doc. RNDr. Petr Holub, Ph.D.


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Curriculum vitae

Person Identification
  • assoc. prof. RNDr. Petr Holub, Ph.D., born on 15. 6. 1979 in Brno, Czechoslovakia
    married, 2 children.
Workplace
  • Institute of Computer Science
    Masaryk University
    Botanicka 68a, 60200 Brno, CZ
    email: hopet@ics.muni.cz
    phone: +420-549493944
    fax: +420-541212747
Employment Position
  • head of Communication Infrastructure Division
Education and Academic Qualifications
  • 2014 - associated professor (docent) in Informatics, Faculty of Informatics, Masaryk University, Brno, Czech Rep.
    2008 - RNDr. in Informatics, Faculty of Informatics, Masaryk University, Brno, Czech Rep.
    2005 - Ph.D. in Informatics, Faculty of Informatics, Masaryk University, Brno, Czech Rep.
    Ph.D. Thesis: Network and Grid Support for Multimedia Distribution and Processing
    2001 - Mgr. (MSc. equiv.) in Physical Chemistry (with honors), Faculty of Science, Masaryk University, Brno, Czech Rep.
    Thesis: Calculation of hyperfine splitting constants on beta-protones in EPR spectra of substituted cationradicals of pyrrol
Employment Summary
  • 2015-: BBMRI-ERIC (Biobanking and Biomolecular Resources Research Infrastructure, Graz, Rakousko)
    Senior IT and Data Protection Manager
    CIO of BBMRI-ERIC Common Service IT
  • 2015-: Institute of Computer Science, Masaryk University
    senior researcher
  • 2013-2014: Institute of Computer Science, Masaryk University
    senior researcher
    Head of Communication Infrastructure Division ICS MU
  • 2012-2014: CESNET
    senior researcher
    multimedia transmission and collaborative environments, high-speed network technologies, leader of UltraGrid and Shongo development teams multimediální přenosy a prostředí pro spolupráci, technologie vysokorychlostních sítí
  • 2012: Institute of Computer Science, Masaryk University
    senior researcher
    audiovisual technologies, multimedia transmissions, network systems, distributed computing systems
  • 2007-2011: CESNET
    senior researcher
    multimedia transmissions and technologies of high speed networks Multimediální přenosy a technologie vysokorychlostních sítí
  • 2007-2011: Supercomputing Centre Brno Institute of Computer Science, Masaryk University
    senior researcher
    audiovisual and multimedia transmissions, collaborative environments, network technologies and distributed computing systems
  • 2003-2006: specialist - Supercomputing Center Brno, Institute of Computer Science, Masaryk University
    distributed computing and Grids, multimedia, distributed storage, networking
  • 2001-2006: researcher - CESNET
    MetaCentrum Project, Multimedia Technologies
  • 2002-2005: PhD student - Faculty of Informatics, Masaryk University
  • 1999-2003: programmer analyst - Supercomputing Center Brno, Institute of Computer Science, Masaryk University
    UNIX/Win/Internet programming, UNIX - Win integration, security, Grids and distributed computing
  • 1998-2000: software support - Faculty of Science, Masaryk University
    specialization on MS software support, UNIX/Win/Internet programming, network & server administration
Pedagogical Activities
  • Lectures:
    Laboratory of Advanced Network Technologies (PV177)
    Introduction to PhD study (DUVOD)
    GPU Programming (PV197)
    Parallel Technical Systems (PV192)
    Introduction to High-Performance Computing (PA177)
    Computer Networks and Their Applications I (PA159)
    Computer Networks (PB156)
  • Member of Doctoral Committee - Computer Systems and Technologies
  • Consultant of Ph.D. students:
    Milos Liska (grad. 2010)
    Jiri Matela (grad 2017)
    Vit Rusnak (grad. 2016)
Scientific and Research Activities
  • Research interests:
    Network transmissions of multimedia, collaborative environments, network technologies, distributed and parallel processing.
