The International Mouse Phenotyping Consortium (IMPC) portal provides a freely available comprehensive catalogue of mammalian gene function, using the mouse as a model. By applying a standardised phenotyping pipeline to single-gene knockout mouse lines, the IMPC identifies the physiological systems that are disrupted when a gene is disabled and thus establish gene-phenotype associations. This course will show you how to navigate the IMPC portal to find phenotypes, disease models and knockout mouse strains for a gene of interest.

By the end of the course you will be able to:
Describe what the IMPC is and what data you can find within the IMPC portal
Determine whether there are phenotypes and/or potential disease models for your gene of interest
Identify whether there are genes associated with a phenotype you are interested in
Establish whether there are knockout mouse strains available for your gene of interest and know how to order them

The IMPC is an international research infrastructure, comprised by 21 of the leading mouse genetics centres worldwide, that is systematically identifying the function of every protein-coding gene in the mouse genome. Despite having sequenced the entire genomes of many species, the exact function of most genes remains unknown. To address this, the IMPC is coordinating the production of a knockout mouse strain per protein-coding gene, which are then characterised using a standardised, broad-based phenotyping pipeline, giving insights into the function for genes for which very little is known. Our open-access database now includes phenotyping data for nearly 6,500 mouse genes.

This webinar will discuss some of the exciting discoveries in genetic disease, development and sexual dimorphism that biologists and clinical researchers are making using IMPC resources. The IMPC strives to generate data that ultimately help understand human health and disease and identify new targets for therapeutic intervention. This data is also useful for research focusing on other mammalian species, including evolutionary research studies seeking to understand adaptation.

All IMPC data is freely available to use and can be accessed at www.mousephenotype.org. The IMPC would like to encourage researchers to get in touch via the IMPC website if they are interested in using IMPC data and would like further guidance on how to use our data.

Who is this course for?
This webinar is suitable for anyone interested in learning more about the IMPC. No prior knowledge of bioinformatics is required but an undergraduate-level knowledge of biology is recommended.

Outcomes
By the end of the webinar you will be able to:

List the aims of the IMPC
Describe discoveries made using IMPC resources
Navigate www.mousephenotype.org to access IMPC data

This webinar will provide an interactive introduction to the new UniProt Disease Portal: a single centralised resource of UniProt disease-centric information which has been developed with the help of our users to better serve the needs of the research community and facilitate protein discoverability.

The UniProt knowledgebase (UniProtKB) supports biomedical research by providing a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. To do this, UniProt integrates, interprets and standardises data from a range of sources including scientific literature, protein sequence analysis tools, other databases and automatic annotation systems to provide a detailed overview of the available protein knowledge.

This webinar will introduce you to the UniProt Disease Portal which aims to help researchers explore and access current genomic disease-related data from the UniProtKB database, but in a single centralised resource. The portal incorporates UniProt functional annotations, protein network visualisations, genomic variant and drug-related data, and organises in a way that allows users to easily visualise and compare data to identify similarities using variants, protein interactions, diseases, and drug data.

The Disease Portal is currently in its first beta release, so we hope that this interactive introduction will give you an understanding of how to access disease-centric protein data in UniProt and encourage your feedback to assist ongoing development of the Portal to further suit the requirements of our users.

Who is this course for?
This webinar is aimed at individuals who have an interest in protein disease biology, would like an interactive introduction to the new disease portal, and/or wish to learn about how disease data is collected and annotated in UniProt. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

Outcomes
By the end of the webinar you will be able to:

Navigate the beta UniProt disease portal to find and discover information on proteins and therapeutic drugs of interest
Understand how UniProt annotates disease data and identify where the data comes from
Help us develop the UniProt Disease Portal by providing valuable feedback

This webinar will give an introduction to programmatic access at PDBe, highlighting the type of data that is available and how this can be utilised.

This webinar is part of a 6-part PDBe API webinar series, introducing different levels of programmatic access at PDBe.The series will range from basic data retrieval and search using the PDBe API to more advanced features, including access and reuse of PDBe data visualisation components.

Who is this course for?
This webinar is open to anyone who is interested in learning about the programmatic access of PDBe.

Outcomes
By the end of the webinar you will be able to:

Discover how to programmatically access data at PDBe
Explore the type of data available at PDBe

European Genome-phenome Archive (EGA) is a permanent repository for all types of potentially identifiable genetic and phenotypic data from biomedical research projects.

