This series of workshops will explore EMBL-EBI data resources for genomics, transcriptomics, protein sequences, structures and interactions, and chemical biology. Each half-day workshop will introduce participants to browsing, searching, retrieving, and conducting a basic analysis of a wide range of biological data types. 

Two workshops will cover the Ensembl genome browser, where researchers can explore annotated genomes and features of interest including genes, transcripts, and variants. Participants will also be introduced to the Variant Effect Predictor (VEP) tool and BioMart for bulk data download.

Functional genomics resources - Array Express, Expression Atlas - will introduce public data derived from transcriptomics experiments and provide instruction on how to begin investigating biological functions. Participants will also cover the Single-cell Expression Atlas and the expression data from individual cell sequencing.

Three workshops will explore resources dedicated to protein data, covering UniProt, the PDBe, IntAct, the Complex Portal, and Reactome. These topics will provide overviews of protein sequence, structure, and interactions; allowing participants to gain a greater understanding of the role played by proteins in the cell.

The final workshop will cover the EBI's chemical biology resources ChEBI and MetaboLights. Participants will learn how to access information on chemical entities of biological interest, and the myriad metabolites found in metabolomics experiements.

Virtual workshop

Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through trainer-led demonstrations and personal exercises on each resource. Live sessions will be delivered using Zoom with additional support and communication from the host, trainer and, resource specialists in the chat stream.

Who is this course for?

This workshop is aimed at PhD students within the PhD programme "Genetics, Molecular and Cellular Biology" (University of Pavia) and the PhD programmme "Biomolecular Sciences and Biotechnology" (IUSS, University School for Advanced Studies Pavia.

No knowledge of programming is required, but an undergraduate level knowledge of biology or molecular biology would be useful.

What will I learn?

Learning outcomes

After this workshop you should be able to:

• View genomic regions and manipulate data features
• Analyse genomic variants and associated phenotypes
• Locate gene expression data and relate to genomic function
• Discover and analyse protein sequence data
• Search, retrieve and assess the quality of protein structural data
• Describe molecular interaction and biomolecular complex data
• Locate chemical entity and metabolite data 

Course content

This workshop covers:

• Ensembl
• PDBe
• ArrayExpress, Expression Atlas, Single Cell Expression Atlas
• UniProt
• IntAct, Complex Portal, Reactome
• ChEBI, MetaboLights

Trainers

This course is available to students within University of Pavia and IUSS/IGM CNR only.

Please contact Professor Binda for eligibility, availability, and registration details.