  • Participation in Projects:
    2019-: IMI ConcePTION (task leader)
    2019-: EU EJP RD (task leader)
    2019-: EU H2020 EOSC-Life (WP leader)
    2018-: EU H2020 EOSChub
    2017-2018: EU H2020 AARC2
    2017-2018: EU H2020 EOSCpilot
    2017-2018: EU H2020 CETOCOEN Excellence
    2015-2019: EU H2020 CORBEL
    2015-2019: EU H2020 ADOPT BBMRI-ERIC
    2015-2018: EU H2020 PhenoMeNal
    2015-2017: EU H2020 EGI-Engage (Competence Center leader)
    2012-2017: EU FP7 THALAMOSS (WP leader)
    2012-2015: GAČR DYSCHNET
    2006-2008 : EU Ithanet
    2006-2008 : EU EuroCareCF
    2004-2011 : Optical Network of National Research and Its New Applications, MŠM 6383917201
    2004-2008 : European Research Network on Foundations, Software Infrastructures and Applications for large scale distributed, Grid and Peer-to-Peer Technologies (CoreGRID), 6th Specific RTD Programme 004265
    2002-2005: A Grid Application Toolkit and Testbed (GridLab), IST-2001-32133
    2003-2004: Implementation of Editing Workplace and Development of Distributed Encoding Environment for Preparing Video on Demand at ICS MU Brno, CESNET FR 017/2002
    2003-2004: Mobile node of AccessGrid, CESNET FR 023/2002
    2003-2004: Distributed Data Storage, CESNET FR 018/2002
    2001-2003: High-Speed Research Network and its New Applications, MŠM000000001
Academical Stays
  • 2006 - Center for Computation & Technology, Lousiana State University, 1 month
Extrauniversity Activities
  • 2008: reviewer: Future Generation Computer Systems journal, Elsevier Science
  • 2008: program committee member: IADIS International Conference Telecommunications, Networks and Systems 2008
Appreciation of Science Community
  • 2012: ACM Multimedia: Best Open-Source Software Competition Award
  • 2007: Dean's Award (Faculty of Informatics, Masaryk University)
  • 2001: Dean's Award (Faculty of Science, Masaryk University)
  • 2001: 1. place - SVOČ: "Calculation of hyperfine splitting constants on beta-protones in EPR spectra of substituted cationradicals of pyrrol"
  • 2000: Dean's Award (Faculty of Science, Masaryk University)
  • 2000: 2. place - SVOČ: "Calculation of hyperfine splitting constants on beta-protones in EPR spectra of substituted cationradicals of pyrrol"
  • 1998: 4. place - SVOČ: "Bonding in the Molecule of Hexafluorocyclotriphosphazene in the View of Post-Hartree-Fock Calculations"
  • 1997: 4. place on the republic SOČ: "Modeling Atomic and Molecular Orbitals in Maple V"
Selected Publications
  • PETERS, K, J BRADBURY, S BERGMANN, M CAPUCCINI, M CASCANTE, Atauri P DE, TMD EBBELS, C FOGUET, R GLEN, A GONZALEZ-BELTRAN, UL GUNTHER, E HANDAKAS, T HANKEMEIER, K HAUG, S HERMAN, Petr HOLUB, M IZZO, D JACOB, D JOHNSON, F JOURDAN, N KALE, I KARAMAN, B KHALILI, PE KHONSARI, K KULTIMA, S LAMPA, A LARSSON, C LUDWIG, P MORENO, S NEUMANN, JA NOVELLA, O Donovan C, JTM PEARCE, A PELUSO, ME PIRAS, L PIREDDU, MAC REED, P ROCCA-SERRA, P ROGER, A ROSATO, R RUEEDI, C RUTTKIES, N SADAWI, RM SALEK, SA SANSONE, V SELIVANOV, O SPJUTH, D SCHOBER, EA THEVENOT, M TOMASONI, M VAN RIJSWIJK, M VAN VLIET, MR VIANT, RJM WEBER, G ZANETTI a C STEINBECK. PhenoMeNal: processing and analysis of metabolomics data in the cloud. GIGASCIENCE, OXFORD: OXFORD UNIV PRESS, 2019, roč. 8, č. 2. ISSN 2047-217X. doi:10.1093/gigascience/giy149. URL info
