Large scale biomedical computation on OMERO

OMERO Biobank

Large scale biomedical computation on OMERO



The number of domains affected by the big data phenomenon is constantly increasing, both in science and industry, with high-throughput DNA sequencers being among the most massive data producers. Building analysis frameworks that can keep up with such a high production rate, however, is only part of the problem: current challenges include dealing with articulated data repositories where objects are connected by multiple relationships, managing complex processing pipelines where each step depends on a large number of configuration parameters and ensuring reproducibility, error control and usability by non technical staff.


OMERO.biobank is a robust, extensible and scalable traceability framework developed to support large-scale experiments in data-intensive biology. The data management system is built on top of the core services of OME Remote Objects (OMERO), an open source software platform that includes a number of storage mechanisms, remoting middleware, an API and client applications.

Innovative features

  • OMERO.biobank’s kernel is complemented with an indexing system that maintains a persistent version of the traceability structure by mapping entities to nodes and actions to edges in a graph database;
  • it is implemented with Neo4j;
  • the indexing system can manage a large number of items.

Potential users

Researchers, developers

Impact sectors

Health - ICT

Other resources

  2. G. Cuccuru, S. Leo, L. Lianas, M. Muggiri, A. Pinna, L. Pireddu, P. Uva, A. Angius, G. Fotia, G. Zanetti, "An automated infrastructure to support high-throughput bioinformatics", 2014 International Conference on High Performance Computing Simulation (HPCS), pp. 600-607, July 2014.
  3. G. Cuccuru, P. Uva, S. Onano, R. Atzeni, S. Leo, L.Lianas, Manuela Oppo, Luca Pireddu, Andrea Angius, Laura Crisponi, Gianluigi Zanetti, Giorgio Fotia, Exploiting a large scale biodata management system to support NGS variant detection studies. Poster presentation at ISMB/ECCB, 10-14 July 2015, Dublin - 2015. 

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