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PaRI Project Final Report

Abdulrahman Azab

Project member(s)
Björn Grüning; Christine O. Rasmussen; Fabian Leonardo Martinez Bernal; Giani Conzett; Johan Viklund; Kjell Petersen; Wolfgang Maier; Ott Eric Oopkaup; Ulvi Gerst Talas; Wolmar Nyberg Åkerström

By embracing and aligning with other European initiatives who contribute to the struggle against COVID-19, such as ELIXIR and EOSC-Life, PaRI facilitates pandemic research for Nordic researchers. The one-year project has built a secure platform for managing and executing tools and workflows for cross-border pandemic data processing. Data processing means collecting, quality controlling, analysing and securely storing data. Making it possible for multiple organisations in the Nordic region to have the same processes enables more seamless and efficient collaboration in further research. One of the PaRI project’s objectives was to implement Nordic pilots and best practices for FAIR data that benefit from these technical results. The project benefits greatly from the outcomes of NeIC’s Tryggve project.

 

NeIC PaRI project contributed to NeIC Strategic objectives, which are aligned with PaRI partners objectives, as follows :

 

  • Facilitate collection and storage of sequence and other human related COVID-19 data

  • Facilitate Nordic analysis of Nordic pandemic data using Galaxy and a research e-infrastructure in the Nordics

  • Deploy Secure cloud infrastructure for sharing and presentation of pandemic research datasets and results

  • Contribute to building the evolutionary tree of viral strains, based on RNA sequences of patient samples infected with coronavirus as they become known and shared.

  • Intend to make the viral and host data collected during pandemic findable, accessible, interoperable and reusable (FAIR) by supporting seamless cross-border access, and adopting data representation standards by existing federated sharing platforms, e.g. EGA.

  • Work in close collaboration with other nordic e-Infrastructure projects in addition to EU projects to support the use cases.

 

PaRI partners are: University of Oslo (UiO), University of Bergen (UiB), Technical University of Denmark (DTU), Estonian Scientific Compute Infrastructure (ETAIS), German Network for Bioinformatics Infrastructure (de.NBI), National Bioinformatics Infrastructure Sweden (NBIS). 

 

Among the most important achievements of the project and its collaborators is the Galaxy Nordic COVID-19 portal. The portal monitors the public output of viral genome sequencing projects that is submitted to the ENA and makes the data more accessible for further use. The portal also demonstrates the feasibility of tracking the output of national genome surveillance projects. The Nordic COVID-19 portal is part of the international Galaxy network. Galaxy helps researchers perform computational analyses with their data without having to have expertise in informatics, programming or data visualization. The platform is open source and enables accessible, reproducible and transparent computational research.

 

Another output of the PaRI project is the PaRI dashboard, a visualisation tool designed to help stakeholders such as epidemiologists, state institutions and researchers monitor the pandemic locally, down to regional and municipality levels. The dashboard is based on the NextStrain tool and visualizes Nordic COVID-19 data (raw sequencing data brokered into ENA or consensus sequences from the Galaxy pipeline). The dashboard visualizes the data as well as any connected metadata, allowing for filtering of created visualisation. Furthermore, it even allows adding sensitive metadata to the sequences, with the key feature that this additional metadata will only be stored in the user’s browser and thus aligned with any local legislation about sensitive data sharing.

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