This webinar aims to cover a quick introduction to EGA by exploring topics ranging from searching and accessing data in EGA to interpreting Data Use Ontology (DUO) codes. We will also demonstrate downloading data with an EGA test account.

Who is this course for?
Anyone who is interested in secure archiving or accessing distribution services for controlled access to human biomedical omics data. An undergraduate level knowledge of biology, and in particular some knowledge of genetics and genomics, would be an advantage.

Outcomes
By the end of the webinar you will be able to:

Explore the scope of EGA
Explain the usage of DUO codes
Access and download data from EGA

This webinar will introduce the Complex Portal, an encyclopaedic database for information on macromolecular complexes. In this webinar we will explain the coverage and curation priorities of the Complex Portal, show how to search for complexes using a variety of accession numbers, keywords and how to use the organism search. We will also demonstrate examples of complex details pages that include visualisation tools and link-outs to related database.

Who is this course for?
This webinar is aimed at individuals who wish to learn more about the Complex Portal. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

Outcomes
By the end of the webinar you will be able to:

Explore the Complex Portal resource
Search for the information on macromolecular complexes
Identify data visualisation tools

This curated pathway brings together a number of online tutorials and recorded webinars to provide an introduction to bioinformatics, a brief tour of the resources available from EMBL-EBI and more details about some of those resources, including Ensembl, UniProt and Expression Atlas.

By the end of the course you will be able to:
Outline what bioinformatics is
Describe the importance of data management
Recall which resources are available from EMBL-EBI
Know where to find information about genes
View information on gene expression
Search for protein information
Know where to find out more about EMBL-EBI resources

This webinar will include a brief introduction to the GWAS Catalog, followed by hands-on demonstrations and exercises covering different methods for accessing GWAS Catalog data, focusing on the most common use-cases. This will include our web-based search interface, with a number of different tools for data access and visualisation, and download of filtered datasets. We will also briefly introduce and describe how to submit your own data.

Who is this course for?
This webinar will be suitable to a wide range of scientists, clinicians and statisticians who are interested in the applications of GWAS Catalog that includes prioritising candidate loci, gathering statistics on traits or populations of interest, exploring disease mechanisms, predicting risk of disease, and discovering drug targets, among other goals.

Outcomes
By the end of the webinar you will be able to:

Describe the role of the GWAS Catalog
Search the GWAS Catalog website
Know how to submit data

Explore gene expression profiles across various species and conditions at single cell resolution.

Single Cell Expression Atlas (SCEA) is an open resource committed to making the information from single cell sequencing datasets readily accessible to the research community and beyond. At SCEA we accumulate, curate and re-analyse available raw single-cell sequencing data from multiple species and across experimental conditions to make them cross-comparable and we present the analysis results in a user-friendly interface for public consumption. This allows researchers to gain a quick insight into the expression pattern of their gene of interest at the level of individual cells across different species from human to Saccharomyces.

At SCEA we aim to keep pace with the rapidly growing single cell transcriptomics research and to make the knowledge thus obtained truly open and widely available so that it can serve as basis for further studies.

The webinar will provide a quick overview of:

Different single cell sequencing methods
Various ways of searching SCEA
How to filter and interpret the analysis results on the experiment page
Additional features and resources available on the experiment page
Who is this course for?
This webinar is for individuals who wish to learn more about Single Cell Expression Atlas. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

This webinar will provide an overview of the MGnify API. MGnify offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository.

The webinar will include how to utilise the API using a browser, where to find documentation, how to use filtering and pagination, available output formats, and scripting examples in Python.

Who is this course for?
This webinar is aimed at individuals who would like to learn more about using the MGnify API, however some familiarity with MGnify and programmatic access methods is recommended.

Outcomes
By the end of the webinar you will be able to:

Access the MGnify API
Find documentation for the MGnify API

This quick tour provides a brief introduction to MGnify - a free resource for analysis, visualisation and discovery of microbiome (metagenomic, metatranscriptomic, amplicon and assembly) datasets.

By the end of the course you will be able to:
Identify what data the MGnify resource provides
Employ MGnify to search for and interpret microbiome data analysis
Describe the various data-types and analysis results available within MGnify

This tutorial provides you with a step-by-step guide for submitting metagenomics data to the European Nucleotide Archive (ENA) in order for it to be analysed by the MGnify resource.

