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

The NHGRI-EBI GWAS Catalog is a publicly available resource of Genome Wide Association Studies (GWAS) and their results. This course provides an introduction of how to browse SNP-trait associations using the NHGRI-EBI GWAS Catalog.

By the end of the course you will be able to:
recall the purpose and function of the NHGRI-EBI GWAS Catalog
recall the type and scope of the data which it contains
search the Catalog to identify variants associated with particular traits
know where to get help and support on the GWAS Catalog

Genome3D provides consensus structural annotations and 3D models for sequences from ten model organisms, including human. These data are generated by several UK-based resources that together form the Genome3D consortium: SCOP, CATH, SUPERFAMILY, Gene3D, FUGUE, pDomTHREADER and PHYRE. InterPro, meanwhile, provides functional analysis of proteins by classifying them into homologous superfamilies and families, and by predicting domains, repeats and important sites, based on data from 14 member databases.

This webinar presents the new InterPro entry type, Homologous superfamily, as well as describing domain and structure predictions from Genome3D annotations, and how they are integrated in InterPro.

Who is this course for?
This webinar is aimed at individuals working with variation data who wish to learn about Genome3D and InterPro's Homologous superfamily. No prior knowledge of bioinformatics is required, but undergraduate level knowledge of biology would be useful.

The new Genome3D annotations provide information on the likely structure of proteins, and the predictions made can guide the design of protein constructs for structural studies.

By the end of the course you will be able to:
explain the role of Genome3D annotations in InterPro

This quick tour provides a brief introduction to Genome Properties, a resource for assigning pathway function to species based on the presence or absence of defined molecular markers, as detected by the protein signature models contained within InterPro.

By the end of the course you will be able to:
Describe the data contained in Genome Properties
Summarise how Genome Properties data can be accessed

Genome Properties allows you to infer the presence of pathways and systems within a species, based on the occurrence of a set of underlying molecular markers.

By the end of the course you will be able to:
Describe the data contained in Genome Properties
Demonstrate various ways to search the resource
Propose ways to use Genome Properties in your own research

This course reviews the key genomic technologies and computational approaches that are driving advances in prognostics, diagnostics, and treatment. Throughout the semester, emphasis will return to issues surrounding the context of genomics in medicine including: what does a physician need to know? what sorts of questions will s/he likely encounter from patients? how should s/he respond? Lecturers will guide the student through real world patient-doctor interactions. Outcome considerations and socioeconomic implications of personalized medicine are also discussed. The first part of the course introduces key basic concepts of molecular biology, computational biology, and genomics. Continuing in the informatics applications portion of the course, lecturers begin each lecture block with a scenario, in order to set the stage and engage the student by showing: why is this important to know? how will the information presented be brought to bear on medical practice? The final section presents the ethical, legal, and social issues surrounding genomic medicine. A vision of how genomic medicine relates to preventative care and public health is presented in a discussion forum with the students where the following questions are explored: what is your level of preparedness now? what challenges must be met by the healthcare industry to get to where it needs to be?

Lecturers
Dr. Atul J. Butte
Dr. Steven A. Greenberg
Dr. Alvin Thong-Juak Kho
Dr. Peter Park
Dr. Marco F. Ramoni
Dr. Alberto A. Riva
Dr. Zoltan Szallasi
Dr. Jeffrey Mark Drazen
Dr. Todd Golub
Dr. Joel Hirschhorn
Dr. Greg Tucker-Kellogg
Dr. Scott Weiss

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 microbial compositions of hot springs are strongly influenced by temperature and pH. _Acidithiobacillus_ bacteria are found in diverse hot springs, but the genomic features that enable their adaptability are unclear. A recent DNA sequencing study analyzed the genomes of _Acidithiobacillus_ from hot springs in New Zealand and compared them to published non-hot-spring _Acidithiobacillus_ sequences. _Acidithiobacillus_ typically accounted for over 10% of the prokaryote abundance in the springs. Three species, including two novel species (TVZ\\_G2 and TVZ\\_G3), accounted for over 90% of _Acidithiobacillus _and were found in springs with wide-ranging characteristics. A fourth related novel species was also found, although in low abundance. All four species were found at temperatures and pHs above the known limits for _Acidithiobacillus, _likely because they had more GC bases and proline codons in their DNA than other species, increasing their thermostability..."

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

Gene expression is controlled by a complicated network of transcription factors and repressors, interacting with genomic features such as promoters and enhancers, dependant on epigenetic marks at those loci. Ensembl provides access to epigenomic data on histone modifications and protein binding across the genome, integrated with data on genes and genetic variation.

Join Ensembl to investigate a genomic region which controls gene expression, determine its activity in different cell types and view the epigenomic markers at that locus, plus see how to access these data in bulk.

Who is this course for?
No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

This course will focus on understanding aspects of modern technology displaying exponential growth curves and the impact on global quality of life through a weekly updated class project integrating knowledge and providing practical tools for political and business decision-making concerning new aspects of bioengineering, personalized medicine, genetically modified organisms, and stem cells. Interplays of economic, ethical, ecological, and biophysical modeling will be explored through multi-disciplinary teams of students, and individual brief reports.

The Greenomes site is part of a laboratory- and Internet-based curriculum to bring college students up to the minute with modern plant research. Plant molecular genetic and genomic research still lags behind medically-oriented research on microbes and higher animals. As a result, there are relatively few lab experiences that expose college-level students to the growing insights into plants offered by genomic biology.

