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Bioinformatics Training

Bioinformatics course timetable

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Sat 19 Jan – Thu 2 May

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January 2019

Thu 24
Exploring, visualising and analysing proteomics data in R new [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course will present a set of R/Bioconductor packages to access, manipulate, visualise and analyse mass spectrometry (MS) and quantitative proteomics data.

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 25
CRUK: Image Analysis with Fiji [Full] 12:00 - 17:30 eLearning 1 - School of Clinical Medicine

Fiji/ImageJ is a popular open-source image analysis software application. This course will briefly cover introductory aspects of image processing and analysis theory, but will focus on practical sessions where participants will gain hands on experience with Fiji.

This course is run by the CRUK CI Light microscopy core facility.

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: Introduction to Command Line Linux [Places] 13:00 - 16:30 Room 009, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

This short (0.5 day) intensive course serves to introduce you to the command-line interface in Linux.

It is based upon elements of the Software Carpentries Shell(novice) and Shell(extras) courses. It is recommended for those CI personnel planning on attending the CI High Performance Computing facilities (Cluster) course.

This course is run by the CRUK CI Bioinformatics and IT core.

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 30
Data Manipulation and Visualisation in R [Full] 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.

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.

February 2019

Tue 19
Data Carpentry in R (1 of 2) [Full] 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, 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 and the Software Sustainability Institute.

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 20
Data Carpentry in R (2 of 2) [Full] 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, 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 and the Software Sustainability Institute.

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 27
An Introduction to Solving Biological Problems with Python (1 of 2) [Full] 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 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.

Thu 28
An Introduction to Solving Biological Problems with Python (2 of 2) [Full] 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 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.

March 2019

Fri 1
Extracting biological information from gene lists new [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists.

This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication.

Course materials 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 your interest by linking here.

Mon 25
An Introduction to Solving Biological Problems with R (1 of 2) [Full] 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.

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.

Tue 26
An Introduction to Solving Biological Problems with R (2 of 2) [Full] 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.

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 27
Introduction to RNA-seq data analysis (1 of 3) [Full] 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 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.

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 28
Introduction to RNA-seq data analysis (2 of 3) [Full] 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 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.

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 29
Introduction to RNA-seq data analysis (3 of 3) [Full] 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 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.

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.

April 2019

Wed 3
Molecular Phylogenetics (1 of 3) [Places] 09:00 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 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.

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 4
Molecular Phylogenetics (2 of 3) [Places] 09:00 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 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.

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 5
Molecular Phylogenetics (3 of 3) [Places] 09:00 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 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.

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 8
Data Science in Python (1 of 2) [Full] 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Tue 9
Data Science in Python (2 of 2) [Full] 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Wed 10
Using the Ensembl Genome Browser [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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

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

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 11
Ensembl REST API workshop [Places] 09:30 - 15:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences.

This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write scripts to call them.

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 15
Transcriptome Analysis for Non-Model Organisms new (1 of 3) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

RNA-Seq technology has been transformative in our ability to explore gene content and gene expression in all realms of biology, and de novo transcriptome assembly has enabled opportunities to expand transcriptome analysis to non-model organisms.

This course provides an overview of modern applications of transcriptome sequencing and popular tools, and algorithms, for exploring transcript reconstruction and expression analysis in a genome-free manner.

Attendees will perform quality assessment and upstream analysis of both Illumina and long reads single molecule sequencing data; the derived transcriptomes will be compared, annotated and used as reference for quantifying transcript expression, leveraging on Bioconductor tools for differential expression analysis. Additional methods will be explored for characterising the assembled transcriptome and revealing biological findings.

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 clicking here.

Tue 16
Transcriptome Analysis for Non-Model Organisms new (2 of 3) [Places] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

RNA-Seq technology has been transformative in our ability to explore gene content and gene expression in all realms of biology, and de novo transcriptome assembly has enabled opportunities to expand transcriptome analysis to non-model organisms.

This course provides an overview of modern applications of transcriptome sequencing and popular tools, and algorithms, for exploring transcript reconstruction and expression analysis in a genome-free manner.

