Course outside EMBL-EBI

Exploring Biodiversity through Bioinformatics

Welcome to the new EMBL-EBI Training site. Please tell us what you think!

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.

Who is this course for?

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.

What will I learn?

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

Trainers

Jan Kreuze
International Potato Center (CIP), Peru
Noelle Anglin
International Potato Center (CIP), Peru
Guilherme Oliveira
Instituto Tecnológico Vale - ITV, Brazil
Marco Cristancho
Universidad de Los Andes, Colombia
Hannele Lindqvist-Kreuze
International Potato Center (CIP), Peru

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 Santelmo Vasconcelos
11:00-11:30 Coffee Break
11:30-13:00 DNA barcodes - experimental design Santelmo Vasconcelos
13:00-14:00 Lunch CIP Cafeteria
14:00-15:30 DNA barcodes - sampling methodology Santelmo Vasconcelos
15:30-16:00 Coffee Break  
16:00-17:30 Data cleaning Santelmo Vasconcelos
17:30 End of day 1  
Day 2 – Wednesday 10 April
08:30-09:30 What is a barcode and how to select markers Santelmo Vasconcelos
09:30-10:30 Choosing and using markers for DNA barcodes Santelmo Vasconcelos
10:30-11:00 Coffee Break
11:00-11:30 Choosing and using markers for DNA barcodes Santelmo Vasconcelos
11:30-13:00 Developing new DNA barcodes Santelmo Vasconcelos
13:00-14:00 Lunch CIP Cafeteria
14:00-15:00 Analyzing DNA barcodes Santelmo Vasconcelos
15:00-16:00 Exercise: obtaining a dataset, and running the analyses Santelmo Vasconcelos
16:00-16:30 Coffee Break  
16:30-17:30 Exercise: obtaining a dataset, and running the analyses Santelmo Vasconcelos
17:30 End of day 2  
Day 3 – Thursday 11 April
08:30-09:30 Phylogeny and species definition by DNA barcodes Santelmo Vasconcelos
09:30-10:30 Exercise: phylogeny and barcode gap Santelmo Vasconcelos
10:30-11:00 Coffee Break
11:00-11:30 Exercise: phylogeny and barcode gap Santelmo Vasconcelos
11:30-12:00 Final Questions Santelmo Vasconcelos
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 Introduction to genome wide association studies (GWAS)

Hannele Lindqvist-Kreuze

11:30-13:00 Practical: GWAS in polyploid potato using RStudio and GWASPoly Hannele Lindqvist-Kreuze
13:00-14:00 Lunch CIP Cafeteria
14:00-14:30 Q&A on Molecular markers Hannele Lindqvist-Kreuze
14:30-15:00 Introduction to viral metagenomics Jan Kreuze
15:00-16:00 Practical: viral metagenomics using VirusDetect Jorge Villacorta
16:00-16:15 Coffee Break  
16:15-17:00 Practical: viral metagenomics using VirusDetect Jorge Villacorta
17:00-17:30 Course wrap-up and feedback Jan Kreuze / Trainers

In order to be considered for a place on this course applicants must complete the online application form.

Incomplete applications will NOT be considered. 

If you have any queries about the registration process please email Piv Gopalasingam.

The registration fee includes:

  • Tea/coffee and lunches will be provided for the duration of the course
  • Course dinner on Thursday 11th April
  • Use of the course training room and computers
  • Course materials provided
  • Course certificate
This course has ended

09 - 12 April 2019
International Potato Center (CIP) Peru
$120 PEN
Contact
Jan Kreuze

Organisers
  • Jan Kreuze
    International Potato Center (CIP), Peru
  • Noelle Anglin
    International Potato Center (CIP), Peru
  • Hannele Lindqvist-Kreuze
    International Potato Center (CIP), Peru
  • Guilherme Oliveira
    Instituto Tecnológico Vale - ITV, Brazil
  • Selene Fernandez-Valverde
    LANGEBIO, Cinvestav, Mexico
  • Marco Cristancho
    Universidad de Los Andes, Colombia
  • Piraveen Gopalasingam
    EMBL-EBI, UK

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