CABANA: Understanding biodiversity through bioinformatics based approaches (Cancelled)

Date:

 Monday 18 Friday 22 May 2020

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday 12 August 2019

Application deadline: 

Friday 31 January 2020

Participation: 

Open application with selection

Contact: 

Marina Pujol

Registration fee: 

£300

Registration closed

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Overview

This course covers aspects of biodiversity and how bioinformatics plays a role in our understanding of the natural world. The content will introduce participants to approaches for analysing genetic barcodes in metagenomics studies, exploring genomic data, and how international sequencing projects aim sequence large numbers of species in particular environments. It will also cover simple bioinformatics tools and resources for examining small sets of biological sequences, and present keynote talks on how the modern biological sciences are changing how we view and interpret the world around us in the face of rapid climate change, and the loss of habitats and key species.

Audience

This course is aimed at PhD students and postdoctoral researchers wanting to use bioinformatics approaches as part of their research in biodiversity. It will enable those wanting to start undertaking basic identification of genetic variation, annotating function to genomic data, and using public data to interpret new findings.

Participants will require a basic knowledge of the Unix command line, the Ubuntu 18 operating system and the R statistical packages. We recommend these free tutorials:



Regardless of your current knowledge we encourage successful participants to use these, and other materials, to prepare for attending the course and future work in this area.
We strongly encourage applications from Latin American students who will be able to benefit from the CABANA funding available as part of this course. For more information and links to apply for the Train the Trainer portion of this course and fellowships, visit the CABANA webpage.

Syllabus, tools and resources

This course covers aspects of biodiversity and how bioinformatics plays a role in our understanding of the natural world.

During this course you will learn about:

  • Approaches for genetic barcoding and meta-barcoding
  • Methods for NGS read mapping, variant calling and analysis
  • Genomics projects supporting biodiversity research
  • EMBL-EBI data resources

Outcomes

By the end of this course participants will be able to:

  • Define challenges around obtaining biological samples and generating biodiversity data
  • Create and critically assess phylogenetic trees; generate a multiple sequence alignment; use simple bioinformatics tools
  • Run a barcoding analysis workflow
  • Utilise genome sequencing approaches as related to biodiversity

Additional information

Participants have the opportunity to display an A2 (420x594mm - portrait) poster for the duration of the course. We will ask you to submit your poster before the course for printing on site. It is not possible to display posters of a different size or orientation.

Accommodation will be provided in the Wellcome Genome Campus Conference Centre Monday-Friday inclusive. Please contact the Conference Centre directly if you wish to arrange to stay additional nights. The course fee includes breakfast and evening meals at Hinxton Hall, as well as breaks and lunches outside the EMBL-EBI training rooms.

Programme

Day 1 – Monday 18 May 2020
Welcome, introductions and overview of bioinformatics
10:00-11:00 Arrival, registration and refreshments  
11:00-12:15 Welcome, introduction to EMBL-EBI and networking Tom Hancocks
12:15-12:30 The CABANA Project and biodiversity Cath Brooksbank
12:30-13:30 Lunch and posters  
13:30-14:30 Keynote talk: Biodiversity, bioinformatics and the bioeconomy Federica Di Palma
14:30-15:30 Keynote talk: to be confirmed Paul Flicek
15:30-16:00 Break  
16:00-18:00 Bioinformatics fundamentals for biodiversity
  • BLAST/FASTA, Multiple sequence alignments, and phylogenetics
Tom Hancocks & CABANA Trainers
18:00 End of day  
18:15 Check-in to accommodation  
18:30-19:30 Welcome drinks Hinxton Hall Lounges
19:30-21:00 Evening meal Hinxton Hall Restaurant
Day 2 – Tuesday 19 May 2020
DNA barcoding for biodiversity
08:45-09:00 Arrival and registration  
09:00-10:00 Keynote talk: Barcoding and biodiversity Guilherme Oliveira
10:00-10:30 Experimental design for DNA barcodes Santelmo Vasconcelos & Guilherme Oliveira
10:30-11:00 Break  
11:00-13:00 Barcoding practical Santelmo Vasconcelos & Guilherme Oliveira
13:00-14:00 Lunch and posters  
14:00-16:00 Barcoding practical Santelmo Vasconcelos & Guilherme Oliveira
16:00-16:30 Break  
16:30-17:30 Barcoding use cases To be confirmed
17:30-18:30 Keynote talk To be confirmed
18:30 End of day  
19:30-21:00 Evening meal Hinxton Hall Restaurant
Day 3 – Wednesday 20 May 2020
Metabarcoding and metagenomics
08:45-09:00 Arrival and registration  
09:00-10:30 Metabarcoding Santelmo Vasconcelos & Guilherme Oliveira
10:30-11:00 Break  
11:00-13:00 Metabarcoding practical Santelmo Vasconcelos & Guilherme Oliveira
13:00-14:00 Lunch and posters  
14:00-16:00 To be confirmed To be confirmed
16:00-16:30 Break  
16:30-17:30 European Nucleotide Archive and geo-location ENA Team
17:30-18:30 Metagenomes and food sustainability Alfredo Herrera-Estrella
18:30 End of day  
19:30-21:00 Evening meal Hinxton Hall Restaurant
Day 4 – Thursday 21 May 2020
Whole genome sequencing of species
08:45-09:00 Arrival and registration  
09:00-10:30 To be confirmed To be confirmed
10:30-11:00 Break  
11:00-13:00 To be confirmed To be confirmed
13:00-14:00 Lunch and posters  
14:00-15:00 Keynote talk: Crop sequencing and biodiversity  Paul Kersey
15:00-16:00 International sequencing projects To be confirmed
16:00-16:30 Break  
16:45 Shuttle to The Backs, Queen's Road, Cambridge  
17:15-19:30 Free time in Cambridge  
19:30 Evening meal Dining at a University of Cambridge college
22:00 Shuttle to Wellcome Genome Campus  
Day 5 – Friday 22 May 2020
Bringing data and research approaches together
08:30 Check out of accommodation  
08:45-09:00 Arrival and registration  
09:00-10:30 Personal data plans: discussion All
10:30-11:00 Break  
11:00-12:30 Biodiversity & bioinformatics use cases To be confirmed
12:30-12:45 Feedback and course wrap-up Tom Hancocks
12:45-13:30 Lunch  
13:30 End of course  
13:45 Shuttle to Station Road, Cambridge