  • SAUNDERS, Gary, Michael BAUDIS, Regina BECKER, Sergi BELTRAN, Christophe BÉROUD, Ewan BIRNEY, Cath BROOKSBANK, Søren BRUNAK, Marc Van den BULCKE, Rachel DRYSDALE, Salvador CAPELLA-GUTIERREZ, Paul FLICEK, Francesco FLORINDI, Peter GOODHAND, Ivo GUT, Jaap HERINGA, Petr HOLUB, Jef HOOYBERGHS, Nick JUTY, Thomas M KEANE, Jan O KORBEL, Ilkka LAPPALAINEN, Brane LESKOSEK, Gert MATTHIJS, Michaela Th MAYRHOFER, Andres METSPALU, Arcadi NAVARRO, Steven NEWHOUSE, Tommi NYRÖNEN, Angela PAGE, Bengt PERSSON, Aarno PALOTIE, Helen PARKINSON, Jordi RAMBLA, David SALGADO, Erik STEINFELDER, Morris A SWERTZ, Alfonso VALENCIA, Susheel VARMA, Niklas BLOMBERG a Serena SCOLLEN. Leveraging European infrastructures to access 1 million human genomes by 2022. Nature Reviews Genetics, 2019. ISSN 1471-0064. doi:10.1038/s41576-019-0156-9. info
  • HOLUB, Petr, Florian KOHLMAYER, Fabian PRASSER, Michaela Theresia MAYRHOFER, Irene SCHLUNDER, Gillian M. MARTIN, Sara CASATI, Lefteris KOUMAKIS, Andrea WUTTE, Lukas KOZERA, Dominik STRAPAGIEL, Gabriele ANTON, Gianluigi ZANETTI, Osman Ugur SEZERMAN, Maimuna MENDY, Dalibor VALÍK, Marialuisa LAVITRANO, Georges DAGHER, Kurt ZATLOUKAL, GertJan B. VAN OMMEN a Jan-Eric LITTON. Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health. Biopreservation and Biobanking, NEW ROCHELLE: MARY ANN LIEBERT, INC, 2018, roč. 16, č. 2, s. 97-105. ISSN 1947-5535. doi:10.1089/bio.2017.0110. URL info
  • PANG, Chao, Fleur KELPIN, David VAN ENCKEVORT, Niina EKLUND, Kaisa SILANDER, Dennis HENDRIKSEN, Mark DE HAAN, Jonathan JETTEN, Tommy DE BOER, Bart CHARBON, Petr HOLUB, Hans HILLEGE a Morris A. SWERTZ. BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration. Bioinformatics, Oxford: Oxford University Press, 2017, roč. 33, č. 22, s. 3627-3634. ISSN 1367-4803. doi:10.1093/bioinformatics/btx478. info
  • RUSŇÁK, Vít, Lukáš RUČKA a Petr HOLUB. Toward Natural Multi-User Interaction in Advanced Collaborative Display Environments. Future Generation Computer Systems, Amsterdam, The Netherlands: Elsevier Science, 2016, roč. 54, January 2016, s. 313-325. ISSN 0167-739X. doi:10.1016/j.future.2015.03.019. URL info
  • KABÁT, Milan, Vojtěch DAVID, Petr HOLUB a Martin PULEC. High-performance forward error correction: Enabling multi-gigabit flows and beyond on commodity GPU and CPU hardware in presence of packet loss. Future Generation Computer Systems, Amsterdam, The Netherlands: Elsevier Science, 2016, roč. 54, č. 1, s. 326 - 335. ISSN 0167-739X. doi:10.1016/j.future.2015.04.007. ScienceDirect info
