CSC offered resources in a virtual Biohackathon helping to develop new tools for COVID-19 analysis

CSC offered resources in a virtual Biohackathon helping to develop new tools for COVID-19 analysis

More than 20 different projects and over 500 scientists, software developers and clinicians met in the online event from 5 to 11 April with a goal to improve the accessibility of COVID-19 data, protocols, analysis pipelines and provide dedicated compute resources to execute demanding data analysis tasks.

The hackathon was initiated by Pjotr Prins, USA; Tazro Ohta, Japan; and Leyla Garcia, Germany.

Many ELIXIR Nodes provided resources, HPC clusters and technical assistance during the event. In addition, the ELIXIR Compute Platform set up common access to a virtual cloud environment - virtual machine - with direct access to all relevant data resources, analysis pipelines and computing capacities. Using this virtual machine, researchers were able to explore and analyse the COVID-19 data without the need to download the data or install any specific software or libraries on their computers.

CSC (as an Elixir-Finland Node) participated in this hackathon by offering access to its state-of-the-art cloud computing and data lake services for the hackathon participants.

Following resources were being offered:

  • cPouta IaaS cloud service access
  • Allas Object Storage service access
  • Rahti Container cloud service access
  • Galaxy service in cPouta was setup to be used via European Galaxy workflow portal

After the hackathon, CSC decided to extend Galaxy service setup in cPouta for the duration of the COVID-19 pandemic period. Idea is that researchers having ELIXIR AAI account can use the service to run workflows for COVID-19 research.

During the hackathon CSC’s specialists also provided support to hackathon participants for queries related to usage of cloud services, setting up their services, data management & sharing related queries etc. CSC’s Specialists mainly involved in supporting this Biohackathon were Álvaro González, Jarno Laitinen & Shubham Kapoor. Shubham Kapoor & Tommi Nyrönen were also responsible for technical coordination & arrangements within CSC.

- In general hackathon went well with several hundred international researchers, national e-infrastructures & private organisations participating under same event for a novel cause. It was really exciting to help these researchers with CSC’s computing resources, answer their queries & guidance to setup services within modern computing environments, told Shubham Kapoor, ELIXIR-Finland, Systems Specialist from CSC.

The results from the virtual Biohackathon will be published in BioHackrXiv, a pre-publishing server hosted by the Open Science Foundation. This will allow anyone to benefit from the outcomes, many of the groups are already planning longer-term collaboration to build upon the results achieved during the event.

Source: Elixir-Europe: Hacking the pandemic

Picture: Adobe Stock

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Shubham Kapoor, ELIXIR-Finland, Systems Specialist, CSC