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Bioinformatics Training

Bioinformatics course timetable

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Thu 18 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 [Places] 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.