This course provides an introduction to the theory and concepts of network analysis. It explores some of the features of protein-protein interaction networks and their implications for biology. Finally, the course discusses the tools and strategies that can be used to build and analyse biological networks.

By the end of the course you will be able to:
List some types of biological networks
Describe topological features of networks
Compare different sources of protein-protein interaction data
Discuss the features of protein-protein interaction networks and their biological implications
Identify tools used for network analysis and their advantages and disadvantages
Evaluate different network analysis strategies and know when to use them

This quick tour provides a brief introduction to Open Targets, an industry-academia collaboration, and the informatics tools it maintains.

By the end of the course you will be able to:
Explain the vision of the Open Targets consortium
Describe how the Open Targets Platform can help you prioritise targets associated with particular diseases or phenotypes, explore diseases associated with specific targets, and how these are linked to known drugs
Describe how the Open Targets Genetics Portal allows you to investigate evidence on genes, genetic variants, and GWAS studies, and identify prioritised candidate causal variants at trait-associated loci
Determine where to find out more about Open Targets and its informatics ecosystem

As part of EMBL-EBI’s celebration of Open Access week, this special one-off webinar will give you insight into the benefits of open access data, alongside guidance and tips on managing your data.

Featuring four members of EMBL-EBI’s resource teams (from BioSamples, ENA, IntAct/Complex Portal & Europe PMC), you’ll get an overview of Open and FAIR data, insights into submission processes and support, the importance of open literature and some hints, tips and tricks for ensuring your data can easily be made available to others. You’ll also get an opportunity to ask live questions to all four of our speakers, and find out where you can learn more.

Who is this course for?
This webinar is for anyone who is interested in learning more about open access data and how they can make their data available to others.

PDBeChem allows you to search for chemical components (ligands, small molecules and monomers) that appear in PDB entries, and discover which protein structures bind a particular ligand. This course will show you how to use PDBeChem and what you can do with it.

By the end of the course you will be able to:
Evaluate what PDBeChem is and what is can be used for
Launch PDBeChem and use different ways to search for small molecules
Use the SMILES molecular editor to draw parts of your chemical structure to explore related small molecules on PDB
Evaluate your search results from the chemical component summary page

This course will show you how to explore the structural information in a PDB entry using PDBe - EMBL-EBI's resource for the collection, organisation and dissemination of data on biological macromolecular structures.

By the end of the course you will be able to:
Navigate and extract the information from a particular PDB entry using the PDBe
Download data in an appropriate format

PDBeFold can be used to identify structural homologues in the PDB. PDBe's Secondary Structure Matching service (SSM) allows you to interactively compare, align and superimpose protein structures in 3D. This course will show you how to use PDBeFold and what you can do with it.

By the end of the course you will be able to:
Evaluate what PDBeFold is and what it can do
Launch PDBeFold and search for 3D structures that are similar to your protein of interest
Interpret structural similarity of your results based on Q-scores
View and analyse structures from your returned results

This webinar will introduce the concepts of a graph database and describe how we used a graph-approach for integrating the structural data of the Protein Data Bank.

The presented PDBe knowledge graph combines annotations provided by PDBe-KB partners with the core PDB archive. Each PDB entry can be thought of as a tree, with the root being the PDB entry, connected to chains and entities, which are then connected to residues. Each of the more than 150 million PDB residues, the leaves of the tree representation, are linked to annotations that make it easier to answer scientific questions such as: Can we find small molecules which have the same scaffold, and interact with the same binding sites? Or, can we find macromolecular interaction interfaces which have highly conserved residues, and are annotated to be structurally flexible?

The webinar will help the audience answer these, and other similar scientific questions and will provide a solid foundation for taking advantage of the PDBe knowledge graph and use it as an invaluable research tool.

Who is this course for?
This webinar is best suited for bioinformaticians with some experience in analysing structural data from the PDB using programmatic and/or high-throughput data access.

Our understanding of biological function can be advanced by the knowledge of biomolecular structures. Yet, it requires compiling data from individual entries in the Protein Data Bank (PDB), where each entry may represent only a segment of a complete system and may lack biological context.

The Protein Data Bank in Europe - Knowledge Base (PDBe-KB) is a community-driven, integrated resource whose goal is to place macromolecular structures in their biological context and thus promote fundamental and translational research. PDBe-KB combines residue-level structural data with functional annotations and sequence information in a highly interconnected, complex graph database, on the scale of 1 billion nodes and 4 billion edges. PDBe-KB infrastructure allows compilation of data from multiple PDB entries into a context-specific view of the data that is made available via an extensive set of API endpoints and modular web components.

This webinar presents an updated version of the first, protein-specific aggregated view that summarises all the data from the PDB and associated functional annotations from PDBe-KB partner resources in a user-friendly and accessible web-based view, providing a novel way to navigate structural data.

Who is this course for?
This webinar is aimed at individuals working on protein biology. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

PDBePISA allows you to explore macromolecular (protein, DNA/RNA and ligand) interfaces and predict the quaternary structure of your protein. This course will show you how to use PDBePISA and what you can do with it.

By the end of the course you will be able to:
Evaluate what PDBePISA is and what it can do
Launch PDBePISA and search for interfaces related to your structure of interest
Analyse and interpret probable assemblies of your structure of interest

This course will show you how to search the Protein Data Bank in Europe (PDBe) - EMBL-EBI's resource for the collection, organisation and dissemination of data on biological macromolecular structures.

By the end of the course you will be able to:
Search the PDB archive using PDBe’s search and navigation system
Know how to refine and save your search query
Sort and download search results
Evaluate the best representative structure from the search results

This webinar will show you how to access some of the software packages created at PDBe, used to generate the data displayed on our website. This will include a walkthrough of our github repositories, highlighting the types of packages available, how to access them and some examples of how they can be used.