A cornerstone of modern molecular biology is the electronic transfer of annotations form a few experimentally characterised sequences to the vast number being determined from DNA modern sequencing technologies. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software and associated website housed at EMBL-EBI, which in the latest version, uses a combination of sophisticated acceleration heuristics and mathematical and computational optimisations to enable the use of profile hidden Markov models (HMMs) for sequence analysis.

In this webinar, we will cover some of the basics about the HMMER algorithm and the use of the HMMER via the website.

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

Understanding protein functions is crucial to unlocking the value of genomic data for biomedical research and innovation. Delivering personalised health and precision medicine requires a detailed understanding of the consequences of sequence variants in proteins and their impact on phenotype. The widening gap between known proteins and their functions has encouraged the development of methods to automatically infer annotations. Artificial intelligence and machine learning hold a large repertoire of algorithms and methodologies to discover and infer prediction models. Coupled with the new big data technologies for interactive analytics and data transformation, the AI/ML methods represent valuable assets that could enhance the discovery of protein functions.

This tutorial will help you understanding how to use Spark and Interactive Analytics to make sense of protein data and build machine learning models to infer their functions.

Who is this course for?
Scientists and bioinformaticians with an interest in protein functions, machine learning and modelling.

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:

"Host-microbiome interactions are a critical component of host health, and plants have a particularly complex relationship with their microbiomes. Understanding these functional relationships will allow us to predict, and even influence, host fitness. Many ‘-omics’ techniques have been developed, and each is a powerful tool solo, but combining them opens the door to a more holistic, systems-level understanding. This strategy, called holo-omics, requires careful experimental design and faces several challenges as a field. First, it currently lacks well-tested analytical frameworks. Second, there is a need for freely available, specialized bioinformatics tools, as most focus on just one data source and don't integrate host and microbe data. Lastly, the heterogeneous nature of holo-omics data requires a wide range of expertise - including plant biologists, microbe experts, statisticians, and computational biologists..."

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:

"Most current knowledge about gut microbiomes has been obtained from studies on mammals, while the microbiomes of fish, the most diverse group of vertebrates (~33,000 species), are less well understood. Specifically, the major influencing factors and unique features of fish gut microbiomes remain unclear. To bridge this knowledge gap, a recent study analyzed the gut contents of 227 fish representing 85 different freshwater fish (FWF) and saltwater fish (SWF) species. rRNA sequencing revealed that Proteobacteria and Firmicutes were the two most abundant phyla, indicating a different composition from the typical vertebrate microbiome, which is composed mainly of Firmicutes and Bacteroidetes. Habitat (freshwater versus saltwater) more strongly influenced the host microbiome than host taxonomy or trophic level and the microbiome taxonomic and functional profiles were better indicators of a fish’s habitat than of its taxonomy..."

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

This webinar will introduce AlphaFold system for prediction and interpretation of protein structures. This webinar is designed for experimental biologists who wish to understand the strengths and limitations of AlphaFold and use the models to guide their experimental studies.

In this webinar we will provide an overview for the AlphaFold method and statistics that can be used to understand the reliability of the models. We will also introduce the AlphaFold Database, which provides hundreds of thousands of ready-made models across the tree of life, as well as highlight the AlphaFold Open Source and Colab notebooks that can be used to generate structures of sequences not yet available within the AlphaFold Database.

We will conclude by demonstrating a range of use cases followed by a question and answer session with all the presenters.

Who is this course for?
This webinar is suitable for lab-based and computational researchers with an interest in structural biology.

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

Explain basic principles of how AlphaFold 2.0 works
Discuss how to interpret the results of AlphaFold
Identify where to find AlphaFold models at EMBL-EBI
Explore how to easily create AlphaFold models using Open source and Google Colab

There is a wealth of training content developed and delivered across the globe each year, there will be many similar sessions on similar topics all delivered to similar audiences. At the same time, there will be trainers looking for inspiration and ideas on how to approach new topics or on new ways to teach old topics; as well as trainees looking for materials to further their own knowledge. Many trainers (or lecturers/educators etc) do not share their materials, or if materials are shared they are not easily found or re-used by others.

During this webinar, we will give you some tips and suggestions on how you can make more of the training materials you produce and encourage others to do the same. FAIR is not just for data - we can make our training materials FAIR too. Join us to find out the benefits of sharing your FAIR materials and some simple ways you can make it easy for others to use your materials in their teaching, or as aids for individuals to learn more.

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?
This webinar is for anyone who is interested in applying FAIR principles to training materials; no prior skills are required.

Though text mining becomes more widespread in biology, an average researcher can rarely use it to their advantage. In this webinar Europe PMC presents a tool to easily share annotated biological entities and relations with the research community. Europe PMC Annotation Submission System allows text miners and curators in the field of life sciences to make their results available to the public. Annotated concepts can be browsed and searched for both on Europe PMC website as a part of SciLite tool and Advanced search, as well as via the Annotations API.

Who is this course for?
This webinar is aimed at individuals who wish to learn more about sharing and reusing results of biomedical text-mining. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

Genetic variation is fundamental to the evolution of all species and is what makes us individuals. This course focuses on heritable variation and will give you a taste of the resources you can use to explore genetic variation data.

By the end of the course you will be able to:
Review sources of genetic variation
Describe the possible effects of genetic variation
Identify common genetic variation file types and formats
Describe types of genetic variation studies