  • SLOVÁK, Petr, Petr HOLUB a Pavel TROUBIL. Videokonferenční prostředí pro komunikaci vzdálených skupin a způsob komunikace vzdálených skupin v systému videokonferenčního prostředí. 2015. info
  • HOLUB, Petr, Martin ŠROM, Martin PULEC, Jiří MATELA a Martin JIRMAN. GPU-accelerated DXT and JPEG compression schemes for low-latency network transmissions of HD, 2K, and 4K video. Future Generation Computer Systems, Amsterdam, The Netherlands: Elsevier Science, 2013, roč. 29, č. 8, s. 1991-2006. ISSN 0167-739X. doi:10.1016/j.future.2013.06.006. URL info
  • MATELA, Jiří, Martin ŠROM a Petr HOLUB. Low GPU Occupancy Approach to Fast Arithmetic Coding in JPEG2000. In Lecture Notes in Computer Science 7119. Heidelberg: Springer Berlin / Heidelberg, 2012. s. 136-145, 10 s. ISBN 978-3-642-25928-9. doi:10.1007/978-3-642-25929-6_13. SpringerLink info
  • MATELA, Jiří, Petr HOLUB, Martin JIRMAN a Martin ŠROM. GPU-specific reformulations of image compression algorithms. In Tescher, AG. Proceedings of Applications of Digital Image Processing XXXV. 8499. vyd. BELLINGHAM, WA 98227-0010 USA: SPIE-INT SOC OPTICAL ENGINEERING, 2012. s. nestránkováno, 8 s. ISBN 978-0-8194-9216-6. doi:10.1117/12.929971. info
  • HOLUB, Petr, Jiří MATELA, Martin PULEC a Martin ŠROM. UltraGrid: Low-Latency High-Quality Video Transmissions on Commodity Hardware. In Proceedings of the 20th ACM international conference on Multimedia. New York, NY, USA: ACM, 2012. s. 1457-1460. ISBN 978-1-4503-1089-5. doi:10.1145/2393347.2396519. info
  • MATELA, Jiří, Vít RUSŇÁK a Petr HOLUB. Efficient JPEG2000 EBCOT Context Modeling for Massively Parallel Architectures. In Storer, James A. and Marcellin, Michael W.. Data Compression Conference (DCC), 2011. Washington, DC, USA: IEEE Computer Society, 2011. s. 423-432, 10 s. ISBN 978-0-7695-4352-9. doi:10.1109/DCC.2011.49. info
  • HOLUB, Petr, Hana RUDOVÁ a Miloš LIŠKA. Data Transfer Planning with Tree Placement for Collaborative Environments. Constraints, Springer, 2011, roč. 16, č. 3, s. 283-316. ISSN 1383-7133. doi:10.1007/s10601-011-9106-7. info
  • LIŠKA, Miloš, Petr HOLUB, Andrew LAKE a John VOLLBRECHT. CoUniverse Orchestrated Collaborative Environments with Dynamic Circuit Networks. : 2010 Ninth International Conference on Networks, 2010. s. 300-305, 6 s. ISBN 978-0-7695-3979-9. URL info
  • SLOVÁK, Petr, Pavel TROUBIL a Petr HOLUB. GColl: enhancing trust in flexible group-to-group videoconferencing. In Proceedings of the 28th of the international conference extended abstracts on Human factors in computing systems. New York, NY, USA: ACM, 2010. s. 3607-3612, 6 s. ISBN 978-1-60558-930-5. URL info
  • VOJTĚCH, Josef, Miloslav HŮLA, Jan RADIL, Miroslav KARÁSEK, Stanislav ŠÍMA, Jan NEJMAN a Petr HOLUB. Zařízení pro skupinové vysílání optických signálů v Internetu a jiných sítích. 2009. info
