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Bioinformatics 2016

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

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Mon 11 Apr 2016 – Tue 7 Jun 2016

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April 2016

Mon 11
R object-oriented programming and package development Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The course will teach intermediate R object-oriented programming and how to build a fully functional R package.

The course page includes slides and handouts; other relevant teaching materials are available here) and the sequences example package used as template in the 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 register Interest by linking here.

Thu 14
Network Visualisation and Analysis of Biological Data new (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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

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

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

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

A draft agenda can be found here.

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

Fri 15
Network Visualisation and Analysis of Biological Data new (2 of 2) Finished 09:30 - 16:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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

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

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

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

A draft agenda can be found here.

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

Mon 18
Introduction to genome variation analysis using NGS (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:

  • an introduction to genetic variation as well as data formats and analysis workflows commonly used in NGS data analysis;
  • an overview of available analytical tools and discussion of their limitations; and
  • hands-on experience with common computational workflows for analysing genome sequence variation using bioinformatics and computational genomics approaches.

A draft agenda can be found here

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

CRUK: Using the Ensembl Genome Browser Finished 09:30 - 17:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This one-day workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information.

This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes.

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

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

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

Tue 19
Introduction to genome variation analysis using NGS (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:

  • an introduction to genetic variation as well as data formats and analysis workflows commonly used in NGS data analysis;
  • an overview of available analytical tools and discussion of their limitations; and
  • hands-on experience with common computational workflows for analysing genome sequence variation using bioinformatics and computational genomics approaches.

A draft agenda can be found here

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

CRUK: Bioinformatics resources for exploring disease related data Finished 09:30 - 17:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

This course will provide participants with an introduction to EMBL-EBI and its data tools and resources, which cover the whole spectrum of biological / life sciences.

Sessions with trainers from ArrayExpress, Expression Atlas and the GWAS catalog will explore SNP-trait associations and show how further understanding can be gained on the location and level of gene expression across the body.

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

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

Wed 20
Molecular Phylogenetics (1 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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

Course timetable is available here.

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

Thu 21
Molecular Phylogenetics (2 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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

Course timetable is available here.

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

Fri 22
Molecular Phylogenetics (3 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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

Course timetable is available here.

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

Tue 26
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 manual 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.

Wed 27
Analysis of high-throughput sequencing data with Bioconductor (1 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing (HTS) data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in bam format. We will also describe the various resources available through Bioconductor to annotate and visualize HTS data, which can be applied to any type of sequencing experiment.

The course timetable is available here.

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

Thu 28
Analysis of high-throughput sequencing data with Bioconductor (2 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing (HTS) data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in bam format. We will also describe the various resources available through Bioconductor to annotate and visualize HTS data, which can be applied to any type of sequencing experiment.

The course timetable is available here.

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

Fri 29
Analysis of high-throughput sequencing data with Bioconductor (3 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing (HTS) data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in bam format. We will also describe the various resources available through Bioconductor to annotate and visualize HTS data, which can be applied to any type of sequencing experiment.

The course timetable is available here.

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

May 2016

Mon 9
Data Analysis and Visualisation in R new Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

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

Tue 10
EXCELERATE: Train the Trainer (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course aims to provide trainers with guidance and tips for developing and delivering training in bioinformatics, exploring a range of methods appropriate to different learning styles and examining the requirements for a successful course (both scientific and logistic).

This event is organized as part of the Horizon 2020 ELIXIR-EXCELERATE project.

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 11
EXCELERATE: Train the Trainer (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course aims to provide trainers with guidance and tips for developing and delivering training in bioinformatics, exploring a range of methods appropriate to different learning styles and examining the requirements for a successful course (both scientific and logistic).

This event is organized as part of the Horizon 2020 ELIXIR-EXCELERATE project.

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.

Thu 12
BIIT web-tools for high-throughput data analysis from ELIXIR-Estonia new Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

In this course we will introduce web-based, open source tools to analyse and interpret high-throughput biological data.

The main focus will be g:Profiler - a toolset for finding most significant functional groups for a given gene or protein list; MEM - a query engine allowing to mine hundreds of public gene expression datasets to find most co-expressed genes based on a query gene; and ClustVis - a web tool for visualizing clustering of multivariate data using Principal Component Analysis (PCA) plot and heatmap.

MEM and g:Profiler are ELIXIR-Estonia node services.

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

Mon 16
ElixirUK: Data Carpentry (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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. 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.

During this course you will learn about:

  • How to use spreadsheet programs (such as Excel) more effectively, and the limitations of such programs
  • Getting data out of spreadsheets and into more powerful tools (R)
  • Data management and manipulation
  • Data visualization
  • Workflows and automating repetitive tasks, in particular using the command line shell

This event is organized in collaboration with Data Carpentry and is sponsored by the HORIZON 2020 TWINNING Project TrainMalta.

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 by linking here.

Tue 17
ElixirUK: Data Carpentry (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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. 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.

During this course you will learn about:

  • How to use spreadsheet programs (such as Excel) more effectively, and the limitations of such programs
  • Getting data out of spreadsheets and into more powerful tools (R)
  • Data management and manipulation
  • Data visualization
  • Workflows and automating repetitive tasks, in particular using the command line shell

This event is organized in collaboration with Data Carpentry and is sponsored by the HORIZON 2020 TWINNING Project TrainMalta.

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 by linking here.

CRUK: Using Genome Browsers to visualise high-throughput data Finished 10:30 - 17:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

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

In this course, we explain the common file formats generated by sequencing technologies and how they can be manipulated and explored by non bioinformaticians. The main tools that we will use are the Integrative Genomics Viewer (IGV) and University of Santa Cruz (UCSC) genome browser.

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

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

Thu 19
Image Analysis for Biologists (1 of 2) 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).

The timetable can be found here.

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

Fri 20
Image Analysis for Biologists (2 of 2) 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).

The timetable can be found here.

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

June 2016

Mon 6
An Introduction to Solving Biological Problems with R (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to the R programming language and software environment for statistical computing and graphics. A variety of examples with a biological theme will be presented.

The course website providing links to the course materials is here.

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

Tue 7
An Introduction to Solving Biological Problems with R (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to the R programming language and software environment for statistical computing and graphics. A variety of examples with a biological theme will be presented.

The course website providing links to the course materials is here.

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