The Galaxy Community and ELIXIR organise a second webinar series to demonstrate how open software and public research infrastructures can be used in analysing and publishing SARS-CoV2 data.

In a series of six webinar sessions, experts from ELIXIR and the global Galaxy community from the US, Australia and Europe will demonstrate how open access and open science are fundamental for fast and efficient response to public health crises. The series follows on the first Galaxy-ELIXIR webinar series organised in April-May 2020. It will introduce the latest Galaxy tools developed for working with SARS-CoV-2 data and discuss some of the challenges in accessing, analysing and interpreting them.

The kick-off session of the webinar series takes place on 20 January 2021.

More information about Galaxy analyses of COVID-19 data: covid19.galaxyproject.org

Programme

Session 1: COVID-19 analysis in Galaxy: Lessons learned and introduction to the series

20 January 2021, 17.00-18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)

The first session will summarise the developments in Galaxy the past eight months and introduce the latest tools for COVID-19 related research:


    WorkflowHub, Dockstore
    Single-tool view, simplified workflow run-form
    Scaling and performance improvements over the last 9 month
    Paper-Cut event(s)
    Galaxy plans for the next years


Speakers: 


    Anton Nekrutenko
    Marius van den Beek


Register

Session 2: Importance of (open) infrastructures in responding to a pandemic

27 January 2021, 17.00-18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)

The second session will present some of the data resources used to deposit and access SARS-CoV2 data. You will also discuss the critical importance of open access data to respond to epidemic outbreaks efficiently.


    Data resources
    Analysis resources
    Interoperability


Speakers: 


    Andrew Lonie
    Guy Cochrane
    Björn Grüning
    Frederik Coppens


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Session 3: Supporting the COVID-19 Data portal: viral data cleaning from human reads and submission to ENA

3 February 2021, 17.00-18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)

This session will present the COVID-19 Data Portal and the tools clean and submit data to open access repositories:


    Submission tool to European Nucleotide Archive
    Data preprocessing and cleaning


Speakers: 


    Ignacio Eguinoa 
    Bert Droesbeke
    Frederik Coppens


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Session 4: Insights from selection analysis of complete genomes and read-level data

10 February 2021, 17.00-18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)

Speakers: 


    Sergei Pond


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Session 5: Viral Beacon and Galaxy variant workflows

17 February 2021 | 17.00–18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)

Speakers:


    Bjoern Gruening
    Beatriz Serrano-Solano
    Babita Singh


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Session 6: DRS, long-read-sequencing, proteomics and more — an update to recent COVID-19 workflow developments

24 February 2021, 17.00-18.00 CET (starts at 16.00 GMT, 11.00 EST, 8.00 PST)

Speakers: 


    Wolfgang Maier
    Nathan Roach
    Pratik Jagtap
    Subina Mehta


Register

Acknowledgement

The analyses have been performed using the Galaxy platform and open source tools from BioConda. Tools were run using XSEDE resources maintained by the Texas Advanced Computing Center (TACC ), Pittsburgh Supercomputing Center (PSC), and Indiana University in the U.S., de.NBI,  VSC cloud resources and  IFB cluster resources on the European side, STFC-IRIS at the Diamond Light Source, and ARDC cloud resources in Australia.