CABANA Workshop: Resources and tools for functional genomics and chemical biology

Date:

 Monday 15 Tuesday 16 October 2018

Venue: 

Faculty of Natural Sciences - University of Buenos Aires (FCEN-UBA) - Ciudad Universitaria. Nuñez - Ciudad Autónoma de Buenos Aires - Pabellón II, 1428,  Buenos Aires,  Buenos Aires, Argentina

Application opens: 

Thursday May 31 2018

Application deadline: 

Monday September 03 2018

Participation: 

Open application with selection

Registration fee: 

$1000 ARS

Course Overview

In this course participants will explore EMBL-EBI resources for transcriptomics and chemical biology applications. The sessions focus on browsing, searching and retrieving both functional genomics and small molecule 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 chemical biology resources ChEMBL and SUREChEMBL, which aid in the identification and investigation of small molecules with their biological targets, and corresponding bioactivity data.

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 transcriptomic and chemical biology datasets. The second day will be of particular interest to those interested in drug discovery, toxicology, agrochemicals, patents and targets of small molecules. No computational or previous bioinformatics experience is required for this workshop, but an undergraduate level knowledge of biology and chemistry would be an advantage.

Modules

  • introduction-embl-ebi-resources-and-tools
  • arrayexpress-public-database-functional-genomics
  • expression-atlas-gene-expression-across-species-and-biological-conditions
  • chembl-and-surechembl-bioactive-molecules-targets-and-patent-resources

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
  • Identify small molecules that interact with biological systems with applications in drug discovery, agrochemicals and predictive toxicology
  • Extract bioactivity data and identify relevant compounds and their biological targets from literature and patent sources

Programme

Day 1 – Monday 15 October 2018

08:30 Arrival, registration  
09:00-09:45 Welcome and Introduction to EMBL-EBI resources and tools Laura Huerta
09:45-10:30 Data quality: standards, curation and ontologies Laura Huerta
10:30-11:00 Break
11:00-12:30 ArrayExpress Laura Huerta
12:30-13:30 Lunch
13:30-14:30 Annotare: 'your' web-form submission tool Laura Huerta
14:30-15:00 Expression Atlas Laura Huerta
15:00-15:30 Break  
15:30-17:00 Expression Atlas Laura Huerta

17:00

End of day 1  

Day 2 – Tuesday 16 October 2018

09:00-10:30 Introduction to Chemical biology resources Anne Hersey
10:30-11:00 Break
11:00-12:30 ChEMBL & SUREChEMBL Anne Hersey
12:30-13:30 Lunch
13:30-15:00 ChEMBL & SUREChEMBL Anne Hersey
15:00-15:30 Break  
15:30-17:00 Searching Patent resources for drug discovery information Anne Hersey
17:00-17:15 End of day and feedback Anne Hersey / Laura Huerta