CABANA Workshop: Functional genomics, Variation and Genomics resources and tools for plant research

Date:

 Thursday 18 Friday 19 October 2018

Venue: 

Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA) - INTA-Castelar, Calle Repetto y De Los Reseros, Hurlingham, C.P. 1686,  Buenos Aires,  Buenos Aires, Argentina

Application opens: 

Wednesday July 25 2018

Application deadline: 

Friday September 21 2018

Participation: 

Open application with selection

Registration fee: 

$1000 ARS

Registration closed

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Course Overview

In this workshop participants will explore EMBL-EBI resources for genomics, genetic variation and transcriptomics applications. The sessions focus on browsing, searching and retrieving genomics and functional genomics data. 

The first day will cover the functional genomics resources ArrayExpress and Expression Atlas, allowing both retrieval of functional genomics data and interpretation of gene expression analysis results via heat-map visualization. The second day will cover the European Variation Archive, Ensembl Plants genome browser and the Gramene database.

The course will be delivered by experienced and dedicated EMBL-EBI trainers, and will involve presentations, demonstrations and practical exercises to give participants hands-on experience.
 

Audience

This course is aimed at wet-lab researchers at any career stage within Latin America who are working with and/or generating their own plant genomic and transcriptomic datasets. 
No computational or previous bioinformatics experience is required for this workshop, but an undergraduate level knowledge of biology would be an advantage.

A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form.
 

Modules

  • arrayexpress-public-database-functional-genomics
  • expression-atlas-gene-expression-across-species-and-biological-conditions
  • introduction-ensemblensembl-genomes
  • european-variation-archive-eva

Learning outcomes

After this course you should be able to: 

  • Browse, search and retrieve functional genomics data from ArrayExpress and describe the caveats behind database searches
  • Describe and Construct a submission to ArrayExpress using Annotare, should they need to  deposit data to support a journal publication
  • Find and interpret heat-map visualized information on the abundance and localisation of RNA (and proteins) in different species and biological conditions
  • Describe the added value of data curation and annotation to ontologies as well as explore gene co-expression and perform gene set overlap analysis
  • View genomic regions and manipulate the view to add features you are interested in.
  • Find, access and download data from genetic variation studies that have been submitted by the community to EVA.

Programme

Day 1 – Thursday 18 October 2018
08:30 Arrival, registration  
09:00-09:30 Welcome and Introduction to EMBL-EBI resources and tools Cath Brooksbank
09:30-10:30 ArrayExpress: public archive for functional genomics data Laura Huerta
10:30-11:00 Break  
11:00-12:30 Data submission using Annotare Laura Huerta
13:30-14:30 Lunch
14:30-15:00 Expression Atlas: gene expression data across species and biological conditions Laura Huerta
15:00-15:30 Break
15:30-17:00 Expression Atlas Laura Huerta
17:00 End of day 1  
Day 2 – Friday 19th October 2018
08:45 Arrival  
09:00-10:30 European Variation Archive Baron Koylass - EVA Team / Laura Huerta
10:30-11:00 Break
11:00-12:30 Ensembl Plants Laura Huerta
12:30-13:30 Lunch
13:30-14:00 Gramene Database Laura Huerta
14:00-15:00 Introduction to GBS Norma Paniego / Carla Filippi
15:00-15:30 Break  
15:30-17:00 GBS in non-model plant species Carla Filippi / Natalia Aguirre
17:00-17:15 Wrap-up and feedback Laura Huerta