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Pandemic Research Infrastructure (PaRI) joins the NeIC affiliate programme

The one-year PaRI project focused on facilitating Nordic research on pandemics and especially the COVID-19 pandemic”

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1 nov 2021–31 okt 2022

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Presented by Wolmar Nyberg Åkerström (NBIS), NeIC AHM 2022-01-24

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Infrastructure for pandemic data

  • COVID-19 workflows
  • National compute resources
  • Local infrastructure
  • Dashboard: Geographic distribution of virus variants over time
  • Guide to FAIR viral genome data

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A guide to data sharing�

  • Provide guidance to projects, labs and other organisations producing or commissioning viral sequencing data
  • What constitutes good and ultimately (re)usable in a viral genome data record with a Nordic perspective?

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Viral genome data sharing

Data deposit

Metadata �as XML

Compressed �data files

Data analyses

Raw reads

Submission �tooling

Sample description

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A playbook for deploying Galaxy

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Curated tools & workflows

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Data flow for regional surveillance

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PaRI Affiliate activities

Expanded professional network

  • FAIRification of pandemic related genomic data
  • Running and administering COVID-19 workflows in Galaxy
  • Curating pandemic data for visualisations in Nextstrain / Auspice (possibly other visualisation tools)

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Targeted outreach

  • Onboarding new “partners” to our network
  • Merge deliverables into active projects and infrastructures

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Access to tools / workflows

  • Populate a GitHub organisation (pari-neic) with tools and workflows from the partners

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Pandemic Research Infrastructure (PaRI) joins the NeIC affiliate programme

Coordinator: Wolmar Nyberg Åkerström (NBIS)

Project owner: Abdulrahman Azab (NeIC)

Partners: NBIS, ETAIS, DTU, UiO/USIT, UiB

Contact: wolmar.n.akerstrom@uu.se

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FAIR data sharing

Background from ‘FAIR Principles’ by Martínez-Lavanchy, et al (2019), CC-BY 4.0. doi:10.11581/dtu:00000049

Ronot: MetaManMachine by Nikola Vasiljevic (2021), CC BY-SA 4.0, doi:10.5281/zenodo.4471098

Works with my software

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Supporting users FAIRifing data

Online entry points for users to get in contact with support staff related to PaRI are the Covid19 Data Portal network

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  • Advice on localizing data
  • Annotating and submitting data
  • Contact information on how to get support

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Infrastructure (non-sensitive data)

Analysis and storage services of PaRI for non-sensitive data:

  • A mix of ELIXIR developed and operated services
  • National generic e-infrastructure services
  • National Infrastructure for Research Data (NIRD)
  • Norwegian Research and Education Cloud (NREC)
  • SNIC Rackham
  • Estonian Scientific Computing Infrastructure (ETAIS)

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Infrastructure (sensitive data)

The Federated EGA services depend on more generic services offered by existing e-infrastructure service providers in the Nordic countries: TSD in Norway and SNIC/Sunet in Sweden.

  • Tjenester for Sensitive Data (TSD)
  • SNIC Bianca
  • Sunet Cloud

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Samples from Human Hosts

Sample description

  • A positive test result is information about a person’s health and thus it’s sensitive
  • May contain personal identity numbers and other identifiers for an individual
  • Demographic information, such as age, sex, location, date etc. could be used deduce the identity of an individual

Experiment description

  • May contain identifiers or references that could be used to deduce the identity of an individual

Raw reads

  • Genome fragments from the host can be used to identify an individual and should be considered sensitive