All Bioinformatics courses

Please note that this course has been discontinued and has been replaced by the Introduction to R for biologists.

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

Materials for this course can be found here.

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.

Please be aware that this course is currently being re-developed and will not be scheduled to run until redevelopment has been completed. If you are interested in being notified once the course is scheduled, please register your interest.

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim 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 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.

THIS EVENT IS NOW FULLY BOOKED!

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim 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 School aims to familiarise biomedical students and researchers with principles of Data Science. Focusing on utilising machine learning algorithms to handle biomedical data, it will cover: effects of experimental design, data readiness, pipeline implementations, machine learning in Python, and related statistics, as well as Gaussian Process models.

Providing practical experience in the implementation of machine learning methods relevant to biomedical applications, including Gaussian processes, we will illustrate best practices that should be adopted in order to enable reproducibility in any data science application.

This event is sponsored by Cambridge Centre for Data-Driven Discovery (C2D3).

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.

This three day workshop will bring together representatives of the ELIXIR Galaxy Working Group, as well as trainers and developers working on the Galaxy project from Europe and beyond, to:

• Build on an existing collection of Galaxy training materials. During the workshop we will collate additional materials, including topics relevant to the ELIXIR use-cases, and ensure that, for each workflow, a minimum set of training materials is available, including slides, practical exercises, Docker containers, and Galaxy tours.
• Improve materials’ annotations (introducing full BioSchemas compliance) and align them with existing ELIXIR efforts (linking to TeSS). During the workshop materials will be curated to ensure they are properly described, according to the ELIXIR/GOBLET guidelines, and BioSchemas compliant.
• Extend the existing “curated” dataset collection and assign DOI to individual datasets.
• Increase the number of Docker/Virtual Machines available for easy installation of Galaxy training environments.
• Explore the feasibility of developing a toolkit to facilitate plug in of different datasets in existing training material/workflows through a templating approach.

This event is supported by ELIXIR-EXCELERATE, an European Commission grant within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.

This module introduces the area of sequence similarity searching and focuses on how to use tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases, including tips on which tool and database to use, input formats, how to change parameters and how to interpret the results pages.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

This workshop will introduce students to EMBL-EBI, the databases and services it offers, and basic concepts in bioinformatics that will be of use to their disease related research work.

It will explain the role of the EMBL-EBI in curating and sharing biological data with scientists around the world, and introduce concepts for locating relevant data and information of interest.

Sessions with trainers from Ensembl, ArrayExpress and the GWAS catalog will introduce practical skills in browsing genes and variation in a genomic context, in exploring SNP-trait associations and will show how further understanding can be gained on the location and level of gene expression across the body.

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.

Are you aware of the wide range of protein data resources that can easily be accessed and explored to enhance your research? Do you want to know more about the sequence of your protein and its functions? Wondered whether a structure of your protein exists and how to explore it? Want to know more about the potential complexes and reaction pathways your protein of interest is involved in, giving you a better overview of its biological context?

This three day workshop will introduce you to data resources and tools developed by EMBL-EBI that can help you in your protein studies. Each day will focus on a particular protein topic, with the aim of helping you get more from your data and also to explore publically-available data that can further support your research.

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 clicking here.

This interactive workshop offers participants hands-on experience in the use of the Ensembl VEP to annotate genetic variants with the effects they have on Ensembl genes, and the known information about co-located variants. We will also look at known genes and variants, including the types of data available and where they come from.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

This interactive workshop offers participants hands-on experience in the use of the European Variation Archive, EVA. The EVA is an open-access, genetic variation data repository, currently hosting more than 80 studies describing in excess of 520 million unique variants. Participants will be shown how this data can be searched for at the study level via the EVA Study Browser, or at the individual variant level, via our Variant Browser. Finally, participants shall also be shown how to access this wealth of genetic variation data via the EVA API.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

This workshop is aimed at giving life scientists training on how to explore and use protein interaction and pathway bioinformatics resources. This course looks at the data repositories, resources and tools available and shows attendees how to both find information on a single molecule and how to build high-quality networks to enable network analysis.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

This workshop will give an introduction to the protein interaction database IntAct and the Complex Portal service. You will also briefly learn how to visualise protein interactions using the Cytoscape application.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

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

Further information can be found here.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

An introduction to the chemogenomics resources available from the EBI. The workshop will cover resources such as ChEMBL, SureChEMBL, UniChem and Open Targets.

This session is one of a series of short introductions to EBI Services, run together, but bookable separately (see Related Courses section below).

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.

This workshop is an introduction to EMBL-EBI and the life science data resources it provides. Participants will be shown how to navigate the website and search for appropriate database resources and tools, whilst also highlighting resources such as Train online (our e-learning portal) and the literature resources at Europe PMC.

This workshop will not focus on a set of specific resources; for more focused workshops please see the others within this series (see the Related Courses section below)

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

Employ InterPro to help you answer your research questions!

