Petr Holub



Assoc. prof. Petr Holub

Titles of Presentations

“Common Service IT” (Session F2)
“Medical imaging and biobanking (radiology and digital pathology) – a joint BBMI / ESR session” (Session C1)


Date and Place

Sessions F2 & C1


Speaker Biography

Dr. Holub is Associate Professor of computer science at Masaryk University. Since 2015, he has become Senior IT/Data Protection Manager with BBMRI-ERIC, European Research Infrastructure Consortium for Biobanking and BioMolecular Resources. He has background both in sciences and computer science. He was head of the Dept. of Communication Technologies at Inst. of Computers Science, Masaryk University, as well as architect of advanced multimedia and collaborative systems of the Czech national e-infrastructure at CESNET. His research in computer networks and multimedia processing has led to more than 40 research papers in established computer science journals and ranked conferences. He was the architect and team leader of UltraGrid, high-performance media processing and distribution framework, which received Best Open-Source Software Award by ACM Multimedia SIG. He is a co-founder of Comprimato company, which further commercializes research results in acceleration of compression algorithms.


Abstract 1 (Session F2)

During 2015, BBMRI-ERIC has set up its Common Service IT, in order to implement core external and internal IT services. It focuses on delivery of the following main services: (a) Directory – a metadata and public data information service with aggregated information about biobanks, their sample and data collections, as well as additional services (Directory 2.0 covering 515 biobanks with more than 60,000,000 samples was released in December 2015); (b) Sample/Data Negotiator and Locator services to allow for negotiating access of the requesters to samples and data sets hosted by the biobanks and to locate sample and data sets of interest for the requesters; (c) Data harmonization tools middleware services that provide ontology registries and translation tools to be used by other BBMRI-ERIC IT services and possibly also external services in the future; (d) Reference tools for biobanks and national nodes – an integrated toolbox designed to provide basic functionality need by the biobanks, such as biobank information management systems or connectors to BBMRI-ERIC IT services. The CS IT services will rely on detailed and continuous analysis of users’ requirements, as well as evaluation of services on pilot user groups. The IT infrastructure operations are also handled by the CS IT. The presentation will provide an overview of services provided by the CS IT, together with status report of their state of development/deployment.


Abstract 2 (Session C1)

Imaging in biobanks has become important resource for researchers in radiology, pathology and other domains. Joint effort of European Society of Radiology and BBMRI-ERIC to bring ESR imaging biobanks into services increasing their findability and accessibility resulted in setup of MIABIS Imaging Working Group and into implementing the proposed extensions of MIABIS data model into prototype of BBMRI-ERIC Directory 3.0. In this presentation, we will discuss experiences with designing the data model and practical experiences with its deployment.