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Bioinformatics Training

Bioinformatics course timetable

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Wed 12 Jun – Fri 26 Jul

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June 2019

Wed 12
An Introduction to Solving Biological Problems with R (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Please note that this course has been discontinued and has been replaced by the Introduction to R for biologists.

R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research.

In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided.

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

Please note that although we will demonstrate how to perform statistical analysis in R, we will not cover the theory of statistical analysis in this course. Those seeking an in-depth explanation of how to perform and interpret statistical tests are advised to see the list of Related courses. Moreover, those with some programming experience in other languages (e.g. Python, Perl) might wish to attend the follow-on Data Analysis and Visualisation in R course.

This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1).

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Thu 13
Data Science in Python (1 of 2) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course covers concepts and strategies for working more effectively with Python with the aim of writing reusable code, using function and libraries. Participants will acquire a working knowledge of key concepts which are prerequisites for advanced programming in Python e.g. writing modules and classes.

Note: this course is the continuation of the Introduction to Solving Biological Problems with Python; participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Fri 14
Data Science in Python (2 of 2) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course covers concepts and strategies for working more effectively with Python with the aim of writing reusable code, using function and libraries. Participants will acquire a working knowledge of key concepts which are prerequisites for advanced programming in Python e.g. writing modules and classes.

Note: this course is the continuation of the Introduction to Solving Biological Problems with Python; participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Mon 17
An Introduction to MATLAB for biologists (1 of 2) Finished 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.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Tue 18
An Introduction to MATLAB for biologists (2 of 2) Finished 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.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Wed 19
Biological data analysis using InterMine (User Interface) Finished 09:30 - 12:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

InterMine is a freely available data integration and analysis system that has been used to create a suite of databases for the analysis of large and complex biological data sets.

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants, nematodes, fly, zebrafish and more recently human. See here for a comprehensive list of InterMine databases.

The InterMine web interface offers sophisticated query and visualisation tools, as well as comprehensive web services for bioinformaticians. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression.

This course will focus on the InterMine web interface and will introduce participants to all aspects of the user interface, starting with some simple exercises and building up to more complex analysis encompassing several analysis tools and comparative analysis across organisms. The exercises will mainly use the fly, human and mouse databases, but the course is applicable to anyone working with data for which an InterMine database is available.

This event is organised alongside a half day course on Biological data analysis using the InterMine API. More information on this event are available here.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Biological data analysis using the InterMine API new Finished 13:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

InterMine is a freely available data integration and analysis system that has been used to create a suite of databases for the analysis of large and complex biological data sets.

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants, nematodes, fly, zebrafish and more recently human. See here for a comprehensive list of InterMine databases. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression.

InterMine provides sophisticated query and visualisation tools both through a web interface and an extensive API; this course will focus on programmatic access to InterMine through its API and on running InterMine searches using Python, Perl and R scripts. The exercises will mainly use the fly, human and mouse databases, but the course is applicable to anyone working with data for which an InterMine database is available.

This event is organised alongside a half day course on Biological data analysis using the InterMine User Interface. More information on this event are available here.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Thu 20
Protein Structure Analysis new (1 of 2) Finished 10:00 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course covers analytical approaches for the interpretation of biomacromolecular structures including how to find information about the structure and function of your protein sequence using CATH, principles of modern state-of-the-art protein modelling with Phyre2 and methods for predicting the effects of mutations on protein structure and function using the SAAP family of tools. In addition, we will look at mapping genetic variants onto structures as well as visualisation and basic analysis of protein structures.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Fri 21
Protein Structure Analysis new (2 of 2) Finished 10:00 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This course covers analytical approaches for the interpretation of biomacromolecular structures including how to find information about the structure and function of your protein sequence using CATH, principles of modern state-of-the-art protein modelling with Phyre2 and methods for predicting the effects of mutations on protein structure and function using the SAAP family of tools. In addition, we will look at mapping genetic variants onto structures as well as visualisation and basic analysis of protein structures.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Mon 24
Image Analysis for Biologists (1 of 3) Finished 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).

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Tue 25
Image Analysis for Biologists (2 of 3) Finished 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).

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Wed 26
Image Analysis for Biologists (3 of 3) Finished 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).

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Thu 27
An introduction to metabolomics and its application in life-sciences (1 of 2) Finished 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.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Fri 28
An introduction to metabolomics and its application in life-sciences (2 of 2) Finished 09:30 - 17:30 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.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

July 2019

Mon 1
Summer School - Bioinformatics for Biologists: An introduction to Data Exploration, Statistics and Reproducibility charged (1 of 5) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 1-week course aims to provide an introduction to the best practices and tools needed to perform bioinformatics research effectively and reproducibly.

Focusing on solutions around handling biological data, we will cover introductory lessons in data manipulation and visualisation in R, statistical analyses, and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility.

More information about the course can be found here.

