Researchers use cases

HADDOCK and Zenodo

Collaborations made easy using OpenAIRE and EOSC-hub services

Alice and Bob are two structural biologists working on the same field in opposite parts of the world. Alice is a post-doc in a European University, while Bob is setting up a research group in a South American institute. They meet during the poster session of a major scientific conference and, after discovering a common interest in how antibiotics attach to harmful bacteria by binding to the proteins in their membranes, they decide to start working together.

Bob is sitting on a lot of experimental data but has no access to the compute capacity required to analyze the results. Using just his laptop would take months to go through the first simulations. Alice suggests HADDOCK, a web portal that offers computational tools for structural biologists to model the structure of complexes of proteins and other biomolecules.

HADDOCK is one of the thematic services available in the EOSC-hub catalogue, developed by the University of Utrecht and powered by the compute resources of the EGI Federation. HADDOCK is regularly used by thousands of researchers across the world, and most of them won’t know their calculations are processed via High-Throughput Compute: the web portal hides all the complexity behind a user-friendly interface, allowing them to focus on the research instead of IT.

While Bob works on the calculations, Alice opens her account in Zenodo and sets up a community for the project with Bob. Zenodo is an online repository developed by OpenAIRE and CERN, open to all researchers regardless of funding stream, geographical location or scientific field. Free to upload and free to access, Zenodo makes scientific outputs of all kinds citable, shareable and discoverable for the long term.

The end goal is to have their research and data published in open access to comply with their funders’ requirements. But for the moment, while they are working on the project, Bob uploads both the data and the methods he used opting for a restricted access option. This will allow him to share embargoed data with Alice during the paper preparation with the restrictions they need at this stage.

 

Zenodo also assigns a DOI, a persistent identifier, to all datasets and method software, as well as specifying the funders and the specific grants that funded this research. This means that when their paper is submitted they can share a protected link to the DOIs with editors and reviewers. And once the paper is accepted for publication, all that Alice and Bob have to do is set the access rights to “embargoed” and enter the publication date, and then Zenodo will automatically toggle the data and methods to open access on that date to make them public and reusable. Moreover, funders, as well as the coordinators of the projects funding this research, will be able to verify the impact of the grant. Finally, and most importantly, other scientists will be able to reuse Bob and Alice’s work, and Bob and Alice will see their scientific reward blossom also based on usage and citation of their data and methods.

EOSC-hub and OpenAIRE support researchers across the world in many ways. For Alice and Bob, this means:
  • Months-worth of computations completed in a couple of days;
  • Safe space to share data without risks;
  • An effortless way to comply with Open Access requirements.

More information:
Advancing research together: EOSC-hub and OpenAIRE. Blogpost by Najla Rettberg.

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