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Bioinformatics Training

Bioinformatics course timetable

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Thu 20 Feb – Fri 24 Apr

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February 2020

Thu 20
An Introduction to Machine Learning (2 of 3) 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 be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes.

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
An Introduction to Machine Learning (3 of 3) 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 be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes.

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
Statistics bootcamp using R new (1 of 4) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 4-days bootcamp provides an in depth look at statistical analyses using R.

Day 1 aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. As well as introducing core R language concepts, this course also provides the basics of using the Tidyverse for data maniupulation, and ggplot for plotting. It will focus on entering and manipulating data in R and producing simple graphs.

Day 2-4 will focus on the statistical possibilities of R, covering from experimental design to analysis of quantitative and qualitative data. Ample time will be given to participants to practice different type of analysis and interact with the trainers to discuss their statistical problems.

This event is organized in collaboration with the Babraham Institutes's Bioinformatics Group and it 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.

Wed 26
Statistics bootcamp using R new (2 of 4) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 4-days bootcamp provides an in depth look at statistical analyses using R.

Day 1 aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. As well as introducing core R language concepts, this course also provides the basics of using the Tidyverse for data maniupulation, and ggplot for plotting. It will focus on entering and manipulating data in R and producing simple graphs.

Day 2-4 will focus on the statistical possibilities of R, covering from experimental design to analysis of quantitative and qualitative data. Ample time will be given to participants to practice different type of analysis and interact with the trainers to discuss their statistical problems.

This event is organized in collaboration with the Babraham Institutes's Bioinformatics Group and it 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 27
Statistics bootcamp using R new (3 of 4) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 4-days bootcamp provides an in depth look at statistical analyses using R.

Day 1 aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. As well as introducing core R language concepts, this course also provides the basics of using the Tidyverse for data maniupulation, and ggplot for plotting. It will focus on entering and manipulating data in R and producing simple graphs.

Day 2-4 will focus on the statistical possibilities of R, covering from experimental design to analysis of quantitative and qualitative data. Ample time will be given to participants to practice different type of analysis and interact with the trainers to discuss their statistical problems.

This event is organized in collaboration with the Babraham Institutes's Bioinformatics Group and it 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 28
Statistics bootcamp using R new (4 of 4) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This 4-days bootcamp provides an in depth look at statistical analyses using R.

Day 1 aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. As well as introducing core R language concepts, this course also provides the basics of using the Tidyverse for data maniupulation, and ggplot for plotting. It will focus on entering and manipulating data in R and producing simple graphs.

Day 2-4 will focus on the statistical possibilities of R, covering from experimental design to analysis of quantitative and qualitative data. Ample time will be given to participants to practice different type of analysis and interact with the trainers to discuss their statistical problems.

This event is organized in collaboration with the Babraham Institutes's Bioinformatics Group and it 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.

March 2020

Tue 10
Using CellProfiler and CellProfiler Analyst to analyse biological images (1 of 2) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Microscopy experiments have proven to be a powerful means of generating information-rich data for biological applications. From small-scale microscopy experiments to time-lapse movies and high-throughput screens, automatic image analysis is more objective and quantitative and less tedious than visual inspection.

This course will introduce users to the free open-source image analysis program CellProfiler and its companion data exploration program CellProfiler Analyst. We will show how CellProfiler can be used to analyse a variety of types of imaging experiments. We will also briefly discuss the basic principles of supervised machine learning with CellProfiler Analyst in order to score complex and subtle phenotypes.

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 11
Using CellProfiler and CellProfiler Analyst to analyse biological images (2 of 2) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Microscopy experiments have proven to be a powerful means of generating information-rich data for biological applications. From small-scale microscopy experiments to time-lapse movies and high-throughput screens, automatic image analysis is more objective and quantitative and less tedious than visual inspection.

This course will introduce users to the free open-source image analysis program CellProfiler and its companion data exploration program CellProfiler Analyst. We will show how CellProfiler can be used to analyse a variety of types of imaging experiments. We will also briefly discuss the basic principles of supervised machine learning with CellProfiler Analyst in order to score complex and subtle phenotypes.

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 12
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. Concepts and strategies for working more effectively with Python are now the focus of a new 2-days course, Data Science 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 or register your interest by linking here.

Fri 13
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. Concepts and strategies for working more effectively with Python are now the focus of a new 2-days course, Data Science 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 or register your interest by linking here.

Mon 23
Introduction to R for Biologists (1 of 2) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard.

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 24
Introduction to R for Biologists (2 of 2) [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard.

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 25
Analysis of bulk RNA-seq data (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.

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 26
Analysis of bulk RNA-seq data (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.

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 27
Analysis of bulk RNA-seq data (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.

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.

April 2020

Wed 1
Molecular Phylogenetics (1 of 3) [Places] 09:00 - 17:00 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.

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 2
Molecular Phylogenetics (2 of 3) [Places] 09:00 - 17:00 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.

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 3
Molecular Phylogenetics (3 of 3) [Places] 09:00 - 17:00 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.

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 6
Data Science in Python (1 of 2) [Places] 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 or register your interest by linking here.

Tue 7
Data Science in Python (2 of 2) [Places] 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 or register your interest by linking here.

Thu 16
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.

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 17
Ensembl REST API workshop [Places] 09:30 - 15:30 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 is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write scripts to call them.

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 22
Extracting biological information from gene lists [Full] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists.

This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication.

Course materials 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 your interest by linking here.

Thu 23
Introduction to metagenomics new (1 of 2) [Full] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This two days course will focus on the theory and applications of metagenomics, for the analysis of complex microbiomes (microbial communities). The course will include theoretical (~40%) and practical (~60%) training. We will start with the fastest, simplest and cheapest amplicon based methods and will go up to the Hi-C metagenomics methods that give highly detailed results on the complex microbial communities. The practical component will cover bioinformatics analysis of metagenomics.

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 24
Introduction to metagenomics new (2 of 2) [Full] 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This two days course will focus on the theory and applications of metagenomics, for the analysis of complex microbiomes (microbial communities). The course will include theoretical (~40%) and practical (~60%) training. We will start with the fastest, simplest and cheapest amplicon based methods and will go up to the Hi-C metagenomics methods that give highly detailed results on the complex microbial communities. The practical component will cover bioinformatics analysis of metagenomics.

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.