University of Cambridge Bioinformatics Training
We offer a broad range of undergraduate and postgraduate hands-on training courses focused on bioinformatics and computational biology. These training activities aim at enabling life scientists to effectively handle and interpret biological data.
University of Cambridge Bioinformatics Training
http://training.csx.cam.ac.uk/bioinformatics/
https://tess.elixir-europe.org/content_providers/university-of-cambridge-bioinformatics-training
We offer a broad range of undergraduate and postgraduate hands-on training courses focused on bioinformatics and computational biology. These training activities aim at enabling life scientists to effectively handle and interpret biological data.
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An Introduction to Solving Biological Problems with R
14 - 15 June 2018
Cambridge, United Kingdom
An Introduction to Solving Biological Problems with R http://training.csx.cam.ac.uk/bioinformatics/event/2469414 https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-r-f5a8ccbb-243d-4201-b59e-3dda9bedfe40 [R](https://www.r-project.org/) 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](http://cambiotraining.github.io/r-intro/). 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](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-intR) course. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2469414&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20R).'' 2018-06-14 08:30:00 UTC 2018-06-15 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Open Targets: Integrating genetics and genomics for disease biology and translational medicine
12 June 2018
Cambridge, United Kingdom
Open Targets: Integrating genetics and genomics for disease biology and translational medicine http://training.csx.cam.ac.uk/bioinformatics/event/2487585 https://tess.elixir-europe.org/events/mining-gene-disease-associations-and-drug-target-validation-with-open-targets-90729d53-0eaf-43b3-880e-9ca711ec5453 Open Targets is a public-private partnership to use human genetics, genomic data and drug information for systematic identification and prioritisation of therapeutic targets. The consortium was founded in 2014 by GSK, EMBL-EBI and the Wellcome Sanger Institute. Two additional partners joined Open Targets in 2016 and 2017, Biogen and Takeda, respectively. Underpinning this partnership is the [Open Targets Platform](https://www.targetvalidation.org/), an open source, user-friendly web interface to investigate causal links between genes, pathways and diseases. These links are computed, scored and ranked using biological evidence integrated from many public [data sources](https://www.targetvalidation.org/data-sources), including the NHGRI-EBI GWAS Catalog, Genomics England, PheWAS, ClinVar, Expression Atlas, UniProt, and ChEMBL to name a few. In addition to data integration, Open Targets also generates new data using human cellular models (e.g. organoids, iPSCs) and genome editing (CRISPR/Cas9) to identify drug targets in oncology, immunology and neurodegenerative diseases. This will be publicly available in the public domain and integrated into the Open Targets Platform. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2487585&course-title=OpenTargets%20workshop).'' 2018-06-12 12:00:00 UTC 2018-06-12 15:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Pharmacogenomics Genotype and phenotype Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] This course is suitable for all users who have an interest in biomedical research and therapeutics. A special emphasis will be given on drug discovery and target validation. It will also be useful to those who seek for practical examples on how large-scale genomic experiments and computational techniques are integrated and visualised in a web platform.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Statistics for Biologists in R
21 - 22 June 2018
Cambridge, United Kingdom
Statistics for Biologists in R http://training.csx.cam.ac.uk/bioinformatics/event/2534302 https://tess.elixir-europe.org/events/statistics-for-biologists-in-r This course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences using the R software package. In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to generalised linear model analysis. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2534302&course-title=Statistics%20for%20Biologists%20in%20R).'' 2018-06-21 08:30:00 UTC 2018-06-22 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Analysis of DNA Methylation using Sequencing
27 June 2018
Cambridge, United Kingdom
Analysis of DNA Methylation using Sequencing http://training.csx.cam.ac.uk/bioinformatics/event/2426618 https://tess.elixir-europe.org/events/analysis-of-dna-methylation-using-sequencing-827a3be6-8191-4d6f-abfe-0d401570d477 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. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2426618&course-title=Analysis%20of%20DNA%20Methylation%20using%20Sequencing).'' 2018-06-27 08:30:00 UTC 2018-06-27 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Epigenetics Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
