Exploring Biodiversity through Bioinformatics

Date:

 Tuesday 9 Friday 12 April 2019

Venue: 

International Potato Center (CIP) - Avenida La Molina 1895,  1558,  LIM,  La Molina,  Peru

Application opens: 

Friday 14 December 2018

Application deadline: 

Sunday 03 February 2019

Participation: 

By invitation

Contact: 

Jan Kreuze

Registration fee: 

$120 PEN

Course Overview

Many Latin American countries are hotspots for biodiversity, most of which have been characterized only to a very limited extent. This course aims to provide knowledge on available approaches, methods and tools to perform studies on biodiversity employing modern high-throughput sequencing approaches. After the course, participants will have learnt how to select the appropriate sequencing approach and experimental setup, how to access, control quality and clean data, and to analyze and interpret results using available bioinformatics tools.

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/or microbial genomic/transcriptomic datasets.


Basic computational or previous bioinformatics experience is required for this workshop, and 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.

Learning outcomes

After this course you should be able to:

  • Select an appropriate sequencing approach and study design to address your specific biodiversity questions
  • Access a range of data types from leading public repositories
  • Process sequence data from various approaches for biodiversity analysis using Galaxy pipelines
  • Interpret results of DNA based biodiversity analysis

Programme

Day 1 – Tuesday 9 April
08:30-09:00 Arrival, registration  
09:00-10:00 Welcome and introductions Jan Kreuze / Noelle Anglin
10:00-11:00 An overview of different sequencing approaches to analyze biodiversity Guilherme Oliveira
11:00-11:30 Coffee Break
11:30-13:00 Experimental design Guilherme Oliveira
13:00-14:00 Lunch CIP Cafeteria
14:00-15:30 Sampling methodology and design Guilherme Oliveira
15:30-16:00 Coffee Break  
16:00-17:30 Data cleaning Guilherme Oliveira
17:30 End of day 1  
Day 2 – Wednesday 10 April
08:30-09:30 What is a barcode and how to select markers Guilherme Oliveira
09:30-10:30 How to develop new barcode markers Guilherme Oliveira
10:30-11:00 Coffee Break
11:00-11:30 Producing DNA barcodes Guilherme Oliveira
11:30-13:00 Automating DNA barcode production Guilherme Oliveira
13:00-14:00 Lunch CIP Cafeteria
14:00-15:00 Using Pipebar/Overlaper Guilherme Oliveira
15:00-16:00 Exercise: obtaining a dataset, and running the pipeline Guilherme Oliveira
16:00-16:30 Coffee Break  
16:30-17:30 Exercise: obtaining a dataset, and running the pipeline Guilherme Oliveira
17:30 End of day 2  
Day 3 – Thursday 11 April
08:30-09:30 Phylogeny and species definition by DNA barcodes Guilherme Oliveira
09:30-10:30 Exercise: DNA barcoding phylogeny Guilherme Oliveira
10:30-11:00 Coffee Break
11:00-11:30 Exercise: DNA barcoding phylogeny Guilherme Oliveira
11:30-12:00 Final Questions Guilherme Oliveira
12:00-13:00 Introduction to Metagenomics data, databases and molecular data formats Marco Cristancho
13:00-14:00 Lunch CIP Cafeteria
14:00-15:00 Software for Metagenomics analysis Marco Cristancho
15:00-16:00 Introduction to Galaxy Marco Cristancho
16:00-16:30 Coffee Break  
16:30-17:30 Practical: Analysis of Metagenomics Data with Galaxy Marco Cristancho
17:30 End of day 3  
18:00-20:00 Course dinner  
Day 4 – Friday 12 April
08:30-09:30 Practical: Analysis of Metagenomics Data with Galaxy Marco Cristancho
09:30-10:00 Q&A on Metagegenomics analysis Marco Cristancho
10:00-10:30 Coffee Break
10:30-11:30 Molecular marckers applied to Biodiversity studies

Hannele Lindqvist-Kreuze

11:30-13:00 GWAS Hannele Lindqvist-Kreuze
13:00-14:00 Lunch CIP Cafeteria
14:00-15:30 Practical: Molecular markers pipelines in Galaxy Hannele Lindqvist-Kreuze
15:30-16:00 Q&A on Molecular markers Hannele Lindqvist-Kreuze
16:00-16:30 Coffee Break  
16:30-17:00 Course wrap-up and feedback Jan Kreuze / Trainers
17:00 End of course