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

In this activity, students are assigned different alleles of the gene for phenylalanine hydroxylase to research using OMIM (Online Mendelian Inheritance in Man). They are then asked to both explain and illustrate how this mutation may cause the disease phenylketonuria (PKU).

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

Preprints enable researchers to rapidly share their work publicly before the formal peer review process. This webinar will demonstrate how to incorporate preprints in your literature search routine by using the discovery tools developed by Europe PMC.

Europe PMC indexes preprints abstracts and full text COVID-19 preprints from many life sciences preprint servers alongside published articles. Preprints in Europe PMC are linked to data and platforms that comment on or peer review preprints. We will demonstrate how to find the data behind preprints as well as comments and reviews associated with a given preprint. We will also share useful tips for posting your pre-prints, claiming a pre-print to your ORCID and tracking your pre-prints’ citations, revisions or recommendations by readers.

To learn more about using Europe PMC in your research try our Europe PMC: Quick tour or our webinar Using Europe PMC for effective literature research.

Who is this course for?
This webinar is suitable to any biological researchers who wish to learn more about incorporating pre-prints 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
Identify how to search for relevant preprints
Find data behind the preprint
Find comments or reviews associated with a preprint
Demonstrate how to add a preprint publication to your publication list
Describe how to cite a preprint

In this activity students explore the evolution of proteins by comparing 2D and 3D alignments of orthologs and paralogs.

This course will provide an introduction to protein classification and basic concepts, such as proteins families, domains and sequence features.

By the end of the course you will be able to:
Describe the importance of classifying proteins
Explain how protein families, domains and sequence features can be defined, and how these can be used to classify proteins
Describe the different predictive methods you can use to help classify proteins: patterns, profiles, fingerprints and hidden Markov models (HMMs)
List which resources for classifying proteins according to family, domain and sequence features are available at the EMBL-EBI

This course will provide an introduction to molecular interactions, their importance and the methodologies use to generate and capture interaction data.

By the end of the course you will be able to:
Know the importance of molecular interaction information and be able to provide examples of different types of molecular interaction
List the main experimental methodologies used to study protein-protein interactions
Describe of the limitations that these methodologies have
Determine where to find molecular interaction data at EMBL-EBI

This course will provide an overview of proteomics and introduce resources related to proteomics that are provided by EMBL-EBI.

By the end of the course you will be able to:
Describe what is meant by 'proteomics'
List proteomics resources that are available at the EBI
Describe what UniProtKB, IntAct, Reactome and PRIDE databases are
Know the differences between the UniProtKB, IntAct, Reactome and PRIDE databases are, and when to use each database

Psychological sciences preprints from PsyArXiv are now searchable in Europe PMC, an open database of life sciences literature. Join us for this live demo to learn how to find PsyArXiv preprints in Europe PMC, how to explore links to data, citations, comments or open peer reviews, how to claim preprints to your ORCID record, and more.

Who is this course for?
This webinar is aimed at psychology researchers.

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

find PsyArXiv preprints in Europe PMC
explore links to data, citations, comments or open peer reviews
claim preprints to your ORCID record

This webinar focuses on how to use QuickGO, our online browser for viewing the gene ontology (GO) and GO annotations. We will be reviewing what GO is, how to read an annotation, and how you can use QuickGO to find the information youneed.

The Gene Ontology Annotation (GOA) project provides high-quality functional annotations to gene products, such as proteins, protein complexes and non-coding RNAs. Currently our database contains over 390 million annotations to 60 million distinct gene products from almost 725,000 taxa. It is therefore critical to be able to easily and quickly mine and visualise the available information.

Who is this course for?
This webinar is aimed at anyone who wants to learn more about gene ontology annotation. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

Non-coding RNAs (ncRNAs) are essential for all life and carry out a wide range of functions. RNAcentral is a database of ncRNA sequences that provides a unified access point to ncRNA annotations from more than forty member databases and helps provide insight into RNA function.

