workshop will bring together representatives of the ELIXIR Galaxy Working Group, as well as trainers and developers working on the Galaxy project from Europe and beyond, to:

  • Build on an existing collection of Galaxy training materials. During the workshop we will collate additional materials, including topics relevant to the ELIXIR use-cases, and ensure that, for each workflow, a minimum set of training materials is available, including slides, practical exercises, Docker containers, and Galaxy tours.
  • Improve materials’ annotations (introducing full BioSchemas compliance) and align them with existing ELIXIR efforts (linking to TeSS). During the workshop materials will be curated to ensure they are properly described, according to the ELIXIR/GOBLET guidelines, and BioSchemas compliant.
  • Extend the existing “curated” dataset collection and assign DOI to individual datasets.
  • Increase the number of Docker/Virtual Machines available for easy installation of Galaxy training environments.
  • Explore the feasibility of developing a toolkit to facilitate plug in of different datasets in existing training material/workflows through a templating approach.

This event is supported by ELIXIR-EXCELERATE, an European Commission grant within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.

EMBL-EBI: An Introduction to Sequence Searching Fri 12 Apr 2019   09:00 Finished

This module introduces the area of sequence similarity searching and focuses on how to use tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases, including tips on which tool and database to use, input formats, how to change parameters and how to interpret the results pages.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

EMBL-EBI: Bioinformatics resources for protein biology new Mon 29 Apr 2019   09:30 Finished

Are you aware of the wide range of protein data resources that can easily be accessed and explored to enhance your research? Do you want to know more about the sequence of your protein and its functions? Wondered whether a structure of your protein exists and how to explore it? Want to know more about the potential complexes and reaction pathways your protein of interest is involved in, giving you a better overview of its biological context?

This three day workshop will introduce you to data resources and tools developed by EMBL-EBI that can help you in your protein studies. Each day will focus on a particular protein topic, with the aim of helping you get more from your data and also to explore publically-available data that can further support your research.

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 clicking here.

EMBL-EBI: Ensembl Variant Effect Predictor (VEP) new Thu 15 Feb 2018   13:30 Finished

This interactive workshop offers participants hands-on experience in the use of the Ensembl VEP to annotate genetic variants with the effects they have on Ensembl genes, and the known information about co-located variants. We will also look at known genes and variants, including the types of data available and where they come from.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

EMBL-EBI: European Variation Archive Thu 15 Feb 2018   09:30 CANCELLED

This interactive workshop offers participants hands-on experience in the use of the European Variation Archive, EVA. The EVA is an open-access, genetic variation data repository, currently hosting more than 80 studies describing in excess of 520 million unique variants. Participants will be shown how this data can be searched for at the study level via the EVA Study Browser, or at the individual variant level, via our Variant Browser. Finally, participants shall also be shown how to access this wealth of genetic variation data via the EVA API.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

EMBL-EBI: Interactions & Pathways Tue 13 Mar 2018   09:30 Finished

This workshop is aimed at giving life scientists training on how to explore and use protein interaction and pathway bioinformatics resources. This course looks at the data repositories, resources and tools available and shows attendees how to both find information on a single molecule and how to build high-quality networks to enable network analysis.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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 give an introduction to the protein interaction database IntAct and the Complex Portal service. You will also briefly learn how to visualise protein interactions using the Cytoscape application.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

EMBL-EBI: Interactions & Pathways - Reactome Tue 28 Feb 2017   09:00 Finished

This workshop will give an introduction to the Reactome pathway database website and analysis tools, using short presentations and practical hands-on exercises. The session will also explain where to learn more, get help, and how to become involved in adding more pathway information to Reactome.

Further information can be found here.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

EMBL-EBI: Introduction to Chemogenomics Resources Mon 6 Feb 2017   09:30 Finished

An introduction to the chemogenomics resources available from the EBI. The workshop will cover resources such as ChEMBL, SureChEMBL, UniChem and Open Targets.

This session is one of a series of short introductions to EBI Services, run together, but bookable separately (see Related Courses section below).

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.

EMBL-EBI: Introduction to EMBL-EBI resources Mon 23 Jan 2017   09:30 Finished

This workshop is an introduction to EMBL-EBI and the life science data resources it provides. Participants will be shown how to navigate the website and search for appropriate database resources and tools, whilst also highlighting resources such as Train online (our e-learning portal) and the literature resources at Europe PMC.

This workshop will not focus on a set of specific resources; for more focused workshops please see the others within this series (see the Related Courses section below)

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

EMBL-EBI: Introduction to Interpro new Tue 27 Feb 2018   09:00 Finished

Employ InterPro to help you answer your research questions!

