The new EurOPDX Research Infrastructure (RI), funded by the European Union Horizon 2020 programme, aims to improve cancer drug development success rates through the enablement of collaborative cancer research using patient-derived xenograft (PDX) models. In particular, we are developing efficient and user-friendly IT tools to optimise access to, and data searching of the collection of PDX models and their clinical, molecular and pharmacological annotations. We will be presenting the EurOPDX RI and the possibilities of access to PDX models, as well as the functionalities of the EurOPDX Data Portal, with the objective to support future applicants to our PDX access grant programme.

Who is this course for?
This webinar is for individuals who are working with patient-derived xenograft models in the context of cancer drug discovery. No prior knowledge of bioinformatics is required but an undergraduate-level knowledge of biology is recommended. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

The new EurOPDX Research Infrastructure (RI), funded by the European Union Horizon 2020 programme, aims to improve cancer drug development success rates through the enablement of collaborative cancer research using patient-derived xenograft (PDX) models. In particular, we are developing efficient and user-friendly IT tools to optimise access to, and data searching of the collection of PDX models and their clinical, molecular and pharmacological annotations.

Following a first webinar in October 2019 introducing the new EurOPDX Data Portal, we will present the latest data and functionalities added to the repository, and associated IT tools to browse molecular data associated with the models: the EurOPDX instance of the well-known cBioPortal, and the GenomeCruzer for 3D interrogation of data.

The webinar will in particular support the last applicants to our PDX access grant programme (last deadline on 18th September 2020, https://www.europdx.eu/europdxri-ta).

Who is this course for?
This webinar is for individuals who are working with patient-derived xenograft models in the context of cancer drug discovery. No prior knowledge of bioinformatics is required but an undergraduate-level knowledge of biology is recommended.

Europe PMC is an open repository, providing access to worldwide biomedical literature, including articles, preprints, books, patents, and clinical guidelines. This webinar will introduce the Europe PMC Articles RESTful API and show how to programmatically access publications and related information, such as citations, references, data links, or text-mined terms.

Who is this course for?
This webinar is for those who want to learn about accessing the Europe PMC search programmatically. Some prior knowledge of programmatic access is recommended.

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

Use RESTful API calls that are relevant for your use case
Understand RESTful web service output
Make literature searches programmatically
Know where to find help

This quick tour gives a brief introduction to Europe PMC, an open science platform that enables access to a worldwide collection of life science publications and preprints from trusted sources around the globe. Free, transparent, and community-driven, Europe PMC is your gateway to life science research.

By the end of the course you will be able to:
Explain the role of Europe PMC
Search Europe PMC for biomedical literature
Outline some advanced features including citations, database cross-links and annotations
Determine where to find out more about Europe PMC

This quick tour provides a brief introduction to the European Genome-phenome Archive (EGA), a permanent repository for all types of potentially identifiable genetic and phenotypic data from biomedical research projects.

By the end of the course you will be able to:
Explore the EGA resource
Identify how to access and submit data
Find out how data access is controlled in the EGA

The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation.

In this webinar, get acquainted with what the European Nucleotide Archive is and how our services can support your work. Learn about how to submit your data to our open-access archive, or how to search interesting data submitted by others.

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

This quick tour provides a brief introduction to the European Nucleotide Archive (ENA), which provides a comprehensive record of the world's nucleotide sequencing information. This course will get you started in finding interesting data, and also in how to submit your own data and share it with the world.

By the end of the course you will be able to:
Describe the basics of what the European Nucleotide Archive (ENA) is
Be able to discuss in overview submission and retrieval of ENA data
Know how to find out more about ENA

This quick tour provides a brief introduction to the European Variation Archive (EVA) which is an open-access repository for genetic variation archiving and accessioning for all species.

By the end of the course you will be able to:
Recognise what the European Variation Archive is
Identify which channel is best suited for you to consume/submit variation data
Know where to get help and find out more about the European Variation Archive resource

Expression Atlas is an open resource that incorporates high quality gene expression data from ArrayExpress as well as other data archives and sources. Our mission is to provide the scientific community with a tool that allows users to visualise the abundance and localisation of gene and protein expression data across over 60 different species and thousands of different biological conditions. Expression Atlas aims to help answer questions such as "where is my favourite gene expressed?" or "how does expression of my favourite gene change in response to disease?"

