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Bioinformatics Training

Bioinformatics course timetable

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Wed 17 Jan – Thu 5 Apr

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January 2018

Thu 18
An Introduction to Machine Learning new (2 of 2) In progress 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Machine learning gives computers the ability to learn without being explicitly programmed. It encompasses a broad range of approaches to data analysis with applicability across the biological sciences. Lectures will introduce commonly used algorithms and provide insight into their theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment.

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

Thu 25
High Performance Computing: An Introduction [Places] 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The course aims to give an introductory overview of High Performance Computing (HPC) in general, and of the facilities of the High Performance Computing Service (HPCS) available at the University of Cambridge.

Practical examples of using the HPCS clusters will be used throughout, although it is hoped that much of the content will have applicability to systems elsewhere.

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

February 2018

Fri 2
EMBL-EBI: Ontologies in life sciences - examples from GO and EFO new [Places] 13:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course will give an introduction to the basic concepts of ontologies and how they are useful in biological applications. We will explain what a biomedical ontology is and present the two primary types of ontology: (i) domain ontology and (ii) application ontology, using examples as Gene Ontology (GO) and Experimental Factor Ontology (EFO). The module will also go into details of why big data need ontologies and the ontology capabilities in advanced computational biology.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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
EMBL-EBI: Protein Sequence Databases with UniProt [Places] 09:30 - 12:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop aims to give the scientific community hands on experience on how to access and effectively use protein data in UniProt. UniProt is a high-quality, comprehensively and thoroughly annotated protein resource. Participants will be able to access detailed information on protein function and millions of protein sequences in the UniProt knowledgebase, including isoforms and disease variants.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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
EMBL-EBI: Introduction to the European Nucleotide Sequence Archive new [Places] 09:30 - 12:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The European Nucleotide Sequence Archive (ENA) is a global database for storing experimental nucleotide data and also interpreted data (alignment files, variant calling, analysis results). The data is submitted by scientists conducting sequencing experiments and publishing research in the area. Data is fully searchable and available for download. Sequence data includes raw NGS files (FastQ, BAM…), assembled genomes and transcriptomes, and annotated sequences (protein coding genes, non coding RNA, barcode genes, HLA genes)

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

EMBL-EBI: An Introduction to Sequence Searching [Places] 13:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This module introduces the area of sequence similarity searching and focuses on how to use tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases, including tips on which tool and database to use, input formats, how to change parameters and how to interpret the results pages.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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 7
EMBL-EBI: Array Express and Expression Atlas [Places] 14:00 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop is designed for researchers interested in learning about functional genomics data, how to access, retrieve and use the data from ArrayExpress and hands-on experience in using Expression Atlas, a resource to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others. This will include an overview on how gene expression data is curated and analysed in Expression Atlas and a practical activity to demonstrate how to access and visualise gene expression analysis results. These activities should help you answer questions such as "where is my favourite gene expressed?" or "how does its expression change in a disease?".

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

Thu 15
EMBL-EBI: European Variation Archive [Places] 09:30 - 12:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This interactive workshop offers participants hands-on experience in the use of the European Variation Archive, EVA. The EVA is an open-access, genetic variation data repository, currently hosting more than 80 studies describing in excess of 520 million unique variants. Participants will be shown how this data can be searched for at the study level via the EVA Study Browser, or at the individual variant level, via our Variant Browser. Finally, participants shall also be shown how to access this wealth of genetic variation data via the EVA API.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

EMBL-EBI: Ensembl Variant Effect Predictor (VEP) new [Places] 13:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This interactive workshop offers participants hands-on experience in the use of the Ensembl VEP to annotate genetic variants with the effects they have on Ensembl genes, and the known information about co-located variants. We will also look at known genes and variants, including the types of data available and where they come from.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

Tue 20
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.

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 21
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.

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 22
Advanced ChIP-seq data analysis new (1 of 2) [Places] 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 data and provide hands-on training on the latest analytical approaches.

The course starts with an introduction to ChIP-seq experiments and discusses quality control issues. We first show 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. We then focus on the analysis of differential binding when comparing between different samples. In addition, there is a short introduction to ATAC-seq data analysis for the detection of regions of open chromatin.

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 23
Advanced ChIP-seq data analysis new (2 of 2) [Places] 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 data and provide hands-on training on the latest analytical approaches.

The course starts with an introduction to ChIP-seq experiments and discusses quality control issues. We first show 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. We then focus on the analysis of differential binding when comparing between different samples. In addition, there is a short introduction to ATAC-seq data analysis for the detection of regions of open chromatin.

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 27
EMBL-EBI: Introduction to Interpro new [Places] 09:00 - 12:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Employ InterPro to help you answer your research questions!

This workshop will help you find out why there is a need to automatically annotate proteins, how protein family databases can help meet this challenge, and how InterPro pulls together a number of such databases, allowing you to classify unknown protein sequences and identify their function. The module is a combination of presentations and hands-on practical exercises. You will explore the various features of an InterPro entry, and design a workflow to utilise InterPro in the analysis of real world data.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

Wed 28
Basic statistics and data handling (1 of 3) [Full] 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 lectures, workshops and hands-on practicals – 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 we will continue to explore core concepts of statistics, focusing on linear regression and multiple testing correction.

Course materials are available here.

This event is supported by a BBSRC Strategic Training Awards for Research Skills (STARS) grant.

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

March 2018

Thu 1
Basic statistics and data handling (2 of 3) [Full] 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 lectures, workshops and hands-on practicals – 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 we will continue to explore core concepts of statistics, focusing on linear regression and multiple testing correction.

Course materials are available here.