This course is run in collaboration with the Institute of Continuing Education.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Tue 2
Summer School - Bioinformatics for Biologists: An introduction to Data Exploration, Statistics and Reproducibility charged (2 of 5) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 1-week course aims to provide an introduction to the best practices and tools needed to perform bioinformatics research effectively and reproducibly.

Focusing on solutions around handling biological data, we will cover introductory lessons in data manipulation and visualisation in R, statistical analyses, and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility.

More information about the course can be found here.

This course is run in collaboration with the Institute of Continuing Education.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Wed 3
Summer School - Bioinformatics for Biologists: An introduction to Data Exploration, Statistics and Reproducibility charged (3 of 5) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 1-week course aims to provide an introduction to the best practices and tools needed to perform bioinformatics research effectively and reproducibly.

Focusing on solutions around handling biological data, we will cover introductory lessons in data manipulation and visualisation in R, statistical analyses, and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility.

More information about the course can be found here.

This course is run in collaboration with the Institute of Continuing Education.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Thu 4
Summer School - Bioinformatics for Biologists: An introduction to Data Exploration, Statistics and Reproducibility charged (4 of 5) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 1-week course aims to provide an introduction to the best practices and tools needed to perform bioinformatics research effectively and reproducibly.

Focusing on solutions around handling biological data, we will cover introductory lessons in data manipulation and visualisation in R, statistical analyses, and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility.

More information about the course can be found here.

This course is run in collaboration with the Institute of Continuing Education.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Fri 5
Summer School - Bioinformatics for Biologists: An introduction to Data Exploration, Statistics and Reproducibility charged (5 of 5) Finished 09:30 - 17:15 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 1-week course aims to provide an introduction to the best practices and tools needed to perform bioinformatics research effectively and reproducibly.

Focusing on solutions around handling biological data, we will cover introductory lessons in data manipulation and visualisation in R, statistical analyses, and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility.

More information about the course can be found here.

This course is run in collaboration with the Institute of Continuing Education.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Mon 8
Variant Discovery with GATK4 (1 of 4) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will focus on the core steps involved in calling germline short variants, somatic short variants, and copy number alterations with the Broad’s Genome Analysis Toolkit (GATK), using “Best Practices” developed by the GATK methods development team. A team of methods developers and instructors from the Data Sciences Platform at Broad will give talks explaining the rationale, theory, and real-world applications of the GATK Best Practices. You will learn why each step is essential to the variant-calling process, what key operations are performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. If you are an experienced GATK user, you will gain a deeper understanding of how the GATK works under-the-hood and how to improve your results further, especially with respect to the latest innovations.

  • Day 1: Introductory and Overview. The first day of the workshop gives a high-level overview of various topics in the morning, and in the afternoon we show how these concepts apply to a case study. The case study is tailored based on the audience, as represented by their answers in our pre-workshop survey.
  • Day 2: Germline Short Variant Discovery. Today we dive deep into the tools that make up the GATK Best Practices Pipeline. In the morning we discuss variant discovery, and in the afternoon we look at refinement and filtering. You will have the opportunity both in the morning and in the afternoon to get hands-on with these tools and run them yourself.
  • Day 3: Somatic Variant Discovery. Today we will cover Somatic Variant Discovery in more depth. In the morning we primarily focus on calling short variants with Mutect2, and in the afternoon we look at copy number alterations. Both sections have a paired hands-on activity.
  • Day 4: Pipelining. Over the first three days, you would have learned a lot about different pipelines and tools that you can use in GATK. Today we will be learning all about how those pipelines are written in a language called WDL. In the afternoon we cover other useful topics to working on the cloud, including Docker and BigQuery.

Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.

The hands-on GATK tutorials in this workshop will be conducted on Terra, a new platform developed at Broad in collaboration with Verily Life Sciences for accessing data, running analysis tools and collaborating securely and seamlessly.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Tue 9
Variant Discovery with GATK4 (2 of 4) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will focus on the core steps involved in calling germline short variants, somatic short variants, and copy number alterations with the Broad’s Genome Analysis Toolkit (GATK), using “Best Practices” developed by the GATK methods development team. A team of methods developers and instructors from the Data Sciences Platform at Broad will give talks explaining the rationale, theory, and real-world applications of the GATK Best Practices. You will learn why each step is essential to the variant-calling process, what key operations are performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. If you are an experienced GATK user, you will gain a deeper understanding of how the GATK works under-the-hood and how to improve your results further, especially with respect to the latest innovations.

  • Day 1: Introductory and Overview. The first day of the workshop gives a high-level overview of various topics in the morning, and in the afternoon we show how these concepts apply to a case study. The case study is tailored based on the audience, as represented by their answers in our pre-workshop survey.
  • Day 2: Germline Short Variant Discovery. Today we dive deep into the tools that make up the GATK Best Practices Pipeline. In the morning we discuss variant discovery, and in the afternoon we look at refinement and filtering. You will have the opportunity both in the morning and in the afternoon to get hands-on with these tools and run them yourself.
  • Day 3: Somatic Variant Discovery. Today we will cover Somatic Variant Discovery in more depth. In the morning we primarily focus on calling short variants with Mutect2, and in the afternoon we look at copy number alterations. Both sections have a paired hands-on activity.
  • Day 4: Pipelining. Over the first three days, you would have learned a lot about different pipelines and tools that you can use in GATK. Today we will be learning all about how those pipelines are written in a language called WDL. In the afternoon we cover other useful topics to working on the cloud, including Docker and BigQuery.

Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.

The hands-on GATK tutorials in this workshop will be conducted on Terra, a new platform developed at Broad in collaboration with Verily Life Sciences for accessing data, running analysis tools and collaborating securely and seamlessly.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Wed 10
Variant Discovery with GATK4 (3 of 4) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will focus on the core steps involved in calling germline short variants, somatic short variants, and copy number alterations with the Broad’s Genome Analysis Toolkit (GATK), using “Best Practices” developed by the GATK methods development team. A team of methods developers and instructors from the Data Sciences Platform at Broad will give talks explaining the rationale, theory, and real-world applications of the GATK Best Practices. You will learn why each step is essential to the variant-calling process, what key operations are performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. If you are an experienced GATK user, you will gain a deeper understanding of how the GATK works under-the-hood and how to improve your results further, especially with respect to the latest innovations.

  • Day 1: Introductory and Overview. The first day of the workshop gives a high-level overview of various topics in the morning, and in the afternoon we show how these concepts apply to a case study. The case study is tailored based on the audience, as represented by their answers in our pre-workshop survey.
  • Day 2: Germline Short Variant Discovery. Today we dive deep into the tools that make up the GATK Best Practices Pipeline. In the morning we discuss variant discovery, and in the afternoon we look at refinement and filtering. You will have the opportunity both in the morning and in the afternoon to get hands-on with these tools and run them yourself.
  • Day 3: Somatic Variant Discovery. Today we will cover Somatic Variant Discovery in more depth. In the morning we primarily focus on calling short variants with Mutect2, and in the afternoon we look at copy number alterations. Both sections have a paired hands-on activity.
  • Day 4: Pipelining. Over the first three days, you would have learned a lot about different pipelines and tools that you can use in GATK. Today we will be learning all about how those pipelines are written in a language called WDL. In the afternoon we cover other useful topics to working on the cloud, including Docker and BigQuery.

Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.

The hands-on GATK tutorials in this workshop will be conducted on Terra, a new platform developed at Broad in collaboration with Verily Life Sciences for accessing data, running analysis tools and collaborating securely and seamlessly.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Thu 11
Variant Discovery with GATK4 (4 of 4) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will focus on the core steps involved in calling germline short variants, somatic short variants, and copy number alterations with the Broad’s Genome Analysis Toolkit (GATK), using “Best Practices” developed by the GATK methods development team. A team of methods developers and instructors from the Data Sciences Platform at Broad will give talks explaining the rationale, theory, and real-world applications of the GATK Best Practices. You will learn why each step is essential to the variant-calling process, what key operations are performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. If you are an experienced GATK user, you will gain a deeper understanding of how the GATK works under-the-hood and how to improve your results further, especially with respect to the latest innovations.

  • Day 1: Introductory and Overview. The first day of the workshop gives a high-level overview of various topics in the morning, and in the afternoon we show how these concepts apply to a case study. The case study is tailored based on the audience, as represented by their answers in our pre-workshop survey.
  • Day 2: Germline Short Variant Discovery. Today we dive deep into the tools that make up the GATK Best Practices Pipeline. In the morning we discuss variant discovery, and in the afternoon we look at refinement and filtering. You will have the opportunity both in the morning and in the afternoon to get hands-on with these tools and run them yourself.
  • Day 3: Somatic Variant Discovery. Today we will cover Somatic Variant Discovery in more depth. In the morning we primarily focus on calling short variants with Mutect2, and in the afternoon we look at copy number alterations. Both sections have a paired hands-on activity.
  • Day 4: Pipelining. Over the first three days, you would have learned a lot about different pipelines and tools that you can use in GATK. Today we will be learning all about how those pipelines are written in a language called WDL. In the afternoon we cover other useful topics to working on the cloud, including Docker and BigQuery.

Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.

The hands-on GATK tutorials in this workshop will be conducted on Terra, a new platform developed at Broad in collaboration with Verily Life Sciences for accessing data, running analysis tools and collaborating securely and seamlessly.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Fri 12
Statistical Analysis using R Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Statistics are an important part of most modern studies and being able to effectively use a statistical package will help you to understand your results.

This course provides an introduction to some statistical techniques through the use of the R language. Topics covered include: Chi2 and Fisher tests, descriptive statistics, t-test, analysis of variance and regression.

Students will run analyses using statistical and graphical skills taught during the session.

The course manual can be found here.

This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1).

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Fri 26
CRUK: Image Analysis with Fiji Finished 12:30 - 17:00 eLearning 1 - School of Clinical Medicine

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

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

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