CABANA Workshop: Applied bioinformatics, molecular epidemiology, and the SARS-CoV-2 Pandemic
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Date:
Tuesday 1 - Friday 4 December 2020Venue:
Virtual - EMBL-EBI, Hinxton, CB10 1SD, United KingdomApplication opens:
Thursday 15 October 2020Application deadline:
Monday 16 November 2020Participation:
Open application with selectionRegistration fee:
FreeRegistration closed
Dates additional information:
This workshop will take place between Tuesday 1st - Friday 4th December, each day running for up to 3 hours.Course Overview
This workshop will provide training on the use of bioinformatic tools for the design and analysis of research and diagnostic molecular assays. Trainees will receive training on viral genome assembly, comparative viral genomics and downstream applications of this data in research and applied contexts. Trainers will focus practical sessions on the analysis of Illumina SARS-CoV-2 sequences.
This online workshop will be delivered on Zoom and comprise a blend of live lectures and hands-on practicals delivered by trainers across Latin America. Certificates will be provided to mark successful completion of this workshop. Sessions on Friday 4th December will be livestreamed on YouTube and made freely available on the platform thereafter. There will be an opportunity to deliver a short presentation about your work to other trainees.
Resources
During this course you will learn about:
- Viral genome assembly
- Comparative analysis of viral genomes
- Primer design for qPCR
- Point of care molecular testing
- Standards for reporting of molecular epidemiology studies
Audience
This course is suitable for postgraduate (MSc-level and above) scientists within Latin America (excluding Chile and Uruguay) who are working with or generating genomic datasets related to SARS-CoV-2. Ideally, trainees will be working in the field of virology, and performing sequencing and/or analysing viral sequences, especially those within the coronaviridae family. We welcome applications from universities, research centres, hospitals, public health, and private laboratories.
Scientists from underrepresented ethnic and gender groups are especially encouraged to apply for this workshop.
Please note this course will be taught in English, however the trainers are fluent in either Spanish or Portuguese and can offer language support where feasible. Attendance priority will be given to those who have not attended a CABANA event yet.
Prerequisites
Undergraduate-level knowledge of biology would be advantageous. You will also require access to a computer for the duration of the workshop. While most practicals are browser-based, a few will require a UNIX environment. Trainees will therefore require a basic knowledge of the Unix command line.
We recommend these free tutorials:
- Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
- Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training
Training will be delivered via Zoom; trainees need to ensure they have working audio and microphones.
Learning outcomes
After this course you should be able to:
- Know the main public repositories for virus sequences
- Analyse genomic sequences of viruses
- Design PCR primers following international recommendations
- Apply international standards for the reporting of molecular epidemiology studies
Programme
Day 1 – Tuesday 1 December 2020 |
||
|---|---|---|
| 08:45-09:00 | Welcome and introductions | Marco Cristancho & Diego Forero |
| 09:00-09:45 | Sequencing technologies (Theoretical) | Dario Fernandez |
| 09:45-10:30 | Viral genomes databases – GISAID and other repositories | Priscila Born |
| 10:30-10:45 | Break | |
| 10:45-11:30 | DNA sequence Quality Control (Theoretical - Practical) | Gisele Nunes & Gilderlanio Araujo |
| 11:30-12:00 | Trainee presentations | Trainees |
| 12:00 | End of day 1 | |
Day 2 – Wednesday 2 December 2020 |
||
|---|---|---|
| 09:00-11:00 | Assembly of viral genomes (Theoretical - Practical) | Jan Kreuze & Segundo Fuentes |
| 11:00-11:15 | Break | |
| 11:15-12:00 | Trainee presentations | Trainees |
| 12:00 | End of day 2 | |
Day 3 – Thursday 3 December 2020 |
||
| 09:00-10:00 | Comparative analysis of viral genomes (Theoretical - Practical) | Dario Fernandez |
| 10:00-11:00 | Phylogenomics of viral genomes (Theoretical - Practical) | Dario Fernandez |
| 11:00-11:15 | Break | |
| 11:15-11:45 | Trainee presentations | Trainees |
| 11:45 | End of day 3 | |
Day 4 – Friday 4 December 2020 |
||
| 08:45-09:30 | Primer design for qPCR (Theoretical) | Segundo Fuentes & Ana Perez |
| 09:30-10:15 | Point of care molecular testing (Point of care isothermal amplification protocols) - LAMP (Theoretical) | Segundo Fuentes - Ana Perez |
| 10:15-10:30 | Break | |
| 10:30-11:15 | Standards for reporting of molecular epidemiology studies - STROBE-ME (Theoretical) | Valentina Gallo |
| 11:15-11:45 | Trainee presentations | Trainees |
| 11:45-12:00 | End of workshop: feedback and certificates | Marco Cristancho & Diego Forero |
Additional information:
This workshop is part supported by the ITV-Fiocruz coronavirus genome initiative.
In association with
How to apply
In order to be considered for a place in this workshop applicants must complete the online application form.
Incomplete applications will NOT be considered.
If you have any queries about the application process please email Guilherme Oliveira and Piv Gopalasingam.
Please note there is NO registration fee and you will not be asked to pay for this workshop.
There will be a maximum of 30 trainees on this workshop and registration is dependent on selection after successful completion of the application process.
Applications will close on Monday 16th November 2020 at 18:30 (COT).
Notification emails will be sent approximately 1 week after the application deadline.
Application deadline
16 November 2020
Number of places
30 places
Organisers
Piraveen Gopalasingam - EMBL-EBI, UK
Marco Cristancho - Universidad de Los Andes
Diego Forero - Fundación Universitaria del Área Andina
Trainers
Marco Cristancho - Universidad de Los Andes
Diego Forero - Fundación Universitaria del Área Andina
Jan Kreuze - International Potato Center (CIP)
Segundo Fuentes - International Potato Center (CIP)
Gisele Nunes Lopes - Instituto Tecnológico Vale (ITV)
Dario Fernández Do Porto - IC-UBA
Gilderlanio Santana de Araujo - Universidade Federal do Pará (UFPA)
Priscila Born - Fundação Oswaldo Cruz (Fiocruz) Rio de Janeiro
Valentina Gallo - University of Groningen
Agustin Pardo - FCEN-UBA
Claudio Schuster - IQUIBICEN-UBA