This workshop will help you find out why there is a need to automatically annotate proteins, how protein family databases can help meet this challenge, and how InterPro pulls together a number of such databases, allowing you to classify unknown protein sequences and identify their function. The module is a combination of presentations and hands-on practical exercises. You will explore the various features of an InterPro entry, and design a workflow to utilise InterPro in the analysis of real world data.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

The European Nucleotide Sequence Archive (ENA) is a global database for storing experimental nucleotide data and also interpreted data (alignment files, variant calling, analysis results). The data is submitted by scientists conducting sequencing experiments and publishing research in the area. Data is fully searchable and available for download. Sequence data includes raw NGS files (FastQ, BAM…), assembled genomes and transcriptomes, and annotated sequences (protein coding genes, non coding RNA, barcode genes, HLA genes)

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

EMBL-EBI: Network Analysis with Cytoscape and PSICQUIC Wed 22 May 2019   09:30 Finished

This module provides an introduction to the theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to analyse large-scale datasets generated these to by techniques such as RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of Cytoscape and selected network analysis apps.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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 will give an introduction to the basic concepts of ontologies and how they are useful in biological applications. We will explain what a biomedical ontology is and present the two primary types of ontology: (i) domain ontology and (ii) application ontology, using examples as Gene Ontology (GO) and Experimental Factor Ontology (EFO). The module will also go into details of why big data need ontologies and the ontology capabilities in advanced computational biology.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

EMBL-EBI: Protein Sequence Databases with UniProt Mon 5 Feb 2018   09:30 Finished

This workshop aims to give the scientific community hands on experience on how to access and effectively use protein data in UniProt. UniProt is a high-quality, comprehensively and thoroughly annotated protein resource. Participants will be able to access detailed information on protein function and millions of protein sequences in the UniProt knowledgebase, including isoforms and disease variants.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

EMBL-EBI: Transcriptomics Data and Tools Fri 17 May 2019   09:30 Finished

This workshop is designed for researchers interested in learning about functional genomics data, how to access, retrieve and use the data from ArrayExpress and hands-on experience in using Expression Atlas, a resource to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others. This will include an overview on how gene expression data is curated and analysed in Expression Atlas and a practical activity to demonstrate how to access and visualise gene expression analysis results. These activities should help you answer questions such as "where is my favourite gene expressed?" or "how does its expression change in a disease?".

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

Ensembl REST API workshop Thu 11 Apr 2019   09:30 Finished

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.

What are the cognitive differences between novices, competent practitioners, and experts? Do different people really have different learning styles? Do flipped classrooms actually work better than regular lectures? This tutorial will explore recent research in these areas and more, and show participants how to apply that research in the classroom to improve teaching.

This tutorial is a condensed version of the instructor training program that Software Carpentry has been running for the past three years. In it, we will explore a handful of research results in educational psychology, and see how to use those findings to build more effective lessons.

Greg Wilson is the Executive Director of the Software Carpentry Foundation, a volunteer non-profit organization that teaches researchers basic lab skills for scientific computing.

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

This event will consist of two parts. The first part of the workshop aims to provide new trainers with guidance and tips for developing and delivering training in bioinformatics, exploring a range of methods appropriate to different learning styles and examining the requirements for a successful course (both scientific and logistic). It will be based on the EXCELERATE Train-the-Trainer (TtT) course materials and content will be tailored to trainers that are involved in teaching bioinformatics to clinical audiences.

The second part of the workshop will focus on "Best practices in clinical bioinformatics training", providing an opportunity for people already involved in this kind of training, or in the process of developing it, to come together and exchange best practice/experiences. Participants will include training providers of the Health Education England’s MSc in Genomics Medicine from several UK Universities as well as other providers active in this area, from around Europe and beyond.

This event is co-sponsored by ELIXIR-EXCELERATE and Health Education England (HEE).

This course will present a set of R/Bioconductor packages to access, manipulate, visualise and analyse mass spectrometry (MS) and quantitative proteomics data.

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.

Extracting biological information from gene lists Thu 23 Jan 2020   09:30 [Full]

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.

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.

Finding and accessing human genome data new Mon 13 Mar 2017   09:30 Finished

Researchers rely on acquiring external data to validate, benchmark and supplement research findings. Funders require researchers to make their datasets accessible for further reuse.

The goal of this workshop is to bring to the fore existing challenges with genomic data access and reuse. We will introduce a number of tools and resources to simplify #dataaccess and #datasharing.

