Large scale biomedical computation on OMERO

OMERO Biobank

Large scale biomedical computation on OMERO

Contacts

Challenge

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.

Overview

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

  1. https://github.com/crs4/omero.biobank
  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. 

Questo sito utilizza cookie tecnici e assimilati. Possono essere presenti anche cookie profilazione di terze parti. Se vuoi saperne di più o negare il consenso a tutti o ad alcuni cookie leggi l'informativa completa. Proseguendo nella navigazione (anche con il semplice scrolling) acconsenti all'uso dei cookie. This site uses technical and anonymized analytics cookies only. There may also be profiling third-party cookies. Please read the cookie information page to learn more about how we use cookies or blocking them. more information

The cookie settings on this website are set to "allow cookies" to give you the best browsing experience possible. If you continue to use this website without changing your cookie settings or you click "Accept" below then you are consenting to this.

Close