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Bioinformatics Training

Bioinformatics course timetable

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Sun 26 Feb – Thu 20 Apr

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February 2017

Tue 28
EMBL-EBI: Interactions & Pathways - Reactome [Places] 09:00 - 11:45 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will give an introduction to the Reactome pathway database website and analysis tools, using short presentations and practical hands-on exercises. The session will also explain where to learn more, get help, and how to become involved in adding more pathway information to Reactome.

Further information can be found here.

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.

March 2017

Fri 3
Using the Ensembl Genome Browser [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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

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

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 7
CRUK: Introduction to Galaxy: Data Manipulation and Visualisation [Places] 09:30 - 16:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

Galaxy is an open, web-based platform for data-intensive life science research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses.

This introductory course will cover Galaxy's basic functionality, simple data manipulation and visualisation. This event is mostly targeted at first time users.

Further information is available from the course website.

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

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

Mon 13
Finding and accessing human genome data new [Places] 09:30 - 12:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Researchers rely on acquiring external data to validate, benchmark and supplement research findings. Funders require researchers to make their datasets accessible for further reuse.

The goal of this workshop is to bring to the fore existing challenges with genomic data access and reuse. We will introduce a number of tools and resources to simplify #dataaccess and #datasharing.

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

CRUK: Basic Unix [Full] 11:00 - 17:00 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

The Unix shell has existed since the early days of computers, and yet is still the preferred way to run many popular Bioinformatics tools. This course aims to take the novice and turn them into a beginning Linux user. We will describe the Linux environment so they can start to utilise command-line tools and feel comfortable using a text-based way of interacting with a computer.

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

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

Tue 14
An Introduction to Solving Biological Problems with PERL (1 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course is aimed at those new to programming and provides an introduction to programming using Perl.

During this course you will learn the basics of the Perl programming language, including how to store data in Perl’s standard data structures such as arrays and hashes, and how to process data using loops, functions, and many of Perl’s built in operators. You will learn how to write and run your own Perl scripts and how to pass options and files to them. The course also covers sorting, regular expressions, references and multi-dimensional data structures.

The course will be taught using the online Learning Perl materials created by Sofia Robb of the University of California Riverside.

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

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

Wed 15
An Introduction to Solving Biological Problems with PERL (2 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course is aimed at those new to programming and provides an introduction to programming using Perl.

During this course you will learn the basics of the Perl programming language, including how to store data in Perl’s standard data structures such as arrays and hashes, and how to process data using loops, functions, and many of Perl’s built in operators. You will learn how to write and run your own Perl scripts and how to pass options and files to them. The course also covers sorting, regular expressions, references and multi-dimensional data structures.

The course will be taught using the online Learning Perl materials created by Sofia Robb of the University of California Riverside.

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

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

Thu 16
Analysis of single cell RNA-seq data new (1 of 2) [Places] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging.

In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq.

The course website providing links to the course materials can be found here.

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

Fri 17
Analysis of single cell RNA-seq data new (2 of 2) [Places] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging.

In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq.

The course website providing links to the course materials can be found here.

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

Mon 27
Python functions and modules: best practices new [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.

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.

CRUK: Data Analysis and Visualisation in R new [Full] 09:30 - 17:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

This course introduces some relatively new additions to the R programming language: dplyr and ggplot2. In combination these R packages provide a powerful toolkit to make the process of manipulating and visualising data easy and intuitive.

Materials for this course can be found here.

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

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

Tue 28
Introduction to high-throughput sequencing data analysis (1 of 4) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to high-throughput sequencing (HTS) data analysis methodologies. Lectures will give insight into how biological knowledge can be generated from RNA-seq, ChIP-seq and DNA-seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq, ChIP-seq and DNA-seq data under the guidance of the lecturers and teaching assistants. It is aimed at researchers who are applying or planning to apply HTS technologies and bioinformatics methods in their research.

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 29
Introduction to high-throughput sequencing data analysis (2 of 4) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to high-throughput sequencing (HTS) data analysis methodologies. Lectures will give insight into how biological knowledge can be generated from RNA-seq, ChIP-seq and DNA-seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq, ChIP-seq and DNA-seq data under the guidance of the lecturers and teaching assistants. It is aimed at researchers who are applying or planning to apply HTS technologies and bioinformatics methods in their research.

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 30
Introduction to high-throughput sequencing data analysis (3 of 4) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to high-throughput sequencing (HTS) data analysis methodologies. Lectures will give insight into how biological knowledge can be generated from RNA-seq, ChIP-seq and DNA-seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq, ChIP-seq and DNA-seq data under the guidance of the lecturers and teaching assistants. It is aimed at researchers who are applying or planning to apply HTS technologies and bioinformatics methods in their research.

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 31
Introduction to high-throughput sequencing data analysis (4 of 4) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course provides an introduction to high-throughput sequencing (HTS) data analysis methodologies. Lectures will give insight into how biological knowledge can be generated from RNA-seq, ChIP-seq and DNA-seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq, ChIP-seq and DNA-seq data under the guidance of the lecturers and teaching assistants. It is aimed at researchers who are applying or planning to apply HTS technologies and bioinformatics methods in their research.

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

April 2017

Mon 3
Basic statistics and data handling new charged (1 of 3) [Places] 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 statistic, focusing on linear regression and multiple testing correction.

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.

Tue 4
Basic statistics and data handling new charged (2 of 3) [Places] 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 statistic, focusing on linear regression and multiple testing correction.

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.

CRUK: Introduction to visualising Next Generation Sequencing data with IGV [Full] 12:30 - 17:00 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

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

In this course, we explain the common file formats generated by sequencing technologies and how they can be manipulated and explored by non-bioinformaticians. The tool that we will use is the Integrative Genomics Viewer (IGV).

If time allows, there will be time at the end of the session for you to explore your own datasets with the assistance of the instructors.

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

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

Wed 5
Basic statistics and data handling new charged (3 of 3) [Places] 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 statistic, focusing on linear regression and multiple testing correction.

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.

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

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

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

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

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

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

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

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

Mon 10
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 from scratch and to customize more complex code to fit their needs.

The Course Web Site providing links to the course materials is 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, Python functions and modules: best practices.

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

Tue 11
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 from scratch and to customize more complex code to fit their needs.

The Course Web Site providing links to the course materials is 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, Python functions and modules: best practices.

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

Wed 19
Molecular Phylogenetics (1 of 3) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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

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

Thu 20
Molecular Phylogenetics (2 of 3) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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

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