Theme: Specialised Research Topics

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.

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.

InterMine is a freely available open-source data warehouse built specifically for the integration and analysis of complex biological data.

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants (over 87 plant genomes), nematodes, fly, zebrafishHymenoptera, Planaria, and more recently human.

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 a powerful web service API, with multiple language bindings including Python and R.

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 (a comprehensive list of InterMine databases is available here.)

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

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.

This course will provide participants with an introduction to EMBL-EBI and its data tools and resources, which cover the whole spectrum of biological / life sciences.

Sessions with trainers from ArrayExpress, Expression Atlas and the GWAS catalog will explore SNP-trait associations and show how further understanding can be gained on the location and level of gene expression across the body.

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

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

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

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

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

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

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

The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This one-day 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.

There may be some tools and topics that do not apply to non-vertebrates; if you have any questions about this, please email the Ensembl Outreach Project Leader, Emily Perry.

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

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

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 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.

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.

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.

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 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.

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.

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.

This one day workshop aims to give an introduction to Artemis and ACT (Artemis Comparison Tool). Both tools enable the visualization, analysis and comparison of genome data. They are freely available for all operating systems and can be downloaded here. This is a hands-on course with short talks introducing the tools. The course is taught by members of the Pathogen and Parasite Genomic Teams from the Wellcome Trust Sanger Institute.

Further information is available here.

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

DECIPHER is a collaborative data sharing and interpretation platform that enables the secure upload, analysis and subsequent sharing of anonymised phenotype-linked patient variant data in rare genetic disorders.

DECIPHER is a worldwide user community of over 250 clinical genetics centres and research groups from over 40 countries that utilise the built-in tools for aiding the interpretation of variants as well as to discover other patients that share similar phenotype and genomic findings.

DECIPHER facilitates collaboration and exchange of information between a global community of clinical centers and researchers leading thereby accelerating discovery and diagnosis. Access to consented anonymised records is free to all users. User accounts are provided to bona-fide clinicians and lab scientists to enable deposition and sharing of anonymised patient data.

The purpose of this half-day workshop is to acquaint participants with the DECIPHER website and database and introduce the various built-in tools for visualisation and interpretation of phenotype-linked genomic variation in anonymised consented patient data. It is hoped that by the end of this workshop, users will be able to carry out effective searches of data, use the built-in genome browser to visualise variation in context of other pathogenic and reference data sources, find other patients with similar variants and shared phenotypes, and identify most likely causes of phenotypic presentation by gene prioritisation.

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.

Mouse Genome Informatics (MGI) is the international database resource for the laboratory mouse and provides integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

MGI is a free, highly curated resource and offers web and programmatic access to a complete catalogue of mouse genes and genome features, functional annotations, a comprehensive catalogue of mutant and knockout alleles, phenotype and human disease model annotations, gene expression, variation and sequence data.

This workshop will be composed of ~20min overview and ~1 hour hands-on, interactive tutorial.

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

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.

Open Targets is a public-private partnership to use human genetics, genomic data and drug information for systematic identification and prioritisation of therapeutic targets. This module introduces the Open Targets partnership, its underlying projects and the bioinformatics resources for researchers studying associations of human genes with diseases.

In this 90 minute long webinar, Denise Carvalho-Silva, will focus on Open Targets Platform and Open Targets Genetics, open source tools of integrated genetic, genomic and chemical data for target-disease associations.

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.

COSMIC, the Catalogue of Somatic Mutations in Cancer, is the world’s largest and most comprehensive expert manually curated resource for exploring the impact of somatic mutations in human cancer. Based at the Wellcome Sanger Institute and available publicly at https://cancer.sanger.ac.uk/cosmic, the latest release includes almost 6 million coding mutations across 1.4 million samples from over 26,000 papers. COSMIC captures the full spectrum of genomic data relating to somatic mutations, so in addition to coding mutations, gene fusions, non-coding mutations, copy-number variants, methylation and drug resistance mutations are included.

This course will use the live COSMIC website and tools to show you how to access and explore this information, seeking to identify genetic causes and targets in all human cancers.

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.

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.

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.

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

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

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

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.

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 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 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.

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.

InterMine is a freely available open-source data warehouse built specifically for the integration and analysis of complex biological data sets.

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants (over 87 plant genomes), nematodes, fly, zebrafish, Hymenoptera, Planaria, and more recently human.

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 a powerful web service API, with multiple language bindings including Python and R.

This course will focus on programmatic access to InterMine through the API and InterMine searches will be done using Python 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 (a comprehensive list of InterMine databases is available here.

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.

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.

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.

Day 1 will introduce you to next generation sequencing technologies (NGS) and how they work, providers, common bioinformatics workflows, standardised file types, quality control. This session will include an introduction to Galaxy. Galaxy is an open, web-based platform for data-intensive life science research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses.

Day 2 will be hands-on practicals on using Galaxy to explore sequencing quality control, before and after removal of low quality samples. This forms the core of all NGS analyses and this day will conclude with how this data pipes into gene expression studies, variant calling and genome assemblies.

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.