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 some of the software packages created at PDBe
Explore PDBe's GitHub repositories to discover types of packages available and their application

This quick tour provides a short introduction to EMBL-EBI's repository for mass spectrometry-based proteomics data, PRIDE.

By the end of the course you will be able to:
Describe what PRIDE is and how data submission and data visualisation work
Search and download datasets from PRIDE Archive
Know where to find out more about PRIDE

This webinar will provide an introduction to proteomics approaches and the PRIDE database, followed by more detailed examples of PRIDE public data re-use, including “big data” approaches.

Who is this course for?
This webinar is suitable for biologists and bioinformaticians with an interest in proteomics, as well as proteomics bioinformaticians or scientific programmers expert in proteomics.

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

Recall the role of the PRIDE database
Describe examples of PRIDE public data re-use

Detection of conserved evolutionary units by profile hidden Markov Models (HMM): discover how different types of entries are created in the Pfam database.

By the end of the course you will be able to:
List the six Pfam entry categories
Describe the concept of Hidden Markov Models
Outline the process of creating a Pfam model
List the features that define a clan of entries

This quick tour provides a brief introduction to the protein families database Pfam, based at EMBL-EBI. Each protein family is represented by multiple sequence alignments and a profile hidden Markov model, which is used to create a probabilistic model that represents the family.

By the end of the course you will be able to:
Provide a basic description of what Pfam provides
Search and discover protein-related information with Pfam
Describe where to find out more about Pfam

This online course provides an introduction to tandem repeats (TR) in proteins. This course offers a description of TRs and their importance in biology. Furthermore, we describe one method of TR detection which is based on sequence homology, as well as discussing the challenges in characterising them.

By the end of the course you will be able to:
list features of tandem repeats
describe the importance of repeats in biology
list the differences between repeats and domains
describe the process used to create repeat entries in Pfam

The PhenoMeNal Gateway is the portal to your own PhenoMeNal Cloud Research Environment (CRE) containing an array of essential metabolomics applications. This course will give you an overview of PhenoMeNal Gateway, how to create your cloud research environment, and how to use the PhenoMeNal Galaxy instance for workflows for metabolomics data.

By the end of the course you will be able to:
Describe what PhenoMeNal is and when to use it
Create your cloud research environment
Use the PhenoMeNal Galaxy instance

This course provides a basic introduction to the field of phylogenetics, with an emphasis on how to read and interpret phylogenetic trees.

By the end of the course you will be able to:
Describe several applications of phylogenetics
Explain how to read simple trees
Identify major stages in phylogenetic analyses
Access bioinformatics tools for phylogenetics

This webinar will focus on practical applications of the FAIR data principles, particularly in the context of clinical bioinformatics. We will highlight several example projects that have put the FAIR principles in practice, and discuss the advantages and some of the challenges involved. ELIXIR Galaxy community (elixir-europe.org/communities/galaxy) promotes the use of Galaxy projects that enhance the FAIRness in data analysis. We will demonstrate the Galaxy services that deliver practical FAIR data analysis with “Single Sign-On” capability provided by ELIXIR-AAI. The aim is to provide (medical) researchers with the practicalities of implementing and using FAIR principles in the context of the CINECA project as applied to translational research at Erasmus University Medical Center.

The “How FAIR are you” webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.

Who is this course for?
Researchers, especially those working in clinical bioinformatics, with an interest in applying FAIR principles to data analysis.

Joint webinar with ASAPbio, Sumeet Pal Singh and Europe PMC

Preprints enable researchers to rapidly share their work publicly before the formal peer review process. In this webinar you will learn more about preprints and their benefits for the research community from ASAPbio (Accelerating Science and Publication in biology); will hear an author’s perspective on posting preprints from Sumeet Pal Singh, a group leader at IRIBHM, ULB; and will find out how to incorporate preprints in your literature search routine by using the preprint discovery tools developed by Europe PMC.

ASAPbio is a scientist-driven nonprofit that promotes the productive use of preprints in the life sciences. ASAPbio coordinates a global community of researchers and stakeholders interested in preprints and develops resources to advance best practices and help researchers make informed decisions about communicating their work via preprints. Iratxe Puebla, Associate Director at ASAPbio, will provide an overview of preprints and their growth in the life sciences, and cover things researchers should consider before posting a preprint.

Sumeet Pal Singh is a group leader at IRIBHM, ULB and an ASAPbio fellow. Sumeet will describe the journey of publishing his first senior author paper from a preprint to a peer-reviewed article, as well as the details related to the timing of posting a preprint and its relationship to the peer-review process. He will outline a new path provided by Review Commons that allows the authors to receive peer reviews for their manuscript prior to a journal submission, as well as post the reviewer’s comments and the authors’ response on preprint server (bioRxiv).

Europe PMC indexes over 300,000 preprints abstracts and full text COVID-19 preprints from 20 life sciences preprint servers alongside published journal articles. Preprints in Europe PMC are linked to citations, data, community peer reviews and more. In this part of the talk we will demonstrate how to find relevant preprints, cite and track preprint citations, claim preprints to ORCID, or discover relevant resources.

Who is this course for?
This webinar is suitable to any biological researchers who wish to learn more about incorporating preprints into their research. No prior knowledge is required.

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

Define what a preprint is
Choose a suitable preprint server for your work
Maximise the options for publication of the preprint at a journal
Decide when to post your manuscript as a preprint
Deal with community reviews and comments
Identify how to search for relevant preprints
Find data behind the preprint
Find comments or reviews associated with a preprint
Add a preprint publication to your publication list
Cite a preprint