A proteome is the set of proteins thought to be expressed by an organism. Through the Proteomes portal, UniProt provides a large collection of proteomes for organisms whose genomes have been sequenced and annotated. Currently, our database contains more than 300,000 proteomes spanning eukaryotes, bacteria, archea and viruses.

This webinar will show you how to retrieve proteomes of interest and download the corresponding datasets. We will also cover where proteomes come from and the features available to help users find the right dataset for their work.

Who is this course for?
This webinar is aimed at students or early stage researchers beginning to use bioinformatics resources in their studies/research who wish to learn more about proteomes. 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:

Navigate the Proteomes portal
Find proteomes of interest
Download datasets

This quick tour provides a brief introduction to UniChem, a compound identifier mapping service. It covers the scientific principles behind the tool, and outlines the use of UniChem and UniChem 'Connectivity Search' to directly locate identical and related molecules in various sources.

By the end of the course you will be able to:
Describe what UniChem is for and the benefits it brings to navigating small molecule resources
Know how to conduct simple searches with UniChem and UniChem Connectivity Search

The new UniProt portal for the SARS-CoV-2 coronavirus and receptor protein entries provides the latest available pre-release UniProtKB data for the SARS-CoV-2 coronavirus and other entries relating to the COVID-19 outbreak. Please join us for a free webinar describing the use of the portal including data release and updates.

Who is this course for?
Any researcher interested in using the Portal.

This course is a guide to the UniProt resource, including what kinds of information it provides and how to access the data using the UniProt website.

By the end of the course you will be able to:
Evaluate what UniProt is and what you can do with it
Explore the wide range of information provided by UniProt and understand where it comes from
Be able to access, navigate and search on the UniProt website
Evaluate the tools provided on the UniProt website
Comprehend how to access completely sequenced proteomes

This webinar will give an overview on how molecular data of proteins associated with neurodegenerative diseases is provided in UniProtKB, including information on molecular protein function, protein-protein interactions, sequence variants, pathways, and drug candidates.

Who is this course for?
This webinar is aimed at researchers studying neurodegenerative diseases who would like to use UniProtKB to find information about the molecular function of proteins involved in disease, and learn what disease-relevant information is available in UniProtKB.

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

Identify where to find molecular data on proteins involved in neurodegenerative diseases
Explore what kind of disease-relevant information is available at UniProtKB
Retrieve information on protein variants and visualise their impact on protein function

This quick tour provides a brief introduction to the Universal Protein Resource, UniProt.

By the end of the course you will be able to:
Explain what UniProt is and what it can do
Determine where to find out more about UniProt

This webinar will cover ongoing curation project at UniProt on proteins involved in Alzheimer's Disease.

We have identified more than 300 proteins, by text mining and from input by experts in the field, to be associated with AD. Using manual curation, information from peer-reviewed literature has been annotated on molecular function and involvement in disease, including disease-associated variant positions and variant characterisation.

By focusing our curation efforts on proteins involved in AD, we hope to shed light on the mechanisms leading to this devastating disease. We focus on a thorough review of available information on sequence variants and associated AD information, as well as normal protein function of proteins associated with the disease. The information on variants together with variant functional description, protein molecular function, structural data and protein-protein interaction should help researchers in the field of neurodegeneration, clinicians and biomedical researchers to gain a global view on the relation between variant and disease and help elucidating disease mechanism.

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

UniProt is a comprehensive, expert-led, publicly available database of protein sequence, function and variation information.

This webinar will give a brief introduction to the UniProt website and then highlight resources available that proteomics scientists or users with large protein datasets may find useful in analysing their data. This will encompass our proteomes service, how to convert and retrieve ID mappings, and how to carry out a peptide search.

The webinar will then go on to introduce the UniProt Proteins API which allows researchers to access and download UniProt data alongside large-scale genomic, proteomics and variation data without needing prior in-depth knowledge of programmatic languages. Data is available for download and querying in a range of formats; including XML, FASTA and PEFF. The API multi-query search functions will be demonstrated and useful features such as searching entries by peptide, and searching for proteomic peptides by protein entry will be explained.

The UniProt Proteins API is available at //www.ebi.ac.uk/proteins/api/doc

Who is this course for?
This webinar is aimed at computational and wet-lab scientists, with no prior knowledge of programming required. An undergraduate level knowledge of protein biology will be useful.

For those already familiar with programming languages that require a more detailed explanation of accessing UniProt programmatically please see the webinar ‘Uniprot: programmatically’.

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

Recall the UniProt services useful for proteomics scientists or users with large protein datasets
Know when and how to use the UniProt Proteins API

This course introduces user experience design (UXD) in the context of bioinformatics tools and service development. It provides an overview of basic concepts and links to external resources on UXD where you can learn more.

By the end of the course you will be able to:
Explain the concept of UXD
Describe the benefits of conducting UXD
Describe different approaches to undertaking UXD

Interested in learning how User Experience (UX) design can help you meet your goals? What are the quick wins for knowing your users, designing with your team and getting feedback on your designs? This webinar is for you if you are involved in maintaining or designing a website, tool or app or alternatively, are in a role where it is key to understand your user (e.g. training or capacity building).

User experience design places the user at the centre of development. Our speakers will discuss tools to profile the user (e.g. personas), to create a user journey, and using sketches and prototypes for usability testing.

We will focus on lean UX tools, and will discuss quick wins for knowing your users, designing with your team and getting feedback on your designs.