By the end of the course you will be able to:
Describe what RNAcentral is and the data it contains
Navigate the RNAcentral website
Perform searches using RNAcentral

This course provides an overview to the Reactome pathway database web interface and the database content. For a short introduction to Reactome, please visit the Reactome quick tour.

By the end of the course you will be able to:
Explain the foundation of Reactome
Describe how data is curated from literature
Navigate the Reactome website
Explore the various forms of data representation in the interface
Use the range of analysis tools

This quick tour provides a brief introduction to Reactome - a manually curated freely available biological pathway knowledgebase.

By the end of the course you will be able to:
Explain the need and significance of Reactome
Describe the range of capabilities of the resource
Search your favourite molecule in Reactome
Perform a basic pathway enrichment analysis and visualise results

This course introduces the analysis tools available via the Reactome pathway database web interface. For a short introduction to Reactome, please visit the Reactome quick tour.

By the end of the course you will be able to:
Explore different types of analysis tools in Reactome website
Identify how to use Reactome interface to submit your own data for analysis
Visualize analysis results at different levels and formats
Find out several complementary tools can help you explore pathway data

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:

"Esophageal cancers are common globally but are difficult to treat and have a poor prognosis. Esophageal squamous cell carcinoma (ESCC) is especially dangerous and has poorly understood molecular mechanisms. A recent study took a comprehensive look at the kappa opioid receptor (KOR), a protein that has been shown to influence the progression of other cancers. First, researchers examined existing patient datasets and found that ESCC tumors had reduced KOR expression and that lower expression of KOR was correlated with reduced patient survival. In the lab, they found that reducing KOR expression in cultured ESCC cells led to increased proliferation, invasion, and metastasis. When looking for potential mechanisms, they found that down-regulation of KOR activated the PDK1-AKT signaling pathway. It also led to invasion-related changes in cells, including invadopodia formation and cytoskeletal rearrangement. Reducing expression of KOR in mice led to increased metastasis and phosphorylation of the AKT enzyme..."

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

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:

"Much like the organisms that flood its instruments the microbiome research community is thriving. But researchers from the UK’s National Institute for Biological Standards and Control (NIBSC) say that it could be doing even better. They’ve developed the first reference reagents for microbiome DNA analysis, Gut-Mix-RR and Gut-HiLo-RR. It’s a move designed to promote standardization and reproducibility across the field of microbiome research as tests revealed drastic variations across shotgun sequencing taxonomic profilers, which could alter conclusions about interactions between different microbes . If researchers can reach a consensus on acceptable levels of errors and begin using the materials in their labs the reference reagents could help standardize downstream gut microbiome analyses. A large open-invite collaborative study for multiple laboratories is slated for later in 2020..."

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

This webinar, will give an overview of BioModels, a popular repository of curated systems biology models. It will also provide a brief introduction to BioModels Parameters, a sub-resource within BioModels that provides model parts, followed by discussion of a study carried out to assess how reproducible systems biology models are, the reasons why mathematical models fail to reproduce simulation results and the solution we propose to tackle lack of reproducibility.

Who is this course for?
This webinar is suitable for any researchers interested in systems biology, computational biology modelling and reproducibility.

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

Describe the role of BioModels
Know when to use the sub-resource BioModels Parameters
Discuss how reproducible systems biology models are

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:

"Solving problems doesn’t always require an entirely new fix -- or new software. A team at IBM recently demonstrated that repurposed software offers improved functional characterization of microbiomes at a fraction of the development time. Currently, microbial functional profiling is typically done by classifying sequencing reads taxonomically, followed by computationally demanding functional analysis. But in a clever twist, researchers opted instead to directly compare sequencing reads to a functionally annotated database. The group developed a tree-shaped functional hierarchy and repurposed taxonomic bioinformatics tools to do the functional annotation. The method was applied to soil samples taken across the globe. This revealed, for example, that antioxidant activity was much higher in polar regions compared with equatorial areas. Next, the team plans to use the technique on other biological samples to further probe the secret lives of microbes..."

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