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

Date:

 Monday 15 Wednesday 17 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: 

Friday September 21 2018

Participation: 

Open application with selection

Registration fee: 

$1000 ARS

Registration closed

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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 course theme will be communicable diseases, with relevant examples and use cases applied throughout. 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.

Please note that attendees of this workshop are invited to attend the 1-day Industry Workshop taking place on Wednesday 17th October 2018 in FCEN-UBA titled, "From Genomics and Bioinformatics to Personalized Medicine". For more information, click here.

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. Ideally, researchers should be working in fields relating to communicable diseases. The second day will be of particular interest to those interested in drug discovery, toxicology, 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.

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

  • 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
  • Explain the important of data reproducibility and the value of biocuration and annotation to ontologies
  • Use Expression Atlas to answer relevant questions about gene expression in your research area of interest
  • Explore gene co-expression and enrichment analysis results
  • 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  
09:00-09:30 Welcome and Introduction to EMBL-EBI resources and tools Cath Brooksbank
09:30-10:30 Data reproducibility: standards and ontologies Laura Huerta
10:30-11:00 Break
11:00-12:00 Discover functional genomics data with ArrayExpress Laura Huerta
12:00-13:00 Lunch
13:00-14:00 Discover functional genomics data with ArrayExpress: Hands-on Laura Huerta
14:00-15:00 Explore expression data with Expression Atlas Laura Huerta
15:00-15:30 Break  
15:30-16:30 Explore expression data with Expression Atlas: Hands-on Laura Huerta

16:30-17:30

Single Cell Expression Atlas: a new tool for single cell transcriptomics Laura Huerta
17:30 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 Target Identification: Exploring target/disease relationships and druggable targets with ChEMBL Anne Hersey
12:30-13:30 Lunch
13:30-15:00 Compound Identification: Exploring compound interactions with protein targets, whole organisms and balancing potency, selectivity and toxicity using ChEMBL Anne Hersey
15:00-15:30 Break  
15:30-17:00 Patent Searching: Exploring the SureChEMBL patent resource for chemical data Anne Hersey
17:00-17:15 End of day and feedback Anne Hersey / Laura Huerta