During this webinar we introduce you to UX design using the Open Targets platform as a case study, showing how UX can be applied and demonstrate how it can make a positive difference.

This webinar was given by Michele Ide-Smith and Nikiforos Karamanis and is a joint webinar between EMBL-EBI and CORBEL.

CORBEL is an initiative of eleven new biological and medical research infrastructures (BMS RIs), which together will create a platform for harmonised user access to biological and medical technologies, biological samples and data services required by cutting-edge biomedical research. CORBEL will boost the efficiency, productivity and impact of European biomedical research.

Who is this course for?
This webinar is for those who are in a role where it is key to understand your user. The target audience for this webinar is academic researchers, technical operators/service providers of biological and medical research infrastructures. No prior knowledge of user experience design is required.

This webinar will explain how to find and access relevant scientific literature and show how you can follow the latest developments in your scientific field. It will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex queries.

Europe PMC (https://europepmc.org/) is an open biomedical literature database including PubMed indexed articles, preprints, micropublications and more.

Who is this course for?
This webinar is aimed at scientists who want to optimise their literature searches. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

Galaxy is an open-source web tool (portal) that organizes bioinformatics work-flows. It provides functionality to:Record workflows (history)Share common sequence data (shared data libraries)Import and use (private) sequence dataShare results with others (shared histories)Integrate new tools into the interfaceRun long analyses using batch queues

This is the second part of a webinar series on InterPro which is held between May 6th 2020 and May 20th 2020.

InterPro is a database that helps users to understand the possible functions of proteins sequence by identifying what family it belongs to or what domains and motifs it contains.

To deal with the growing volume of protein sequence data and an increasing demand to retrieve subsets of the data, the InterPro website has been entirely redesigned. It allows more flexibility and provides additional features to be used by the scientific community working on protein sequences. This webinar will guide you through searching and exploring the data available in the InterPro database and will show you how it can help finding data for your research.

Who is this course for?
This webinar is aimed at scientists with an interest in learning more about the InterPro database. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

This webinar will introduce the PDBe graph API, which is generated from the PDBe graph database and contains an even richer level of data than our standard API. We will highlight how this API supports our PDBe-KB aggregated views, with specific case studies that demonstrate the possibilities through this API.

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:

Explain the advantage of PDBe Graph API over standard API
Identify the function of PDBe Graph API in supporting PDBe-KB aggregated views

The European Variation Archive (EVA) is a primary open repository for archiving, accessioning, and distributing genome variation including single nucleotide variants, short insertions and deletions (indels), and larger structural variants (SVs) in any species. The EVA is in the process of releasing the first dbSNP data release which consists of RS ID-containing VCF files for each non-human species available in dbSNP. This webinar will provide an overview of the European Variation Archive including data ingestion, consumption, and how you can access and utilise dbSNP RS release batch files.

Who is this course for?
This webinar is aimed at individuals working with variation data who wish to learn about submitting and accessing data in the EVA. No prior knowledge of bioinformatics is required, but undergraduate level knowledge of biology would be useful.

This webinar will cover how to access data using the EVA UI/API and the methodology of variant data submission to the EVA, specifically focusing on data transformation and formats. With a new version of the variant ID data release now available, this webinar will also cover what has been updated and what to expect from future releases.

Who is this course for?
This webinar is targeted to those working with genetic variant data from any species, suitable for web lab scientists, bioinformaticians, and clinical specialists.

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

Access variant data using the EVA UI/API
Explore the new version of the variant ID data release

The Ensembl project (www.ensembl.org) offers integrated genome, variation, gene regulation and comparative genomics data of mainly vertebrate genomes on an open access web browser platform. This webinar will introduce you to visualising your own datasets in the genome browser.

Who is this course for?
This webinar is aimed at bioinformaticians and wet-lab biologists. No prior knowledge of bioinformatics is required, but undergraduate level knowledge of biology would be useful.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"The rapid expansion of microbiome science has revealed much about the roles of microbes in health and disease. But the diversity of experimental tools available has made the reproducibility of microbiome studies a serious issue. To minimize bias during DNA extraction, researchers recently developed and tested WC-Gut RR—a whole-cell reference reagent specific to the gut microbiome. Built using 20 strains commonly found in the human gut, WC-Gut RR was designed to evaluate DNA extraction protocols used in microbiome pipelines. Researchers tested WC-Gut RR using 8 commercial DNA extraction kits, which revealed significant differences in, among other things, DNA yield, integrity, and purity. In addition, findings revealed that less complex reagents that do not feature anaerobic and hard-to-lyse strains can inflate the performance of microbiome DNA extraction kits..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

The wheat genome is large, complicated and arguably the most important genome of all in terms of food security.

In this webinar, join Ensembl Plants to learn more about where the latest IWGSC genome came from, how to explore homoeologues in wheat, along with their orthologues in the progenitor species and understand genetic variation in wheat.

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

The eQTL Catalogue is a new project aimed at accelerating the functional interpretation of human GWAS studies and the annotation of common variants through a comprehensive collection of gene expression and transcript splicing QTLs. Public datasets are thus collected then processed with a uniform pipeline to remove analysis artefacts and quality controlled, before being made freely available to all.

In this webinar, we will describe the data and most importantly how to access it. Already, the results of the eQTL Catalogue can be accessed via bulk download, API access and browsed on the Open Targets Genetics platform.

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