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Bioinformatics 2016

Programme of events provided by Bioinformatics
(Mon 18 Jan 2016 - Fri 16 Dec 2016)

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Wed 2 Nov 2016 – Fri 16 Dec 2016

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November 2016

Wed 2
Introduction to RNA-seq and ChIP-seq data analysis (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The aim of this course is to familiarize the participants with the primary analysis of datasets generated through two popular high-throughout 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.

CRUK: Beginners guide to version control with git Finished 13:30 - 17:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

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.

Mon 7
CRUK: Biological data analysis using InterMine Finished 10:00 - 13:00 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

InterMine is a freely available data warehouse and analysis software 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.

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.

We have recently re-designed the InterMine interface to provide a more intuitive user-experience. This workshop will provide an overview of key features of the new interface and how this can be used to interrogate genomic and proteomic data.

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 16
Statistical Analysis using R Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Statistics are an important part of most modern studies and being able to effectively use a statistical package will help you to understand your results.

This course provides an introduction to some statistical techniques through the use of the R language. Topics covered include: Chi2 and Fisher tests, descriptive statistics, t-test, analysis of variance and regression.

Students will run analyses using statistical and graphical skills taught during the session.

The 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.

Mon 21
CRUK: Intermediate Image Analysis new (1 of 2) Finished 12:30 - 17:00 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

This course will cover common image analysis problems including colocalization, segmentation and tracking. We will also cover the handling of large data including registration, fusion and visualization. We will use Fiji and Icy; two leading open source image analysis software applications.

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 22
CRUK: Intermediate Image Analysis new (2 of 2) Finished 12:30 - 17:00 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

This course will cover common image analysis problems including colocalization, segmentation and tracking. We will also cover the handling of large data including registration, fusion and visualization. We will use Fiji and Icy; two leading open source image analysis software applications.

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 24
Analysis of gene regulatory sequencing data: ChIP-seq, ATAC-seq and Hi-C new (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Fri 25
Analysis of gene regulatory sequencing data: ChIP-seq, ATAC-seq and Hi-C new (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Light sheet data processing new Finished 14:30 - 17:30 Department of Genetics, Room G1

This course will focus on handling of large image data including image registration, fusion, deconvolution and visualization. We will use Fiji, an open source image analysis software.

Mon 28
Protein Structure Analysis new (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Tue 29
Protein Structure Analysis new (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Wed 30
An Introduction to Solving Biological Problems with R (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Course materials are available 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.

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.

December 2016

Thu 1
An Introduction to Solving Biological Problems with R (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Course materials are available 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.

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 2
Analysis of DNA Methylation using Sequencing Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

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 by linking here.

Mon 5
An Introduction to Solving Biological Problems with Python (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 from scratch and to customize more complex code to fit their needs.

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 by linking here.

Tue 6
An Introduction to Solving Biological Problems with Python (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 from scratch and to customize more complex code to fit their needs.

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 by linking here.

Wed 7
Basic statistics and data handling new (1 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 lecture, workshop and hands-on practice – 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 will use some practical statistics examples in R to introduce concepts in data presentation for publication. Covering: Some practical examples of statistics in R. Visualising and publishing your data.

Course materials are available here.

This event is sponsored by CRUK.

Thu 8
Basic statistics and data handling new (2 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 lecture, workshop and hands-on practice – 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 will use some practical statistics examples in R to introduce concepts in data presentation for publication. Covering: Some practical examples of statistics in R. Visualising and publishing your data.

Course materials are available here.

This event is sponsored by CRUK.

Fri 9
Basic statistics and data handling new (3 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 lecture, workshop and hands-on practice – 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 will use some practical statistics examples in R to introduce concepts in data presentation for publication. Covering: Some practical examples of statistics in R. Visualising and publishing your data.

Course materials are available here.

This event is sponsored by CRUK.

Mon 12
Image Analysis for Biologists (1 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualization, 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).

On day 3, we will cover time series processing and cell tracking using TrackMate. 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.

A timetable is available here.

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

Tue 13
Image Analysis for Biologists (2 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualization, 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).

On day 3, we will cover time series processing and cell tracking using TrackMate. 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.

A timetable is available here.

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

Wed 14
Image Analysis for Biologists (3 of 3) Finished 09:30 - 16:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualization, 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).

On day 3, we will cover time series processing and cell tracking using TrackMate. 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.

A timetable is available here.

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

Thu 15
Using CellProfiler and CellProfiler Analyst to analyse biological images new (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 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 account you will need to book or register your interest by linking here.

Fri 16
Using CellProfiler and CellProfiler Analyst to analyse biological images new (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 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 account you will need to book or register your interest by linking here.

CRUK: Mining gene-disease associations and drug target validation with Open Targets new Finished 13:00 - 16:00 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

Open Targets was founded by three global leading institutions in the fields of pharmaceuticals, bioinformatics and genomics: GSK, EMBL-EBI, the Wellcome Trust Sanger Institute, and recently joined by Biogen, the world’s oldest independent biotechnology company.

We develop two major areas of work, which are further subdivided into projects. The major areas are the Core Bioinformatics and Computational Pipelines, which created and developed the Target Validation Platform, and Experimental projects, which combine large-scale genomics with statistical and computational techniques to identify and validate the causal links between targets, pathways and diseases. The Target Validation Platform integrates comprehensive datasets from a myriad of renowned public databases, such as UniProt, ChEMBL, Ensembl, NHGRI-EBI GWAS, EuropePMC, COSMIC, amongst others, and will incorporate the newly generated data by our Experimental projects in Oncology, Immunity, Inflammation and other areas for free and open access.

The purpose of this half-day workshop is to acquaint participants with the Open Targets consortium. We will highlight the experimental projects in the Consortium but focus on the Target Validation Platform to introduce the tools for visualisation and interpretation of gene-disease associations and target validation. By the end of this half-day workshop, users will be able to carry out effective searches of data, and use the web application to visualise genes, variants, ontology, pathways (and more) in the context of human disease and therapeutics.

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.