Attendees will perform quality assessment and upstream analysis of both Illumina and long reads single molecule sequencing data; the derived transcriptomes will be compared, annotated and used as reference for quantifying transcript expression, leveraging on Bioconductor tools for differential expression analysis. Additional methods will be explored for characterising the assembled transcriptome and revealing biological findings.

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 clicking here.

Wed 17
Transcriptome Analysis for Non-Model Organisms new (3 of 3) [Places] 09:30 - 12:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

RNA-Seq technology has been transformative in our ability to explore gene content and gene expression in all realms of biology, and de novo transcriptome assembly has enabled opportunities to expand transcriptome analysis to non-model organisms.

This course provides an overview of modern applications of transcriptome sequencing and popular tools, and algorithms, for exploring transcript reconstruction and expression analysis in a genome-free manner.

Attendees will perform quality assessment and upstream analysis of both Illumina and long reads single molecule sequencing data; the derived transcriptomes will be compared, annotated and used as reference for quantifying transcript expression, leveraging on Bioconductor tools for differential expression analysis. Additional methods will be explored for characterising the assembled transcriptome and revealing biological findings.

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 clicking here.

May 2019

Thu 2
ChIP-seq and ATAC-seq analysis (1 of 2) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The primary aim of this course is to familiarise participants with the analysis of ChIP-seq and ATAC-seq data and provide hands-on training on the latest analytical approaches.

The course starts with an introduction to ChIP-seq experiments for the detection of genome-wide DNA binding sites of transcription factors and other proteins. We first show data quality control and basic analytical steps such as alignment, peak calling and motif analysis, followed by practical examples on how to work with biological replicates and fundamental quality metrics for ChIP-seq datasets. On the second day, we then focus on the analysis of differential binding, comparing between different samples. We will also give an introduction to ATAC-seq data analysis for the detection of regions of open chromatin.

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.



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Training events

February 2019

26 26
Bioinformatics Resources for Protein Biology
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
26th 28th Feb

This three day workshop will introduce you to data resources and tools developed by EMBL-EBI that can help you in your protein studies.

First come, first served

26th

March 2019

11 11
Data Visualisation for Biology: a practical workshop on design, techniques and tools
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
11th 15th Mar

This workshop will give insights and practical experience in data visualisation for exploring biological data.

Open application with selection

11th 19 19
Exploring Human Genetic Variation
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
19th 20th Mar

This two-day workshop will data resources and bioinformatics tools available at EMBL-EBI and the Sanger Institute that will aid understanding of human genetic variation.

First come, first served

19th

April 2019

1 1
Livestock Genomics
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
1st 5th Apr

This course will introduce participants to methods and approaches for analysing genomic data from common livestock species.

Open application with selection

1st

May 2019

13 13
Functional Insights Into Biological Data Through Network Analysis
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
13th 17th May

This course will provide life scientists with training on using network and pathway tools to enrich biological data. The content examines the data repositories, resources and tools available to explore and analyse large datasets. The principles of biological network and pathway analysis will be introduced and explained using relevant case studies. Participants will also have the opportunity to either learn how to access public repositories via programmatic methods or spend time analysing data using the approaches covered in the course.

Open application with selection

13th 13 13
Computational Molecular Evolution
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
13th 24th May

This course provides theoretical knowledge and practical experience in conducting molecular evolutionary analyses on sequence data.

13th

June 2019

4 4
Managing a Bioinformatics Core Facility
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
4th 6th Jun

Bioinformatics core facilities play an essential role in enabling research in the molecular life sciences. This is constantly evolving as new research tools emerge, as experiments become increasingly data intensive, and as their clients – experimental researchers – become more exposed to the power of data-driven biology. This is an opportunity for managers of core facilities to learn directly from EMBL-EBI’s service teams, from each other and from potential users. This course is organised in parallel with Bioinformatics for Principal Investigators to maximise opportunities for networking.

Open application with selection

4th 4 4
Bioinformatics for Principal Investigators
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
4th 6th Jun

The aim of this course is to provide principal investigators with an introduction to the challenges of working with biological data as a research leader; to provide guidance on strategies for managing data and the importance of data sharing; how to encourage bioinformatics development in your team and / or work with collaborators and what resources are available across the life sciences. This course will not provide a platform for teaching hands-on bioinformatics analysis. This course is organised in parallel with Bioinformatics for Core Facilities Managers to maximise opportunities for networking.