This event is supported by a BBSRC Strategic Training Awards for Research Skills (STARS) grant.

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

Fri 2
Basic statistics and data handling (3 of 3) [Full] 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 lectures, workshops and hands-on practicals – 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 we will continue to explore core concepts of statistics, focusing on linear regression and multiple testing correction.

Course materials are available here.

This event is supported by a BBSRC Strategic Training Awards for Research Skills (STARS) grant.

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

Mon 12
Introduction to using the Ensembl Genome Browser [Places] 09:30 - 12:30 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.

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
EMBL-EBI: Interactions & Pathways [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop is aimed at giving life scientists training on how to explore and use protein interaction and pathway bioinformatics resources. This course looks at the data repositories, resources and tools available and shows attendees how to both find information on a single molecule and how to build high-quality networks to enable network analysis.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

Wed 14
EMBL-EBI: Network Analysis with Cytoscape and PSICQUIC [Places] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This module provides an introduction to the theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to analyse large-scale datasets generated these to by techniques such as RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of Cytoscape and selected network analysis apps.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

Thu 15
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. Functions and modules are now the focus of a new 1-day course, Working with Python: functions and modules.

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

Fri 16
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. Functions and modules are now the focus of a new 1-day course, Working with Python: functions and modules.

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

Wed 28
Analysis of RNA-seq data with Bioconductor (1 of 2) [Full] 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 bulk RNA-seq data. We will present a workflow for the analysis RNA-seq data starting from aligned reads in bam format and producing a list of differentially-expressed genes. We will also describe the various resources available through Bioconductor to annotate, visualise and gain biological insight from the differential expression results.

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

Thu 29
Analysis of RNA-seq data with Bioconductor (2 of 2) [Full] 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 bulk RNA-seq data. We will present a workflow for the analysis RNA-seq data starting from aligned reads in bam format and producing a list of differentially-expressed genes. We will also describe the various resources available through Bioconductor to annotate, visualise and gain biological insight from the differential expression results.

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

April 2018

Thu 5
Working with Python: functions and modules [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course will cover concepts and strategies for working more effectively with Python with the aim of writing reusable code. In the morning session, we will briefly go over the basic syntax, data structures and control statements. This will be followed by an introduction to writing user-defined functions. We will finish the course by looking into how to incorporate existing python modules and packages into your programs as well as writing you own modules.

Course materials can be found here.

Note: this one-day 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.

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



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Training events

March 2018

6 6
Bioinformatics Resources for Protein Biology
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
6th 8th Mar

Are you aware of the wide range of protein data resources that can easily be accessed and explored to enhance your research? Do you want to know more about the sequence of your protein and its functions? Wondered whether a structure of your protein exists and how to explore it? Want to know more about the potential complexes and reaction pathways your protein of interest is involved in, giving you a better overview of its biological context?

First come, first served

6th 13 13
ENA Sequence Retrieval workshop
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
13th Mar

This free course will introduce users to the powerful search and retrieval methods available within ENA (European Nucleotide Archive) for annotated sequences, genomes, raw data and metadata, as well as download options from the ENA browser and an introduction to the various ENA browser tools.

First come, first served

19 19
Bioinformatics for Discovery
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
19th 20th Mar

An online master’s level short course aimed at providing discovery scientists from a range of fields (e.g. agri-food, pharma and consumer goods) with the skills and knowledge required to apply bioinformatics techniques in their everyday work. The course starts with a 2-day face to face workshop, followed by a 6 month period of online study.

Open application with selection

19th

April 2018

16 16
Advanced RNA-Seq Analysis
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
16th 20th Apr

The aim of this course is to familiarise the participants with advanced data analysis methodologies and provide hands-on training on the latest analytical approaches.

Open application with selection

16th 23 23
Ensembl programmatic access with Perl, April 2018
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
23rd 26th Apr

Work with the Ensembl developers to master the Ensembl Perl APIs and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments.

First come, first served

23rd 25 25
Ensembl Browser workshop, EBI April 2018
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
25th Apr

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

May 2018

14 14
Networks and Pathways
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
14th 18th May

This course will provide life scientists training on exploring and using protein interaction bioinformatics resources. The content examines the data repositories, resources and tools available to explore and analyse large datasets and introduce the principles of biological network and pathway analysis.

Open application with selection

14th

June 2018

3 3
In Silico Systems Biology
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
3rd 8th Jun

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

3rd 4 4
Bioinformatics Resources for Immunologists
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
4th 8th Jun

This course will introduce and explore a number of key bioinformatics tools and resources that can be applied to immunological research.

Open application with selection

4th 12 12
Bioinformatics for Core Facility Managers
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
12th 14th Jun

Bioinformatics core facilities play an essential role in enabling research in the molecular life sciences. 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.

Open application with selection

12th 12 12
Bioinformatics for Principal Investigators
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
12th 14th 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. This course will not provide a platform for teaching hands-on bioinformatics analysis.

Open application with selection

12th 18 18
Cancer Genomics
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
18th 21st Jun

This course will focus on the analysis of data from genomic studies of Cancer.

Open application with selection

18th 25 25
Summer School in Bioinformatics
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
25th 29th Jun

This popular computational course is run jointly with Wellcome Trust Advanced Courses and Scientific Conferences and will provide an introduction to the use of bioinformatics in biological research using publicly available data resources and tools.

Open application with selection

25th

July 2018

15 15
Proteomics Bioinformatics
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
15th 20th Jul

This course provides hands-on training in the basics of mass spectrometry and proteomics bioinformatics.

Open application with selection

15th 17 17
Metagenomics Bioinformatics
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
17th 20th Jul

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

17th

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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

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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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