Bioinformatics 2019
(Wed 9 Jan 2019 - Tue 17 Dec 2019)
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May 2019
| Tue 14 |
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. |
| Wed 15 |
Statistics for Biologists in R
Finished
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. 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. |
| Thu 16 |
Statistics for Biologists in R
Finished
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. 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. |
| Fri 17 |
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. |
| Mon 20 |
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 by linking here. |
| Tue 21 |
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 by linking here. |
| Wed 22 |
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. |
| Thu 23 |
Analysis of single cell RNA-seq data
Finished
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 by linking here. |
| Fri 24 |
Analysis of single cell RNA-seq data
Finished
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 by linking here. |
| Thu 30 |
Train the Trainer for Image Analysts
Finished
 This course aims to provide trainers with guidance and tips for developing and delivering training in image analysis, exploring a range of methods appropriate to different learning styles and examining the requirements for a successful course (both scientific and logistic). The first part of the course will give participants principles of training theory and best practises for developing and delivering their future training content; the second part will be a hackathon to kick start the development of a common set of training materials in image analysis. This event is organized in collaboration with the Image Analysis Focused Interest Group and is supported 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 Interest by linking here. |
| Fri 31 |
Train the Trainer for Image Analysts
Finished
This course aims to provide trainers with guidance and tips for developing and delivering training in image analysis, exploring a range of methods appropriate to different learning styles and examining the requirements for a successful course (both scientific and logistic). The first part of the course will give participants principles of training theory and best practises for developing and delivering their future training content; the second part will be a hackathon to kick start the development of a common set of training materials in image analysis. This event is organized in collaboration with the Image Analysis Focused Interest Group and is supported 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 Interest by linking here. |
June 2019
| Tue 4 |
 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. |
| Mon 10 |
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. |
| Tue 11 |
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. |
| Wed 12 |
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. |
| Thu 13 |
Data Science in Python
Finished
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 by linking here. |
| Fri 14 |
Data Science in Python
Finished
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 by linking here. |
| Mon 17 |
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. |
| Tue 18 |
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. |
| Wed 19 |
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. |
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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. |
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| Thu 20 |
Protein Structure Analysis
Finished
This course covers analytical approaches for the interpretation of biomacromolecular structures including 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. In addition, we will look at mapping genetic variants onto structures as well as visualisation and basic analysis of protein structures. 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. |
| Fri 21 |
Protein Structure Analysis
Finished
This course covers analytical approaches for the interpretation of biomacromolecular structures including 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. In addition, we will look at mapping genetic variants onto structures as well as visualisation and basic analysis of protein structures. 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. |
| Mon 24 |
Image Analysis for Biologists
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. |
| Tue 25 |
Image Analysis for Biologists
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. |