EBI Transcriptomics Data and Tools Workshop Jan 2020

This workshop is jointly hosted by the Shields Library and the Genome Center Bioinformatics Core.

The European Bioinformatics Institute (EMBL-EBI,www.ebi.ac.uk) is part of EMBL, Europe’s flagship laboratory for the life sciences. Part of their mission is to train scientists at all levels to get the most out of publicly available biological data.

 

Description

This workshop will provide an overview of data management and ontology principles in addition to hands-on experience with functional genomics resources at the EBI including data submission, archival and visualisation. It is primarily targeted at wetlab researchers interested in learning about functional genomics data, how to access, retrieve and use the data from ArrayExpress and hands-on experience in using Expression Atlas, a resource to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others. The workshop will include an overview on how gene expression data is curated and analysed in Expression Atlas and a practical activity to demonstrate how to access and visualise gene expression analysis results. These activities should help you answer questions such as "where is my favourite gene expressed?" or "how does its expression change in a disease?".

 

Target Audience

This workshop is aimed at wet-lab scientists and bioinformaticians. Participants should have an understanding of molecular biology/genetics and be comfortable conducting analyses via web browsers.

 

Prerequisites

No previous bioinformatics experience is required, but an undergraduate level understanding of biology would be an advantage.

 

Aims

During this course you will learn about:

• ArrayExpress Archive (http://www.ebi.ac.uk/arrayexpress/)
• Expression Atlas (http://www.ebi.ac.uk/gxa/home)

 

Content

• Introduction to data management good practice, FAIR standards and ontologies
• Annotare: submitting functional genomics data to the EBI in-line with good data practice.
• ArrayExpress: how to find and reuse functional genomics data
• Expression Atlas: overview of the standardised analysis pathway. Introduction to experiment types investigated and features available in visualising bulk RNA-seq data
• Single Cell Expression Atlas: introduction into single-cell sequencing concepts and experiment types followed by overview of the resource and methods of single cell data visualisation
• RNA-seqer API: programmatic access to processed RNA-seq data from ENA. (Inclusion of this module will depend on time available on the day of the workshop.)

 

Learning Outcomes

After this course you should be able to:

• Understand good data management concepts and incorporate them into their
  research practice
• Understanding data submission process at the EBI with the web tool Annotare
• Investigate datasets in ArrayExpress to investigate relevant to users’ research; access and download the raw data and accompanying metadata
• Interpret the results of data visualisation in Expression Atlas and its counterpart Single Cell Expression Atlas to draw conclusions about available data as well as downloading the results of the data analysis
• Be aware of different methods for producing single cell data and the considerations underlying these decisions

 

FAQ

What do I need to bring? … This workshop will be held in a computer classroom at Shields Library. If you want to bring your own laptop to use, it will need to be able to run a current web browser, such as Chrome or Firefox.

Can I bring my own data? … No, but we will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.

How  much does it cost? … The registration fee is $50, which covers the cost of hosting the workshop.

Where is the workshop? … This workshop will be held in a computer classroom at Shields Library and will run from 9:30am to 5:00pm on Friday January 24. Coffee and snacks will be provided.

How do I apply? … All registration is “first-come, first-served”. There is no application process.  So, sign up as soon as possible to ensure your place in the workshop!

Where can I find more information, including your policies?  ... Go to our website (bioinformatics.ucdavis.edu/training/) and check out our FAQ.

 

Questions?

If you have any questions, please don’t hesitate to contact us at training.bioinformatics@ucdavis.edu