R object-oriented programming and package development
6 July 2018
Cambridge, United Kingdom
R object-oriented programming and package development http://training.csx.cam.ac.uk/bioinformatics/event/2480552 https://tess.elixir-europe.org/events/r-object-oriented-programming-and-package-development-84ec7075-b1bc-492e-a71b-d7a8d3800a44 The course will teach intermediate R object-oriented programming and how to build a fully functional R package. Relevant teaching materials are available [here](http://lgatto.github.io/TeachingMaterial/) and the sequences example package used as template in the course can be found [here](http://cran.r-project.org/web/packages/sequences/index.html). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2480552&course-title=R%20object-oriented%20programming%20and%20package%20development).'' 2018-07-06 08:30:00 UTC 2018-07-06 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Software engineering Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Using the Ensembl Genome Browser
20 July 2018
Cambridge, United Kingdom
Using the Ensembl Genome Browser http://training.csx.cam.ac.uk/bioinformatics/event/2526393 https://tess.elixir-europe.org/events/using-the-ensembl-genome-browser-4e8fa566-d250-4e95-9309-42a094810456 The [Ensembl Project](http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2526393&course-title=Using%20the%20Ensembl%20Genome%20Browser).'' 2018-07-20 08:30:00 UTC 2018-07-20 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Gene transcripts Gene structure Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Introduction to Scientific Figure Design
13 June 2018
Cambridge, United Kingdom
Introduction to Scientific Figure Design http://training.csx.cam.ac.uk/bioinformatics/event/2426612 https://tess.elixir-europe.org/events/introduction-to-scientific-figure-design-e416130c-379e-4d39-9114-95f5e23888de 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](http://www.bioinformatics.babraham.ac.uk/training.html#figuredesign). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2426612&course-title=Introduction%20to%20Scientific%20Figure%20Design).'' 2018-06-13 08:30:00 UTC 2018-06-13 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
An Introduction to MATLAB for biologists
25 - 26 June 2018
Cambridge, United Kingdom
An Introduction to MATLAB for biologists http://training.csx.cam.ac.uk/bioinformatics/event/2505664 https://tess.elixir-europe.org/events/an-introduction-to-matlab-for-biologists-26d7fc34-bf4c-4ab5-942b-6fa8b3305c43 This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2505664&course-title=An%20Introduction%20to%20MATLAB).'' 2018-06-25 08:30:00 UTC 2018-06-26 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Data Analysis and Visualisation in R
23 May 2018
Cambridge, United Kingdom
Data Analysis and Visualisation in R http://training.csx.cam.ac.uk/bioinformatics/event/2427471 https://tess.elixir-europe.org/events/data-analysis-and-visualisation-in-r-03eb127f-9e12-4f24-a246-8ec925119d7c 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](http://bioinformatics-core-shared-training.github.io/r-intermediate/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2427471&course-title=Data%20analysis%20and%20visualisation).'' 2018-05-23 08:30:00 UTC 2018-05-23 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation Biology Bioinformatics University of Cambridge Bioinformatics Training [] Existing R users who are not familiar with dplyr and ggplot2Those with programming experience in other languages that want to know what R can offer themGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Big Data and Cloud Computing
1 June 2018
Cambridge, United Kingdom
Big Data and Cloud Computing http://training.csx.cam.ac.uk/bioinformatics/event/2473649 https://tess.elixir-europe.org/events/big-data-and-cloud-computing 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](https://aws.amazon.com/education/awseducate/), 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](https://aws.amazon.com/research-credits/), [Microsoft Azure for Research](https://www.microsoft.com/en-us/research/academic-program/microsoft-azure-for-research/) or [Google Cloud Platform Education Grants](https://cloud.google.com/edu/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2473649&course-title=Big%20Data%20and%20Cloud%20Computing).'' 2018-06-01 08:30:00 UTC 2018-06-01 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Workflows Bioinformatics University of Cambridge Bioinformatics Training [] Researchers in the life sciences with little or no experience of cloud computing.Researchers from other disciplines may find the course usefulbut should be aware that biological data will be used in some of the examples and exercises.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Protein Structure Analysis