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

This 2-days workshop will bring together bioimage analysts, trainers and developers from NEUBIAS, EuroBioImaging and Global BioImaging, as well as ELIXIR’s Bioschemas and TeSS developers, and anyone willing to contribute, to foster new collaborations between ELIXIR and key initiatives from the image analysis community, to:

  • Build a collection of curated image analysis training materials. Many materials are currently available online for several topics but no consistent curation has been applied to them to make them easily discoverable. During the workshop we will collate materials and ensure that, for each image analysis workflow, a minimum set of training materials is available, including slides, practical exercises, Docker container, etc.
  • Improve materials’ annotations (introducing full BioSchemas compliance) and align them with existing ELIXIR efforts (linking to TeSS). During the workshop, materials will be curated to ensure that they are properly described, according to the existing ELIXIR guidelines, and BioSchemas compliant. Consequently the curation will enable materials, hosted by individual providers, to be discoverable via TeSS.
  • Increase the number of Docker/Virtual Machines (VMs) available for easy installation of image analysis training environments. We will focus on: (i) specific pipelines for which containers currently do not exist, (ii) workflows that are of interest to the NEUBIAS/GBI communities and (iii) for which expertise will be available among the workshop participants. This would be incredibly helpful for running future image analysis courses, including the next GBI course planned for October 2018, as it would increase portability of training environments, reducing the burden of lengthy, and often troublesome, software installations.
Genome Annotation with Artemis Thu 28 May 2015   09:30 Finished

This one day workshop aims to give an introduction to Artemis and ACT (Artemis Comparison Tool). Both tools enable the visualization, analysis and comparison of genome data. They are freely available for all operating systems and can be downloaded here. This is a hands-on course with short talks introducing the tools. The course is taught by members of the Pathogen and Parasite Genomic Teams from the Wellcome Trust Sanger Institute.

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 by linking here.

High Performance Computing: An Introduction Thu 18 Oct 2018   09:30 Finished

The course aims to give an introductory overview of High Performance Computing (HPC) in general, and of the facilities of the High Performance Computing Service (HPCS) available at the University of Cambridge.

Practical examples of using the HPCS clusters will be used throughout, although it is hoped that much of the content will have applicability to systems elsewhere.

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.

A hands-on interactive course that will introduce you to how to analyse genomic sequences in the command line environment. Examples will focus on metagenomics data but the course is suitable to anyone starting to analyze high-throughput sequencing data.

This course will be taught by Dr. Adina Howe from Iowa State University. Her group focuses on integrating traditional microbiology approaches with metagenomics and computational biology as investigative tools to understand environmental microbial populations

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

IAFIG-RMS: Bioimage analysis with Python new charged Mon 9 Dec 2019   09:30 [Full]

THIS EVENT IS NOW FULLY BOOKED!

The aim of this 5 days course is to develop motivated participants toward becoming independent BioImage Analysts in an imaging facility or research role. Participants will be taught theory and algorithms relating to bioimage analysis using Python as the primary coding language.

Lectures will focus on image analysis theory and applications. Topics to be covered include: Image Analysis and image processing, Python and Jupyter notebooks, Visualisation, Fiji to Python, Segmentation, Omero and Python, Image Registration, Colocalisation, Time-series analysis, Tracking, Machine Learning, and Applied Machine Learning.

The bulk of the practical work will focus on Python and how to code algorithms and handle data using Python. Fiji will be used as a tool to facilitate image analysis. Omero will be described and used for some interactive coding challenges.

Research spotlight talks will demonstrate research of instructors/scientists using taught techniques in the wild.

This event is organized in collaboration with the Image Analysis Focused Interest Group and is sponsored by the Royal Microscopical Society.

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.

Image Analysis for Biologists Mon 11 Dec 2017   09:30 Finished

This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines.

On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based on Fiji, an extensible open source software package.

On day 2, we will cover time series processing and cell tracking using TrackMate. The afternoon of day two will focus on understanding the basics of deconvolution and colocalisation, using tools in Fiji to look at basic examples of how to apply deconvolution and how to carry out colocalisation analysis in fluorescence microscopy.

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.

Image Analysis for Biologists Mon 24 Jun 2019   09:30 Finished

This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines.

On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based on Fiji, an extensible open source software package.

On day 2, we will cover time series processing and cell tracking using TrackMate and advanced image segmentation using Ilastik. Additionally, in the afternoon we will run a study design and data clinic (sign up will be required) for participants that wish to discuss their experiments.

On day 3, we will describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualisation, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager).

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.

Image Processing and Visualisation with LithoGraphX new Thu 4 Aug 2016   10:00 Finished

LithoGraphX is a software to visualize, process and analyse 3D images and meshes.