The webinar will guide users through:

Introduction to baseline data which investigate gene expression under normal conditions (without experimental interference)
Introduction to differential data which explore gene expression changes in response to perturbations such as disease or compound treatment
Searching for specific genes and conditions
Advanced features: visualising gene information within the Ensembl genome browser; identifying similarly expressed genes to your gene of interest; view variable gene expression and transcript information
Who is this course for?
This webinar is aimed at those with an interest in gene expression data. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available. Its protein sequences are retrieved from predominant, publicly accessible resources. To avoid redundancy, each unique sequence is stored only once with a stable protein identifier. As a result, performing a sequence search against UniParc is equivalent to performing the same search against all databases cross-referenced by UniParc.

UniProt Reference Clusters (UniRef) provides clustered sets of sequences from the UniProt Knowledgebase (UniProtKB) and selected UniParc records to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences. The reduced redundancy increases the speed of similarity searches and improves detection of distant relationships.

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

ChEMBL is a manually curated open database of bioactivity data of molecules with drug-like properties. It enables users to identify data that relates chemical structural information to biological function and used to facilitate the discovery of new drugs.

This webinar will highlight the data that is available in the ChEMBL database and how it can be accessed using the new ChEMBL web interface //www.ebi.ac.uk/chembl/. The webinar will include a walkthrough of several typical drug discovery use cases and will show how the data can be queried via the interface to identify this data.

Who is this course for?
This webinar is for anyone with an interest in using ChEMBL. No prior skills are required.

This webinar will provide a practical overview of how to use the Enzyme Portal to find enzyme-related information about metabolites. The Enzyme Portal is a freely available resource to find and explore enzyme features. It integrates relevant enzyme data for a wide range of species from various resources including UniProt, PDB, Reactome and CHEMBL. We will demonstrate how to use the Enzyme Portal to find relevant enzymes involved in a specific metabolite biosynthesis or catabolism.

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

RNAcentral is a database of non-coding RNA sequences that provides a unified view of >40 specialised databases. This webinar will give an overview of the data found in RNAcentral as well as the RNAcentral website.

The team will share tips on how to efficiently explore the data using text and sequence similarity search, how to visualise RNA secondary structure, and how to access the bulk data in the FTP archive. More advanced functionality, including the programmatic data access and public Postgres database, will also be discussed.

Join the webinar to also learn what's new in RNAcentral or ask any questions you may have.

Who is this course for?
This webinar is aimed at individuals who would like to learn more about using RNAcentral. 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 data found in RNAcentral
Navigate the RNAcentral website
Access data in the RNAcentral FTP archive

This extended quick tour provides an introduction to Expression Atlas, an open resource for finding information about gene expression across species and biological conditions. Expression Atlas aims to help answer questions such as ‘where is a certain gene expressed?’ or ‘how does its expression change in a disease?'.

By the end of the course you will be able to:
Gain a basic understanding of what Expression Atlas is and how it works
Know how to use Expression Atlas to explore gene expression data
Describe where to find out more about Expression Atlas

This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis.

Europe PMC 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 with an interest in learning more about the data-rich literature search tools provided by Europe PMC. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

This course will introduce the field of functional genomics and provide an overview of the different resources at the EBI which are related to this field.

By the end of the course you will be able to:
Know what functional genomics is
Describe which functional genomic resources are available at the EBI
Outline the role of ArrayExpress
Describe what the Gene Expression Atlas is
Know what the difference between ArrayExpress and the Atlas is and when to use them
Outline the role of Single Cell Expression Atlas

This online course introduces common technologies in functional genomics studies, including microarrays and next generation sequencing (NGS), with a special focus on RNA-sequencing (RNA-seq). We look at important considerations when designing your experiments, data analysis methods, and discuss when to use one technology over another.

By the end of the course you will be able to:
Evaluate different functional genomics technologies and know when to use them
List some of the considerations when designing your own functional genomics experiments using these technologies
Describe the steps involved in data analysis of microarray and RNA-seq experiments

In this online course, we will look at why, when, where to submit your functional genomics data.

By the end of the course you will be able to:
Describe the importance of sharing your functional genomics data
Evaluate two functional genomics databases

This online course will give you an introduction to functional genomics. We will introduce you to different types of functional genomics studies and discuss best practices when designing your own experiments. We will also explore some examples of how functional genomics is being applied to drug discovery and plant sciences.

By the end of the course you will be able to:
Describe some types of functional genomics studies
Apply best practices when designing your own functional genomics experiments

This quick tour provides a brief introduction to the Gene Ontology (GO), the Gene Ontology Annotation (GOA) project and QuickGO, a web-based browser for viewing GO annotations.

By the end of the course you will be able to:
Describe basic characteristics of GO
List ways in which GO can help you find out more about your protein data and other gene products
Search for GO using QuickGO
Determine where to find out more about GO