24 - 25 May 2018
Cambridge, United Kingdom
Protein Structure Analysis http://training.csx.cam.ac.uk/bioinformatics/event/2419336 https://tess.elixir-europe.org/events/protein-structure-analysis-c4198c49-a642-4c17-a225-680992e1d4fd 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](http://www.ebi.ac.uk/pdbe/) and [Electron Microscopy Data Bank](https://www.ebi.ac.uk/pdbe/emdb/)) and resources for protein analysis and classification ([Pfam](http://pfam.xfam.org/), [InterPro](https://www.ebi.ac.uk/interpro/) and [HMMER](https://www.ebi.ac.uk/Tools/hmmer)). Day 2 covers how to find information about the structure and function of your protein sequence using [CATH](http://www.cathdb.info/), principles of modern state-of-the-art protein modelling with [ Phyre2](http://www.sbg.bio.ic.ac.uk/phyre2/) and methods for predicting the effects of mutations on protein structure and function using the [SAAP family of tools](http://www.bioinf.org.uk/saap/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2419336&course-title=Protein%20Structure%20Analysis).'' 2018-05-24 08:30:00 UTC 2018-05-25 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Protein structure analysis Data visualisation Data mining Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
An Introduction to Solving Biological Problems with Python
12 - 13 July 2018
Cambridge, United Kingdom
An Introduction to Solving Biological Problems with Python http://training.csx.cam.ac.uk/bioinformatics/event/2480123 https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-python-7125aa8b-0e83-4328-a305-ae7886112283 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](http://pycam.github.io). 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. Functions and modules are now the focus of a new 1-day course, [Working with Python: functions and modules](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-advpython/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2480123&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20Python).'' 2018-07-12 08:30:00 UTC 2018-07-13 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Working with Python: functions and modules
4 July 2018
Cambridge, United Kingdom
Working with Python: functions and modules http://training.csx.cam.ac.uk/bioinformatics/event/2481914 https://tess.elixir-europe.org/events/working-with-python-functions-and-modules-6f2da787-533c-4b79-a1a2-217a822b7a35 This course will cover concepts and strategies for working more effectively with Python with the aim of writing reusable code. In the morning session, we will briefly go over the basic syntax, data structures and control statements. This will be followed by an introduction to writing user-defined functions. We will finish the course by looking into how to incorporate existing python modules and packages into your programs as well as writing you own modules. Course materials can be found [here](https://github.com/pycam/python-functions-and-modules/blob/master/python_fm_intro.ipynb). Note: this one-day course is the continuation of the [Introduction to Solving Biological Problems with Python](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-python/); participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2406617&course-title=Working%20with%20Python:%20functions%20and%20modules).'' 2018-07-04 08:30:00 UTC 2018-07-04 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Working with Python: functions and modules
31 May 2018
Cambridge, United Kingdom
Working with Python: functions and modules http://training.csx.cam.ac.uk/bioinformatics/event/2515419 https://tess.elixir-europe.org/events/working-with-python-functions-and-modules-76641afa-f158-4c75-99b8-87b28cd83213 This course will cover concepts and strategies for working more effectively with Python with the aim of writing reusable code. In the morning session, we will briefly go over the basic syntax, data structures and control statements. This will be followed by an introduction to writing user-defined functions. We will finish the course by looking into how to incorporate existing python modules and packages into your programs as well as writing you own modules. Course materials can be found [here](https://github.com/pycam/python-functions-and-modules/blob/master/python_fm_intro.ipynb). Note: this one-day course is the continuation of the [Introduction to Solving Biological Problems with Python](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-python/); participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2406617&course-title=Working%20with%20Python:%20functions%20and%20modules).'' 2018-05-31 08:30:00 UTC 2018-05-31 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Variant Discovery with GATK4