On the first day of this course, we will demonstrate how to use LithoGraphX to visualize, clean and process 2D and 3D images. We will cover: (i) how to extract cell shape from 2D or 3D images by marking the cell wall or membrane, (ii) how to extract key morphological features and (iii) how to use these features to build a cell classifier. The first day is intended for biologists and computer scientists interested in using LithoGraphX.

On the second day, we will see how to write and distribute extensions to LithoGraphX. To this purpose, we will learn more about the internals of LithoGraphX and its API both in C++ and Python. The second day is intended for computer scientists wanting either to write their own algorithm or automate complex protocols.

Participants can choose to register for both days or for individual days, depending on their interest and background knowledge.

The timetable for this event can be found here.

This course is organized in collaboration with Dr Susana Sauret-Gueto from the OpenPlant Lab of the Department of Plant Sciences of the University of Cambridge.

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.

Interpreting the clinical genome with DECIPHER new Fri 8 Jul 2016   09:30 Finished

DECIPHER is a collaborative data sharing and interpretation platform that enables the secure upload, analysis and subsequent sharing of anonymised phenotype-linked patient variant data in rare genetic disorders.

DECIPHER is a worldwide user community of over 250 clinical genetics centres and research groups from over 40 countries that utilise the built-in tools for aiding the interpretation of variants as well as to discover other patients that share similar phenotype and genomic findings.

DECIPHER facilitates collaboration and exchange of information between a global community of clinical centers and researchers leading thereby accelerating discovery and diagnosis. Access to consented anonymised records is free to all users. User accounts are provided to bona-fide clinicians and lab scientists to enable deposition and sharing of anonymised patient data.

The purpose of this half-day workshop is to acquaint participants with the DECIPHER website and database and introduce the various built-in tools for visualisation and interpretation of phenotype-linked genomic variation in anonymised consented patient data. It is hoped that by the end of this workshop, users will be able to carry out effective searches of data, use the built-in genome browser to visualise variation in context of other pathogenic and reference data sources, find other patients with similar variants and shared phenotypes, and identify most likely causes of phenotypic presentation by gene prioritisation.

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 (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.

Introduction to genome variation analysis using NGS Thu 18 May 2017   09:30 Finished

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.

Introduction to R for Biologists Wed 15 Jan 2020   09:30 [Full]

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.

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.

Introduction to RNA-seq and ChIP-seq data analysis Wed 25 Oct 2017   09:30 Finished

The aim of this course is to familiarize the participants with the primary analysis of datasets generated through two popular high-throughput sequencing (HTS) assays: ChIP-seq and RNA-seq.

This course starts with a brief introduction to the transition from capillary to high-throughput sequencing (HTS) and discusses quality control issues, which are common among all HTS datasets. Next, we will present the alignment step and how it differs between the two analysis workflows. Finally, we focus on dataset specific downstream analysis, including peak calling and motif analysis for ChIP-seq and quantification of expression, transcriptome assembly and differential expression analysis for 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.

Introduction to Scientific Figure Design Fri 11 Oct 2019   09:30 Finished

This course provides a practical guide to producing figures for use in reports and publications.

It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures.

The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools.

Further information and access to the course materials is here.

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 provides a practical guide to producing figures for use in reports and publications.

It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures.

The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools.

Further information and access 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 or register Interest by linking here.

Introduction to Unix shell new Wed 17 Oct 2018   09:30 Finished

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.

Introduction to working with UNIX and bash new Thu 6 Feb 2020   09:30 [Places]

Using the Linux operating system and the bash command line interface, we will demonstrate the basic structure of the UNIX operating system and how we can interact with it using a basic set of commands. Applying this, we will learn how to navigate the filesystem, manipulate text-based data and structure simple pipelines out of these commands.

Building on this foundation, the course will use a bioinformatics example to demonstrate how the skills learnt can be applied to connecting to external resources/servers, installing specialist tools and ultimately combining commands into scripts for automation and reproducibility.

This course is targeted at participants with no prior experience working with UNIX-like systems (OSX, Linux) or command line interfaces.

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.

Molecular Phylogenetics Wed 3 Apr 2019   09:00 Finished

This course will provide training for bench-based biologists to use molecular data to construct and interpret phylogenies, and test their hypotheses. Delegates will gain hands-on practice of using a variety of programs freely-available online and commonly used in molecular studies, interspersed with some lectures.

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.

Mouse Genome Informatics workshop new Tue 27 Oct 2015   10:00 Finished

Mouse Genome Informatics (MGI) is the international database resource for the laboratory mouse and provides integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

MGI is a free, highly curated resource and offers web and programmatic access to a complete catalogue of mouse genes and genome features, functional annotations, a comprehensive catalogue of mutant and knockout alleles, phenotype and human disease model annotations, gene expression, variation and sequence data.

