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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Showing 2 materials.
An overview of Unix and R for bioinformatics
Keywords: Unix, R-programming
Resource type: Training materials
Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R
https://github.com/semacu/20180726_TrainMalta_Unix_R
https://tess.elixir-europe.org/materials/summer-school-2018-trainmalta-epigenomics-introduction-to-unix-and-r
An overview of Unix and R for bioinformatics
Sergio Martínez Cuesta
Luigi Grassi
Unix, R-programming
PhD students
Life Science Researchers
Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover Data organization in spreadsheets, data...
Keywords: Data analysis, Data carpentry, SoftwareCarpentry
Resource type: course materials
Data Carpentry in R
https://tavareshugo.github.io/2018-06-28-cambridge/
https://tess.elixir-europe.org/materials/data-carpentry-in-r
Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover Data organization in spreadsheets, data cleaning with OpenRefine, and learn how to use the statistical program R. If time allows we will also talk about Interacting with databases from R. Participants will be encouraged to help one another and to apply what they have learned to their own research problems
Sandra Cortijo
Hugo Tavares
Sergio Martínez Cuesta
Data analysis, Data carpentry, SoftwareCarpentry
Anyone
Showing 13 upcoming events.
Found 293 past events.
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High Performance Computing: An Introduction
18 October 2018
Cambridge, United Kingdom
High Performance Computing: An Introduction http://training.csx.cam.ac.uk/bioinformatics/event/2652631 https://tess.elixir-europe.org/events/high-performance-computing-an-introduction-aa891ede-7439-43a9-9292-9f70d01db744 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)](https://www.hpc.cam.ac.uk/) 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. 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=2652631&course-title=High%20Performance%20Computing:%20An%20Introduction).'' 2018-10-18 08:30:00 UTC 2018-10-18 15:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Novice users of HPC and anyone who expects to need to use HPC systems at some stage in their researchGraduate 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 R
12 - 13 September 2018
Cambridge, United Kingdom
An Introduction to Solving Biological Problems with R http://training.csx.cam.ac.uk/bioinformatics/event/2649674 https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-r-531d619b-121b-415d-9145-8541ba7afd3f [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=2649674&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20R).'' 2018-09-12 08:30:00 UTC 2018-09-13 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 [] [] -
Introduction to Unix shell
17 October 2018
Cambridge, United Kingdom
Introduction to Unix shell http://training.csx.cam.ac.uk/bioinformatics/event/2652625 https://tess.elixir-europe.org/events/introduction-to-unix-shell-09f4b111-cd12-4f94-890c-6ccadf9282f0 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. 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=2652625&course-title=Introduction%20to%20Unix%20shell).'' 2018-10-17 08:30:00 UTC 2018-10-17 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 [] [] -
An Introduction to Machine Learning
26 - 28 September 2018
Cambridge, United Kingdom
An Introduction to Machine Learning http://training.csx.cam.ac.uk/bioinformatics/event/2601268 https://tess.elixir-europe.org/events/an-introduction-to-machine-learning-0a9d6023-6c96-415d-8baf-e38541d7d80e 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. 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=2601268&course-title=An%20Introduction%20to%20Machine%20Learning).'' 2018-09-26 12:30:00 UTC 2018-09-28 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Machine learning Data mining Bioinformatics University of Cambridge Bioinformatics Training [] This introductory course is aimed at biologists with little or no experience in machine learning.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
6 - 7 September 2018
Cambridge, United Kingdom
An Introduction to Solving Biological Problems with Python http://training.csx.cam.ac.uk/bioinformatics/event/2605767 https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-python-cd031d18-8ff6-479a-8065-588e678376b3 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=2605767&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20Python).'' 2018-09-06 08:30:00 UTC 2018-09-07 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 Manipulation and Visualisation in R
14 September 2018
Cambridge, United Kingdom
Data Manipulation and Visualisation in R http://training.csx.cam.ac.uk/bioinformatics/event/2651197 https://tess.elixir-europe.org/events/data-manipulation-and-visualisation-in-r 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=2651197&course-title=Data%20manipulation%20and%20visualisation).'' 2018-09-14 08:30:00 UTC 2018-09-14 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 [] [] -