16 - 19 July 2018
Cambridge, United Kingdom
Variant Discovery with GATK4 http://training.csx.cam.ac.uk/bioinformatics/event/2483603 https://tess.elixir-europe.org/events/variant-analysis-with-gatk-1c39207f-184f-4cb6-a01e-2e4ee6aa4ee3 This workshop will focus on the core steps involved in calling variants with the [Broad’s Genome Analysis Toolkit](https://www.broadinstitute.org/gatk/), using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows. The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud. This includes the logic of the major pipelines, file formats and data transformations involved, and hands-on operation of the tools using goal-oriented exercises. *Day 1: Introduction to Genomics, GATK Best Practices and Pipelining *Day 2: Germline short variant discovery (SNPs + Indels) *Day 3: Somatic variant discovery (SNVs + Indels + CNVs) *Day 4: Writing pipelines with WDL and running them in FireCloud Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2483603&course-title=Variant%20Discovery%20with%20GATK4).'' 2018-07-16 08:30:00 UTC 2018-07-19 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Genomics Data visualisation Data mining Bioinformatics University of Cambridge Bioinformatics Training [] The course is aimed primarily at mid-career scientists – especially those whose formal education likely included statisticsbut who have not perhaps put this into practice since.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Image Analysis for Biologists
9 - 11 July 2018
Cambridge, United Kingdom
Image Analysis for Biologists http://training.csx.cam.ac.uk/bioinformatics/event/2495657 https://tess.elixir-europe.org/events/image-analysis-for-biologists-2e61e51b-b3c2-44bb-844e-191710e6ffd5 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](http://fiji.sc/), an extensible open source software package. On day 2, we will cover time series processing and cell tracking using [TrackMate](http://imagej.net/TrackMate) and advanced image segmentation using [Ilastik](http://ilastik.org/). 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](http://icy.bioimageanalysis.org/) 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). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2495657&course-title=Image%20Analysis%20for%20Biologists).'' 2018-07-09 08:30:00 UTC 2018-07-11 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation Data mining Biological imaging Bioinformatics University of Cambridge Bioinformatics Training [] Researchers who are applying or planning to apply image analysis in their researchGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
An introduction to metabolomics and its application in life-sciences
2 - 3 July 2018
Cambridge, United Kingdom
An introduction to metabolomics and its application in life-sciences http://training.csx.cam.ac.uk/bioinformatics/event/2463063 https://tess.elixir-europe.org/events/an-introduction-to-metabolomics-and-its-application-in-life-sciences-6f7cb052-d300-4400-899e-82f192acbe98 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. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2463063&course-title=An%20introduction%20to%20metabolomics%20and%20its%20application%20in%20life-sciences).'' 2018-07-02 08:30:00 UTC 2018-07-03 17:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Metabolomics Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] This course is aimed at researchers with an interest in metabolomics and its applicationsGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Data Carpentry in R
28 - 29 June 2018
Cambridge, United Kingdom
Data Carpentry in R http://training.csx.cam.ac.uk/bioinformatics/event/2463814 https://tess.elixir-europe.org/events/data-carpentry-in-r 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, analyzing 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. This course is organized in collaboration with [ElixirUK](http://www.elixir-uk.org/) and the [Software Sustainability Institute](https://www.software.ac.uk/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2463814&course-title=Data%20Carpentry%20in%20R).'' 2018-06-28 08:30:00 UTC 2018-06-29 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Introduction to RNA-seq data analysis
18 - 20 June 2018
Cambridge, United Kingdom
Introduction to RNA-seq data analysis http://training.csx.cam.ac.uk/bioinformatics/event/2505682 https://tess.elixir-europe.org/events/introduction-to-rna-seq-data-analysis-008b588c-002b-4556-a837-f41466461cec The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data. This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2505682&course-title=Introduction%20to%20RNA-seq%20data%20analysis).'' 2018-06-18 08:30:00 UTC 2018-06-20 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR RNA-Seq Data mining Transcriptomics Data visualisation Functional genomics Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] []