Open application with selection

4th 10 10
Metagenomics Bioinformatics 2019
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
10th 13th Jun

This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data, including marker gene, whole gene shotgun (WGS) and assembly-based approaches.

Open application with selection

10th 11 11
Ensembl Browser Course, EBI, 11th June 2019
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
11th Jun

Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart.

First come, first served

17 17
Cancer Genomics
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
17th 21st Jun

This course will focus on the analysis of data from genomic studies of Cancer. Lectures will give an insight into the bioinformatic concepts required to analyze such data, whilst practical sessions will enable the participants to apply statistical methods to the analysis of cancer genomics data under the guidance of the lecturers and teaching assistants.

Open application with selection

17th 24 24
Summer School in Bioinformatics
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
24th 28th Jun

This course provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research.

Open application with selection

24th

July 2019

8 8
Systems Biology: From large datasets to biological insight
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
8th 12th Jul

Run jointly with the Wellcome Trust, this course will provide participants with an introduction to network analysis and an in-depth training in the main modelling approaches used in systems biology.

Open application with selection

8th 15 15
Bioinformatics for Immunologists
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom
15th 19th Jul

This course provides an introduction to immunology bioinformatics and offer opportunities to explore key methods, tools and resources that can be applied to research.

Open application with selection

15th

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CSED 2015 programme

CSED page


COMPUTING FOR RESEARCH
Introduction to NVivo
An Introduction to R  [NEW]
Intermediate Workshop on R [NEW]
An Introduction to PASW (SPSS) [NEW]
Basic Data Analysis PASW (SPSS) [NEW]
Advanced Data Analysis I PASW (SPSS) [NEW]
Advanced Data Analysis II PASW (SPSS) [NEW]
Introduction to Linux [NEW]
Introduction to High Powered Computing [NEW]
Matlab (Online Service) [NEW]

 

Introduction to NVivo

DATE & TIME: Tuesdays 18 & 25 November 2014, 09.30-12.30
REPEATED: Wednesdays 4 & 11 February 2015, 13.30-16.30
REPEATED: Fridays 8 & 15 May 2015, 09.30-12.30
TUTOR: Steve Oldfield, CSED
DURATION: Two half days
VENUE: CSED IT Training Room, 02.01, Library
DETAILS: Nvivo is a software package which makes the task of analysing qualitative data easier. ITCS has arranged a site licence which some Schools at UEA have bought into. It is expected that we will be using version 10 for this course. This course provides a step-by-step introduction to using NVivo for those with little or no experience of it (though some familiarity with analysing qualitative data will be an advantage). Demonstration data will be used, though the techniques and organising principles can be applied to any qualitative data. The course focuses on basic use of the software package; it is not a research methods course.
ADDITIONAL INFORMATION: Participants are expected to attend both parts. A general familiarity with the use of Windows features such as menus, toolbars and dialogue boxes is a prerequisite. Course materials are provided in-session.

[Go to Top of Page]     [Online Course Booking Form]


An Introduction to R [NEW]

DATE & TIME: Wednesday 8 October 2014, 12.00-14.00
VENUE: Room 0.24, Chancellors Drive Annexe
REPEATED: Wednesday 18 February 2015, 12.00-14.00
VENUE: ARTS 1.02
SESSION LEADERS:
Gareth Janacek, CMP
DURATION: 2 hours
RDF Domains: A1, A3
DETAILS: This basic introduction to R aims to get you up and running. We assume some very basic computer skills and a familiarity with data. The topics we expect to cover are;

  • What is R?
  • Basics
  • Preparing and Importing Your Data
  • The Help Files
  • Finding and loading R Packages
  • Graphics
  • Record Keeping
  • Problems/Getting help
  • Examples of analyses: regression and generalised linear models
  • Multivariate techniques (if time permits)

ADDITIONAL INFORMATION: Please feel free to bring your own laptop. The data examples used will be available on Blackboard.