This workshop will be composed of ~20min overview and ~1 hour hands-on, interactive tutorial.

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

MSt in Genomic Medicine - Advanced bioinformatics Mon 20 Mar 2017   09:30 Finished

This module introduces a deeper exploration of bioinformatics analysis of genomic data, providing a greater understanding of the different approaches to mapping and alignment of genome sequence data, programming and scripting, along with approaches for the detection and analysis of genomic changes, gene expression and network analysis.

Network Visualisation and Analysis of Biological Data new Thu 14 Apr 2016   09:30 Finished

This two day course will cover network-based approaches to visualise and analyse complex biological ‘big’ data and model pathway systems. The course will be centred on the use of BioLayout Express3D, a tool developed between scientists at the University of Edinburgh and EBI over the last 10 years.

BioLayout provides rapid and versatile means to explore and integrate very large datasets, providing a stunning interface to visualise the relationships between 10’s of thousands of data points. Originally designed for the analysis of microarray data, it is equally effective in analysing data matrices from other analysis platforms.

Day one of the course will introduce principles of network analysis and their use as a generic medium to understand relationships between entities. We will introduce the basics of network visualisation and navigation within BioLayout and principles of correlation analysis of data matrices. We will then explore how data can be explored and clustered within the tool and how you can use the software to rapidly extract meaning from large and complex datasets.

Day two will focus on pathway modelling. We will explain how to collate information about a given system of interest from the literature, and to turn this information into a logic-based pathway model. We will then explore how these models can be parametrised and imported into BioLayout where simulations can be run that model the dynamics of these systems under different conditions. For more information see: http://www.virtuallyimmune.org/

A draft agenda 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 Interest by linking here.

Next Generation Sequencing data analysis Tue 17 Mar 2015   09:00 Finished

This course provides an introduction to next generation sequencing (NGS) 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 NGS technologies and bioinformatics methods in their research.

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 or register Interest by linking here.

  • Nowomics - Access to the latest data and papers relevant to your research
  • Nowomics is a new website to help biologists stay up to date with the latest data and papers relevant to their research. Try it here.
  • Nowomics tracks new papers and many types of data in online repositories. You ‘follow’ the genes and processes you work on to see a Twitter-like news feed of new papers, annotation, interactions, curated comments and more.
  • For each gene you can also include information from orthologues and related genes directly in your news feed.
  • Data are currently included for human, mouse, rat, fly and plant.
  • This short workshop will show you how to use the Beta version of Nowomics to find the latest information for genes & keywords, how to set up your personalised news feed and configure email alerts. We’ll also demonstrate new portals to help researchers working on Drosophila or Arabidopsis find the latest and most popular papers.

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

Ontologies and ontology-based data analysis Wed 21 Nov 2018   10:00 Finished

Ontologies have long provided a core foundation in the organization of biomedical entities, their attributes, and their relationships. With over 500 biomedical ontologies currently available there are a number of new and exciting opportunities emerging in using ontologies for large scale data sharing and data analysis.

This tutorial will help you understand what ontologies are and how they are being used in computational biology and bioinformatics. It will include hands-on examples and exercises and an introduction to Onto2Vec and OPA2Vec, two methods that can be used to learn semantic similarity measures in a data- and application-driven way.

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.

Open Targets is a public-private partnership to use human genetics, genomic data and drug information for systematic identification and prioritisation of therapeutic targets. This module introduces the Open Targets partnership, its underlying projects and the bioinformatics resources for researchers studying associations of human genes with diseases.

We offer interactive and hands-on experience with Open Targets Platform and Open Targets Genetics, open source tools of integrated biological and chemical data for drug target identification and prioritisation. We cover user cases relevant to the biomedical and pharmaceutical communities and can customise the course according to specific therapeutic areas.

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.

Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA.

Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication.

The course involves of a mixture of talks and hands-on exercises.

Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview.

Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch.

Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues.

There will be opportunities for attendees to get advice on analysis of their own sequence families.

Further information, including some training videos, is also available.

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

Protein Structure Analysis new Thu 24 May 2018   09:30 Finished

This course covers data resources and analytical approaches for the discovery and interpretation of biomacromolecular structures.

Day 1 focuses on public repositories of structural data (Protein Data Bank and Electron Microscopy Data Bank) and resources for protein analysis and classification (Pfam, InterPro and HMMER).

Day 2 covers how to find information about the structure and function of your protein sequence using CATH, principles of modern state-of-the-art protein modelling with Phyre2 and methods for predicting the effects of mutations on protein structure and function using the SAAP family of tools.

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

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