By the end of the course you will be able to:
Submit your metagenomics data to the ENA
Describe why MGnify requires you to archive your data in the ENA
Evaluate why it is important to provide accurate contextual metadata with your metagenomic sequence data

This webinar will describe how MGnify can assist you in your microbiome research by providing a broad overview of resources available in MGnify.

MGnify offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. During this webinar, we will cover what types of microbiome data are included, improvements we have made to our analysis pipeline, as well as ways to search for data.

Who is this course for?
This webinar is aimed at individuals who would like to learn more about using MGnify. No prior knowledge of bioinformatics is required, but undergraduate level knowledge of biology would be useful.

Outcomes
By the end of the webinar you will be able to:

Describe the types of data included in MGnify
Explore the MGnify resources
Search MGnify

What is machine learning and how can it be applied in drug discovery to identify or prioritise new drug targets? Find out more with this introduction to machine learning applications in drug discovery using WEKA.

By the end of the course you will be able to:
Identify common types of ML algorithms that can be applied to tackle drug discovery challenges
Illustrate some applications of machine learning and other artificial intelligence frameworks in drug discovery
Get started with WEKA, an easy-to-use open-source machine learning software
Use standalone web resources to explore the WEKA results and see if the identified genes could be potential targets in drug discovery

This quick tour provides a brief introduction to EMBL-EBI's database for Metabolomics experiments and derived information, MetaboLights.

By the end of the course you will be able to:
Describe what MetaboLights is
Navigate the MetaboLights website
Outline what MetaboLights can be used for

This course provides a basic introduction into the rapidly emerging field of metabolomics and its importance and applications.

By the end of the course you will be able to:
Comprehend the purpose and importance of the field of metabolomics
Describe some principles of metabolomic study design
Evaluate advantages and limitations of some analytical techniques used in metabolomics studies
Discuss some of the modern-day applications of metabolomics
Access metabolomics resources at the EMBL-EBI

Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high-throughput sequencing of the microbial DNA, collecting, archiving and re-sharing the genomic data for taxonomic and functional analysis.

By the end of the course you will be able to:
Conduct appropriate quality control and decontamination of metagenomic data and run simple assembly pipelines on short-read data
Utilise public datasets and resources to identify relevant data for analysis
Apply appropriate tools in the analysis of metagenomic data
Submit metagenomics data to online repositories for sharing and future analysis
Apply relevant knowledge in strain resolution and comparative metagenomic analysis to their own research

This webinar will focus on the use of the online molecular visualisation tool, Mol* at PDBe. We will show basic usage, observation of electron density maps and EM volumes, interrogation of ligand structures, and the visualisation of sequence annotations. We will also highlight the advantages to using Mol* in comparison to other tools and show the different ways the Mol* viewer is presented and accessed on PDBe's pages.

Who is this course for?
This webinar is for individuals with an interest in visualising molecular structures. No prior knowledge of bioinformatics is required, but undergraduate level knowledge of protein biology would be useful.

Outcomes
By the end of the webinar you will be able to:

Visualise molecular structures using Mol*
Identify advantages of using Mol* over other visualisation tools

Ensembl not only provides up-to-date annotation of the mouse reference genome assembly, but also allows you to browse the genomes of 16 other mouse strains.

This webinar will consist of a short presentation that will describe the origin of the data, followed by a demonstration on how to use the Ensembl web browser to browse and compare data between the different strains, looking specifically at homology and variation data.

Who is this course for?
This webinar is for scientists with an interest in mouse strains, genomes and genotypes. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

The webinar will demonstrate how to perform multiomics comparative pathway analyses using ReactomeGSA. This will cover the web interface and R package. We will demonstrate how to use ReactomeGSA to quickly derive novel biological knowledge by combining multiple datasets. In addition, we will also cover the function of ReactomeGSA for investigating scRNA-seq cell clusters at the pathway level.

Who is this course for?
Bioinformaticians and wet-lab scientists who are interested in analysing their proteomics/transcriptomics/scRNA-seq data.

Outcomes
By the end of the webinar you will be able to:

Identify the application of ReactomeGSA
Apply ReactomeGSA to perform multiomics comparative pathway analyses