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Bioinformatics Training

Bioinformatics course timetable

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Tue 3 Mar – Wed 13 May

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March 2020

Tue 10
Using CellProfiler and CellProfiler Analyst to analyse biological images (1 of 2) Finished 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.

CRUK: Introduction to Linear Modelling with R Finished 09:45 - 17:00 eLearning 1 - School of Clinical Medicine

The course will cover ANOVA, linear regression and some extensions. It will be a mixture of lectures and hands-on time using RStudio to analyse data.

This event is part of a series of training courses organized in collaboration with the Bioinformatics Core Facility 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.

Wed 11
Using CellProfiler and CellProfiler Analyst to analyse biological images (2 of 2) Finished 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.

CRUK: Data Carpentry in R (1 of 2) Finished 09:30 - 17:30 eLearning 1 - School of Clinical Medicine

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.

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

Thu 12
An Introduction to Solving Biological Problems with Python (1 of 2) Finished 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.

CRUK: Data Carpentry in R (2 of 2) Finished 09:30 - 17:30 eLearning 1 - School of Clinical Medicine

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.

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) Finished 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.

Thu 19
CRUK: Introduction to Command Line Linux (POSTPONED DATE TBC) Finished 13:00 - 17:00 Room 009, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

This short (0.5 day) intensive course serves to introduce you to the command-line interface in Linux.

It is based upon elements of the Software Carpentries Shell(novice) and Shell(extras) courses. It is recommended for those CI personnel planning on attending the CI High Performance Computing facilities (Cluster) course.

This course is run by the CRUK CI Bioinformatics and IT core.

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.

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

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team are investigating a workable solution to offer some of the courses on a remote basis and will be in contact with updates as soon as possible.

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.

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.

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.

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

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team are investigating a workable solution to offer some of the courses on a remote basis and will be in contact with updates as soon as possible.

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.

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 (FUTURE ONLINE LIVE TRAINING) (1 of 3) Finished 09:00 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team are investigating a workable solution to offer some of the courses on a remote basis and will be in contact with updates as soon as possible.

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 or register your interest by linking here.

Thu 2
Molecular Phylogenetics (FUTURE ONLINE LIVE TRAINING) (2 of 3) Finished 09:00 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team are investigating a workable solution to offer some of the courses on a remote basis and will be in contact with updates as soon as possible.

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 or register your interest by linking here.

Fri 3
Molecular Phylogenetics (FUTURE ONLINE LIVE TRAINING) (3 of 3) Finished 09:00 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team are investigating a workable solution to offer some of the courses on a remote basis and will be in contact with updates as soon as possible.

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 or register your interest by linking here.

Thu 16
Data Science in Python (ONLINE LIVE TRAINING) (1 of 2) Finished 09:30 - 16:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

Discount offer of 50% off normal fees applies to this course.

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.

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
Data Science in Python (ONLINE LIVE TRAINING) (2 of 2) Finished 09:30 - 16:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

Discount offer of 50% off normal fees applies to this course.

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.

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 20
Introduction to R for Biologists (ONLINE LIVE TRAINING) (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

Discount offer of 50% off normal fees applies to this course.

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.

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 21
Introduction to R for Biologists (ONLINE LIVE TRAINING) (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

Discount offer of 50% off normal fees applies to this course.

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.

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 (ONLINE LIVE TRAINING) Finished 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online in conjunction with the presenters.

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.

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.

May 2020

Mon 4
MATLAB: Image Processing Workshop (Online) new Finished 15:00 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

Join us for a two-hour workshop on image processing and analysis in MATLAB. This practical session provides a series of example workflows to extract quantitative data from image files.

This workshop is the first event in Imaging ONE WORLD, a series of events bringing together scientists working from home to deliver workshops and talks on imaging theory and analysis. An initiative made up of scientists, imaging systems and software providers in collaboration to deliver high quality training to the image analysis community.

Although not a necessity, we recommend attending the Introduction to MATLAB course run at the Training Facility and / or the Intro to MATLAB using MathWorks prior to the workshop. For the MathsWorks course you will need to sign up for a MathWorks Account. All University of Cambridge members should be eligible to obtain a MathWorks Account. Create an account using your institution email address.

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 6
Introduction to metagenomics (ONLINE LIVE TRAINING) new (1 of 2) Finished 09:30 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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.

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 7
Introduction to metagenomics (ONLINE LIVE TRAINING) new (2 of 2) Finished 09:30 - 16:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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.

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.

Mon 11
Introduction to R for Biologists (ONLINE LIVE TRAINING) (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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.

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 12
Introduction to R for Biologists (ONLINE LIVE TRAINING) (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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.

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
EMBL-EBI: Introduction to the European Nucleotide Sequence Archive (Online) new Finished 09:30 - 11:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

The European Nucleotide Sequence Archive (ENA) is a global database for storing experimental nucleotide data and also interpreted data (alignment files, variant calling, analysis results). ENA is the database where all raw and consensus viral sequence data should be deposited, including SARS-Cov-2 data. The data is submitted by scientists conducting sequencing experiments and publishing research in the area. Data is fully searchable and available for download. Sequence data includes raw NGS files (FastQ, BAM…), assembled genomes and transcriptomes, and annotated sequences (protein coding genes, non coding RNA, barcode genes, HLA genes).

This training is aimed at a wide range of users that need to retrieve data from ENA, either occasionally or on a regular basis, or those users who will have retrieval needs closer to the course time.

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