This workshop will help you find out why there is a need to automatically annotate proteins, how protein family databases can help meet this challenge, and how InterPro pulls together a number of such databases, allowing you to classify unknown protein sequences and identify their function. The module is a combination of presentations and hands-on practical exercises. You will explore the various features of an InterPro entry, and design a workflow to utilise InterPro in the analysis of real world data.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

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.

This course provides an introduction to the basic theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to overlay large-scale data such as that obtained through RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of one of the most commonly used open source Network Visualisation Platforms, Cytoscape. The course will also access and analyse the data through Cytoscape apps, including IntAct app.

If you do not have a University of Cambridge Raven account please book or register your interest here.

• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.

This course will give an introduction to the basic concepts of ontologies and how they are useful in biological applications. We will explain what a biomedical ontology is and present the two primary types of ontology: (i) domain ontology and (ii) application ontology, using examples as Gene Ontology (GO) and Experimental Factor Ontology (EFO). The module will also go into details of why big data need ontologies and the ontology capabilities in advanced computational biology.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

This workshop aims to give the scientific community hands on experience on how to access and effectively use protein data in UniProt. UniProt is a high-quality, comprehensively and thoroughly annotated protein resource. Participants will be able to access detailed information on protein function and millions of protein sequences in the UniProt knowledgebase, including isoforms and disease variants.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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.

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. We aim 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 workshop is designed for researchers interested in learning about functional genomics data, how to access, retrieve and use the data from ArrayExpress and hands-on experience in using Expression Atlas, a resource to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others. This will include an overview on how gene expression data is curated and analysed in Expression Atlas and a practical activity to demonstrate how to access and visualise gene expression analysis results. These activities should help you answer questions such as "where is my favourite gene expressed?" or "how does its expression change in a disease?".

This workshop is not going to be a session on how to run your own bioinformatics analysis but to use the tools that have been developed in order to be able to take advantage of others’ work and prepare your work to be reproducible.

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.

The Ensembl project provides an interface and an infrastructure for accessing genomic information, including genes, variants, comparative genomics and gene regulation data, covering over 300 vertebrate species.

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.

If you do not have a University of Cambridge Raven account please book or register your interest here.

• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.

What are the cognitive differences between novices, competent practitioners, and experts? Do different people really have different learning styles? Do flipped classrooms actually work better than regular lectures? This tutorial will explore recent research in these areas and more, and show participants how to apply that research in the classroom to improve teaching.

This tutorial is a condensed version of the instructor training program that Software Carpentry has been running for the past three years. In it, we will explore a handful of research results in educational psychology, and see how to use those findings to build more effective lessons.

Greg Wilson is the Executive Director of the Software Carpentry Foundation, a volunteer non-profit organization that teaches researchers basic lab skills for scientific computing.

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

This event will consist of two parts. The first part of the workshop aims to provide new trainers with guidance and tips for developing and delivering training in bioinformatics, exploring a range of methods appropriate to different learning styles and examining the requirements for a successful course (both scientific and logistic). It will be based on the EXCELERATE Train-the-Trainer (TtT) course materials and content will be tailored to trainers that are involved in teaching bioinformatics to clinical audiences.

The second part of the workshop will focus on "Best practices in clinical bioinformatics training", providing an opportunity for people already involved in this kind of training, or in the process of developing it, to come together and exchange best practice/experiences. Participants will include training providers of the Health Education England’s MSc in Genomics Medicine from several UK Universities as well as other providers active in this area, from around Europe and beyond.

This event is co-sponsored by ELIXIR-EXCELERATE and Health Education England (HEE).

This one-day course is primarily aimed at life science researchers, but covers many topics that are applicable to other fields. It combines key theoretical knowledge with practical application, which will aid researchers in designing effective experiments. The focus throughout the course is to link experimental design to a clear analysis strategy. This ensures that the collected data will be suitable for statistical analysis. During this course, we cover:

• Practices in experimental design that lead to high quality research
• Common design pitfalls, and how to avoid or mitigate them
• A brief introduction to more advanced analysis techniques for experiments with unusual or complex designs

Topics included in the course include: crafting a good research question, operationalising variables effectively, identifying and dealing with confounding variables and pseudoreplication, and practical tips for power analysis and piloting.

The course is delivered via a mix of lectures, group discussion and worked examples.

If you do not have a University of Cambridge Raven account please book or register your interest here.

• ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.

Modern technologies are able to deliver an unprecedented amount of data rapidly. However, without due care and attention early in the experimental process, such data are meaningless if they cannot adequately answer the intended research question. This course is aimed at those planning high-throughput experiments and highlights the kinds of questions they should be asking themselves. The course consists of a lecture and small-group discussions led by a member of the Genomics or Bioinformatics Cores.

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 your interest by linking here.