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Bioinformatics Training

Bioinformatics course timetable

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Mon 28 May – Fri 13 Jul

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May 2018

Thu 31
Working with Python: functions and modules POSTPONED 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.

June 2018

Fri 1
Big Data and Cloud Computing new [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Recent advances in genomics, proteomics, imaging and other technologies, have resulted in data being generated at a faster rate than they can be meaningfully analysed. In this course we will show you how cloud computing can be used to meet the challenges of storage, management and analysis of big data. The first half of the course will introduce cloud infrastructure technologies. The second half will cover tools for collaborative working, resource management, and creation of workflows. The instructors will demonstrate how they are using cloud computing in their own research.

N.B. If you sign up for this course, you will be automatically registered for an AWS educate account, which will provide you with sufficient AWS credits to complete the course exercises. If you decide to continue using cloud computing after the course, you will need to either purchase more credits or apply for a grant from programs like: AWS Cloud Credits for Research, Microsoft Azure for Research or Google Cloud Platform Education Grants.

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

Tue 12
Open Targets: Integrating genetics and genomics for disease biology and translational medicine [Places] 13:00 - 16:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Open Targets is a public-private partnership to use human genetics, genomic data and drug information for systematic identification and prioritisation of therapeutic targets. The consortium was founded in 2014 by GSK, EMBL-EBI and the Wellcome Sanger Institute, and later welcomed three new partners, Biogen, Takeda, and Celgene. Underpinning this partnership is the Open Targets Platform, an open source, user-friendly web interface to investigate causal links between genes, pathways and diseases. These links are computed, scored and ranked using biological evidence integrated from many public data sources, including the NHGRI-EBI GWAS Catalog, Genomics England, PheWAS, ClinVar, Expression Atlas, UniProt, and ChEMBL to name a few.

In addition to data integration, Open Targets also generates new data using human cellular models (e.g. organoids, iPSCs) and genome editing (CRISPR/Cas9) to identify drug targets in oncology, immunology and neurodegenerative diseases. This will be publicly available in the public domain and integrated into the Open Targets Platform.

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 13
Introduction to Scientific Figure Design [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides a practical guide to producing figures for use in reports and publications.

It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures.

The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools.

Further information and access to the course materials is here.

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

Thu 14
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.

Fri 15
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.

Mon 18
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.

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 19
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.

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 20
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.

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 21
Statistics for Biologists in R (1 of 2) [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences using the R software package.

In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to generalised linear model analysis. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory.

After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques.

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 22
Statistics for Biologists in R (2 of 2) [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences using the R software package.

In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to generalised linear model analysis. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory.

After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques.

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 MATLAB for biologists (1 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts.

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

Tue 26
An Introduction to MATLAB for biologists (2 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts.

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 27
Analysis of DNA Methylation using Sequencing [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course will cover all aspects of the analysis of DNA methylation using sequencing, including primary analysis, mapping and quality control of BS-Seq data, common pitfalls and complications.

It will also include exploratory analysis of methylation, looking at different methods of quantitation, and a variety of ways of looking more widely at the distribution of methylation over the genome. Finally the course will look at statistical methods to predict differential methylation.

The course will be comprised of a mixture of theoretical lectures and practicals covering a range of different software packages.

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
Data Carpentry in R (1 of 2) [Places] 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.

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

Fri 29
Data Carpentry in R (2 of 2) [Places] 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.

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

July 2018

Mon 2
An introduction to metabolomics and its application in life-sciences (1 of 2) [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The goal of metabolomics is to identify and quantify the complete biochemical composition of a biological sample. With the increase in genomic, transcriptomic and proteomic information there is a growing need to understand the metabolic phenotype that these genes and proteins ultimately control.

The aim of this course is to provide an overview of metabolomics and its applications in life sciences, clinical and environmental settings. Over 2 days we will introduce different techniques used to extract metabolites and analyse samples to collect metabolomic data (such as HPLC or GC-based MS and NMR), present how to analyse such data, how to identify metabolites using online databases and how to map the metabolomic data to metabolic pathways.

The course content will predominantly be based on analysing samples from model plant species such as Arabidopsis thaliana but the procedures are transferable to all other organisms, including clinical and environmental settings.

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

Tue 3
An introduction to metabolomics and its application in life-sciences (2 of 2) [Full] 09:30 - 18:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The goal of metabolomics is to identify and quantify the complete biochemical composition of a biological sample. With the increase in genomic, transcriptomic and proteomic information there is a growing need to understand the metabolic phenotype that these genes and proteins ultimately control.

The aim of this course is to provide an overview of metabolomics and its applications in life sciences, clinical and environmental settings. Over 2 days we will introduce different techniques used to extract metabolites and analyse samples to collect metabolomic data (such as HPLC or GC-based MS and NMR), present how to analyse such data, how to identify metabolites using online databases and how to map the metabolomic data to metabolic pathways.

The course content will predominantly be based on analysing samples from model plant species such as Arabidopsis thaliana but the procedures are transferable to all other organisms, including clinical and environmental settings.

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

Wed 4
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.

Fri 6
R object-oriented programming and package development [Places] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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

Relevant teaching materials are available here and the sequences example package used as template in the course can be found here.

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

Mon 9
Image Analysis for Biologists (1 of 3) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines.

On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based on Fiji, an extensible open source software package.

On day 2, we will cover time series processing and cell tracking using TrackMate and advanced image segmentation using Ilastik. Additionally, in the afternoon we will run a study design and data clinic (sign up will be required) for participants that wish to discuss their experiments.

On day 3, we will describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualisation, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager).

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 10
Image Analysis for Biologists (2 of 3) [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines.

On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based on Fiji, an extensible open source software package.

On day 2, we will cover time series processing and cell tracking using TrackMate and advanced image segmentation using Ilastik. Additionally, in the afternoon we will run a study design and data clinic (sign up will be required) for participants that wish to discuss their experiments.

On day 3, we will describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualisation, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager).

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 11
Image Analysis for Biologists (3 of 3) [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines.

On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based on Fiji, an extensible open source software package.

On day 2, we will cover time series processing and cell tracking using TrackMate and advanced image segmentation using Ilastik. Additionally, in the afternoon we will run a study design and data clinic (sign up will be required) for participants that wish to discuss their experiments.

On day 3, we will describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualisation, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager).

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 12
An Introduction to Solving Biological Problems with Python (1 of 2) [Places] 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 13
An Introduction to Solving Biological Problems with Python (2 of 2) [Places] 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.