[Go to Top of Page]     [Online Course Booking Form]


Intermediate Workshop on R [NEW]

DATE & TIME: Tuesday 11 November 2014, 12.00-14.00
VENUE: BIO 0.12
REPEATED: Wednesday 13 May 2015, 12.00-14.00
VENUE: ARTS 1.02
SESSION LEADER: Gareth Janacek, CMP
DURATION: 2 hours
RDF Domains: A1, A3
DETAILS: The aim of this session is to show how one can use R to perform statistical analyses. This is a huge subject area and we shall aim to show what is available without delving too far into de   tails. Do feel free to bring your own laptop. The approach is example driven and quite practical.

We would aim to cover:

  • Multivariate analysis
  • PCA
  • Factor Analysis
  • Discriminant analysis
  • Time Series Analysis
  • Time series class
  • Plots
  • Time domain modelling – Forecasting
  • The frequency domain
  • Graphics
  • The basic graphic system, devices and output
  • Trellis graphics
  • GGplot
  • Bayesian Methods
  • Introduction and the LearnBayes pac  kage
  • MCMC
  • R functions for Bayesian inference using lm, glm, mer and polr objects.
  • Point out packages that link R to other Bayesian sampling engines such as JAGS , OpenBUGS , and WinBUGS
  • Survival Analysis
  • Censoring
  • Kaplan –Meier
  • Cox Models

We aim to have at least one example data set in each case.

ADDITIONAL INFORMATION: Feel free to bring your own laptop

[Go to Top of Page]     [Online Course Booking Form]


Introduction to PASW (SPSS) [NEW]

DATE & TIME: Wednesday 14 January 2015, 09.30-12.30
VENUE: Arts, 1.02
SESSION LEADER: Simon Poulton, BIO
DURATION: A half day
RDF Domains: A1, A3
DETAILS:This session introduces you to the PASW (SPSS) statistical software and will cover ways to create and interpret histograms, bar charts and scatter plots using the interactive “Chart Builder”, as well as two main themes;

  • Getting started, including an introduction to the PASW environment (windows & settings), definition of variables, opening and saving PASW files and importing data from other software packages.
  • Exploring your data, including how to create summary statistics for your variables and the creation of frequency tables and cross-tabulations between variables.

ADDITIONAL INFORMATION: There are no attendance requirements for this session, prior knowledge of PASW (SPSS) is not essential, and you do not have to attend all four sessions.  The emphasis is on practical use of PASW rather than statistical theory.  The session will have a strong graphical emphasis and include ‘hands-on’ exercises as well as opportunities for feedback and Q&As.

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Basic Data Analysis PASW (SPSS) [NEW]

DATE & TIME: Thursday 15 January 2015, 09.30-12.30
VENUE: BIO, 0.12
SESSION LEADERS: Simon Poulton, BIO
DURATION: A half day
RDF Domains: A1, A3
DETAILS: This session assumes that you have used PASW before and have a basic understanding of statistical analysis and testing methods. It will continue the practical use of PASW and show you how to manage, extract and analyse data as well as generate graphical techniques provided in the “Chart Builder”.
ADDITIONAL INFORMATION: To benefit from this session you should be familiar with using PASW.  If you understand and have successfully completed statistical analyses such as ANOVA and linear regression then this course may not be suitable. The emphasis is on practical use of PASW rather than statistical theory. The session will have a strong graphical emphasis and include ‘hands-on’ exercises as well as opportunities for feedback and Q&As.

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Advanced Data Analysis I PASW (SPSS) [NEW]

DATE & TIME: Wednesday 11 March 2015, 09.30-12.30
VENUE: Arts, 1.02
SESSION LEADER: Simon Poulton, BIO
DURATION: A half day
RDF Domains: A1, A3
DETAILS: This session will introduce the concepts of Analysis-of-Variance, Linear Regression and General Linear Models, how they are run and interpreted in PASW. It will cover advanced PASW data handling methods; transposing data and the comprehensive two-stage process for data validation, including the detection of outliers. It introduces the concepts of ANOVA, then moves forward to two-way and multi-way ANOVA, with particular emphasis on how to arrange your data and explore methods of correlation and multiple regression models.
ADDITIONAL INFORMATION: To benefit from this session you should be well-versed in the use of PASW (SPSS) or other statistical software and confident in manipulating data, although perhaps unsure how to achieve this in PASW. You will require an understanding of concepts such as the sums-of-squares and variances, confidence intervals and how to interpret p-values. If you possess extensive experience in using GLMs for linear modelling, then this course may not be suitable. The emphasis is on practical use of PASW rather than statistical theory. The session will have a strong graphical emphasis and include ‘hands-on’ exercises as well as opportunities for feedback and Q&As.