Ontologies and ontology-based data analysis
21 November 2018
Cambridge, United Kingdom
Ontologies and ontology-based data analysis http://training.csx.cam.ac.uk/bioinformatics/event/2660714 https://tess.elixir-europe.org/events/ontologies-and-ontology-based-data-analysis 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 new 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. 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=2660714&course-title=Ontologies%20and%20ontology-based%20data%20analysis).'' 2018-11-21 10:00:00 UTC 2018-11-21 15:00:00 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 [] The tutorial will be of interest to computational biologists who useproduce or analyse large structured datasets.The tutorial will be at an introductory levelbut will also describe current research directions and challenges that will be of broad interest to researchers in computational biology.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Using CellProfiler and CellProfiler Analyst to analyse biological images
10 - 11 December 2018
Cambridge, United Kingdom
Using CellProfiler and CellProfiler Analyst to analyse biological images http://training.csx.cam.ac.uk/bioinformatics/event/2657149 https://tess.elixir-europe.org/events/using-cellprofiler-and-cellprofiler-analyst-to-analyse-biological-images-784b3b6a-5e06-4064-b715-9c596d8b9d43 Microscopy experiments have proven to be a powerful means of generating information-rich data for biological applications. From small-scale microscopy experiments to time-lapse movies and high-throughput screens, automatic image analysis is more objective and quantitative and less tedious than visual inspection. This course will introduce users to the free open-source image analysis program [CellProfiler](http://cellprofiler.org/) and its companion data exploration program CellProfiler Analyst. We will show how CellProfiler can be used to analyse a variety of types of imaging experiments. We will also briefly discuss the basic principles of supervised machine learning with CellProfiler Analyst in order to score complex and subtle phenotypes. 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=2657149&course-title=Using%20CellProfiler%20and%20CellProfiler%20Analyst%20to%20analyse%20biological%20images).'' 2018-12-10 09:30:00 UTC 2018-12-11 17:30:00 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 want to extract quantitative information from microscopy imagesGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] [] -
Analysis of DNA Methylation using Sequencing
14 December 2018
Cambridge, United Kingdom
Analysis of DNA Methylation using Sequencing http://training.csx.cam.ac.uk/bioinformatics/event/2653218 https://tess.elixir-europe.org/events/analysis-of-dna-methylation-using-sequencing-451867ff-b0e1-4e80-9606-54c7ada67d97 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=2653218&course-title=Analysis%20of%20DNA%20Methylation%20using%20Sequencing).'' 2018-12-14 09:30:00 UTC 2018-12-14 17:30:00 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 [] [] -
Introduction to Scientific Figure Design
14 November 2018
Cambridge, United Kingdom
Introduction to Scientific Figure Design http://training.csx.cam.ac.uk/bioinformatics/event/2653212 https://tess.elixir-europe.org/events/introduction-to-scientific-figure-design-604aab1e-fed2-40e7-b756-93e6f250c78a 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=2653212&course-title=Introduction%20to%20Scientific%20Figure%20Design).'' 2018-11-14 09:30:00 UTC 2018-11-14 17:30:00 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 [] [] -
Statistics for Biologists in R
10 - 11 September 2018
Cambridge, United Kingdom
Statistics for Biologists in R http://training.csx.cam.ac.uk/bioinformatics/event/2601252 https://tess.elixir-europe.org/events/statistics-for-biologists-in-r-5aa81bcb-b0bb-4bc1-8fd5-79d5b405ba3a 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 multiple linear regression. 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=2601252&course-title=Statistics%20for%20Biologists%20in%20R).'' 2018-09-10 08:30:00 UTC 2018-09-11 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 [] [] -
Data Carpentry in R
24 - 25 September 2018
Cambridge, United Kingdom
Data Carpentry in R http://training.csx.cam.ac.uk/bioinformatics/event/2651178 https://tess.elixir-europe.org/events/data-carpentry-in-r-458a5188-0f1e-4328-97fa-5a06ccb3ab7d 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=2651178&course-title=Data%20Carpentry%20in%20R).'' 2018-09-24 08:30:00 UTC 2018-09-25 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
3 - 5 September 2018
Cambridge, United Kingdom
Introduction to RNA-seq data analysis http://training.csx.cam.ac.uk/bioinformatics/event/2605748 https://tess.elixir-europe.org/events/introduction-to-rna-seq-data-analysis-06fe6d04-97b2-42b3-8777-d4a39ce20307 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=2605748&course-title=Introduction%20to%20RNA-seq%20data%20analysis).'' 2018-09-03 08:30:00 UTC 2018-09-05 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 [] []