 

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Advanced Data Analysis II PASW (SPSS) [NEW]

DATE & TIME: Wednesday 27 May 2015, 09.30-12.30
VENUE: Arts, 1.02
SESSION LEADER: Simon Poulton
DURATION: A half day
RDF Domains: A1, A3
DETAILS: This session continues the theme of practical use of the software. It explores the importance of residuals and diagnostic tests in ANOVA and regression models and will also cover a brief introduction to Analysis-of-Covariance (ANCOVA). Emphasis will be on how to organise your data and specify models using the GLM dialogue boxes. It will explore the use of mixed models and repeated-measures models and outline how they are implemented and defined in PASW. If you are curious about residuals plots, post-hoc testing or more complex types of linear models then this session may be for you. There will be a strong emphasis on the interpretation of PASW outputs.
ADDITIONAL INFORMATION: You should possess considerable experience of manipulating data and an understanding of basic linear modelling techniques. Familiarity with interpreting the outputs from simple ANOVA and regression models is also required. The emphasis is on practical use of PASW rather than statistical theory. The session will have a strong graphical emphasis and include ‘hands-on’ exercises as well as opportunities for feedback and Q&As.

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Introduction to Linux [NEW]

RDF Domains: A1, A3
DETAILS: Linux is a powerful and versatile open source operating system frequently found powering desktop computers and servers, including the UEA High Performance Computing Cluster. In one-to-one or small group sessions we will work through the fundamental skills needed to begin working with Linux tailored to the individual: from familiarising participants with the working environment, using common commands and file management to more advanced usage and scripting.
ADDITIONAL INFORMATION: This course is held on a one-to-one basis. For further information and to register your interest, please contact hpc.admin@uea.ac.uk

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Introduction to High Powered Computing [NEW]

RDF Domains: A1, A3
DETAILS: Do you have a computational element to your research? In a one-to-one session we will introduce UEA’s HPC cluster and discuss how it can benefit your research looking at your own specific computational requirements. We will go through the initial steps on using the HPC cluster and help you get started with your own task.
ADDITIONAL INFORMATION: This course is held on a one-to-one basis. For further information and to register your interest, please contact hpc.admin@uea.ac.uk

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Matlab (Online Service) [NEW]

RDF Domains: A1, A3
DETAILS:

Matlab Fundamentals

This online course provides a comprehensive introduction to the MATLAB technical computing environment and is intended for beginners and those looking for a review. No prior programming experience or knowledge of MATLAB is necessary. The course is structured to allow thorough assimilation of ideas through hands-on examples and exercises. MATLAB competency is developed in a natural way, with an emphasis on practical application. Themes of data analysis, visualization, modelling, and programming are explored throughout the course.

Topics include:

  • Working with the MATLAB user interface
  • Entering commands and creating variables
  • Performing analysis on vectors and matrices
  • Visualizing vector and matrix data
  • Working with data files
  • Working with data types
  • Automating commands with scripts
  • Writing programs with logic and flow control
  • Writing functions

Matlab for Data Processing and Visualisation

This course focuses on the details of data management and visualization techniques, from reading arbitrarily formatted text data files to producing customized publication-quality graphics. The course emphasizes creating scripts that extend the basic features provided by MATLAB. Topics include:

  • Importing data
  • Organizing data
  • Visualizing data

Matlab Programming Techniques

This course provides hands-on experience using the features in the MATLAB® language to write efficient, robust, and well-organized code. These concepts form the foundation for writing full applications, developing algorithms, and extending built-in MATLAB capabilities. Details of performance optimization, as well as tools for writing, debugging, and profiling code, are covered. Topics include:

  • Creating robust applications
  • Utilizing development tools
  • Structuring code
  • Structuring data
  • Efficient data management
  • Classes and objects

ADDITIONAL INFORMATION: The Matlab sessions are available to take as an online service. For further information please contact hpc.admin@uea.ac.uk

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