  • HOLUB, Petr, Ravi PARUCHURI, Stacey SIMMONS, Tomáš REBOK, Andrei HUTANU, Daniel EILAND a Miloš LIŠKA. Enabling Technologies for Teaching an HPC Class as a Distributed Course. In SPR2007 - The 9th Annual SURA/ViDe Conference, Atlanta, Internet2, USA. 2007. URL info
  • HOLUB, Petr, Eva HLADKÁ, Michal PROCHÁZKA a Miloš LIŠKA. Secure and Pervasive Collaborative Platform for Medical Applications. Studies in Health Technology and Informatics, Amsterdam, The Netherlands: IOS Press, 2007, roč. 126, č. 1, s. 229-238. ISSN 0926-9630. info
  • EILAND, Daniel, Thomas STERLING, Amy APON, Box LEANGSUKSUN a Petr HOLUB. Community Building in Distance Learning Environments: Using uncompressed high-definition videos as a medium for classroom interactivity. Chicago, USA: AccessGrid Retreat, 2007. AccessGrid Retreat 2007. URL Presentation. Abstract. info
  • HOLUB, Petr a Eva HLADKÁ. Distributed Active Element in 10Gbps Network. In ICT 2007, 14th International Conference on Telecommunications. Penang, Malaysia: IEEE/MICC, 2007. s. 455-460, 6 s. ISBN 978-1-4244-1094-1. URL PDF in IEEE Xplore info
  • MATYSKA, Luděk, Petr HOLUB a Eva HLADKÁ. HD Collaborative Framework for Distributed Distance Learning. In Proceedings of the 4th High-End Visualization Workshop. Rakousko: University of Innsbruck, 2007. s. 40-45, 6 s. ISBN 978-3-86541-216-4. info
  • KAPIČKA, Libor, Pavel KUBÁČEK a Petr HOLUB. Bonding and aromaticity of cyclic phosphazenes viewed as interaction of Dnh fragments. Journal of Molecular Structure (Theochem), Amsterdam: Elsevier Science, 2007, roč. 820, 1-3, s. 148-158. ISSN 0166-1280. info
  • ANTOŠ, David, Vojtěch ŘEHÁK a Petr HOLUB. Packet Filtering for FPGA-Based Routing Accelerator. In CESNET Conference 2006 Proceedings. Prague: CESNET, z. s. p. o., 2006. s. 161--173, 13 s. ISBN 80-239-6533-6. URL info
  • HOLUB, Petr, Eva HLADKÁ, Jiří DENEMARK a Tomáš REBOK. Active Elements for High-Definition Video Distribution. In ICT 2006, 13th International Conference on Telecommunications. Funchal, Madeira: University of Aveiro, Portugal, 2006. s. 1-4, 4 s. ISBN 972-98368-4-1. info
  • HOLUB, Petr. HD Multi-point Videoconferencing. In TERENA Networking Conference 2006. 2006. Presentation. info
  • HOLUB, Petr, Luděk MATYSKA, Miloš LIŠKA, Lukáš HEJTMÁNEK, Jiří DENEMARK, Tomáš REBOK, Andrei HUTANU, Ravi PARUCHURI, Jan RADIL a Eva HLADKÁ. High-definition multimedia for multiparty low-latency interactive communication. Future Generation Computer Systems, Amsterdam, The Netherlands: Elsevier Science, 2006, roč. 22, č. 8, s. 856-861. ISSN 0167-739X. ScienceDirect info
  • HUTANU, Andrei, Gabrielle ALLEN, Stephen D. BECK, Petr HOLUB, Hartmut KAISER, Archit KULSHRESTHA, Miloš LIŠKA, Jon MACLAREN, Luděk MATYSKA, Ravi PARUCHURI, Steffen PROHASKA, Ed SEIDEL, Brygg ULLMER a Shalini VENKATARAMAN. Distributed and collaborative visualization of large data sets using high-speed networks. Future Generation Computer Systems, Amsterdam, The Netherlands: Elsevier Science, 2006, roč. 22, č. 8, s. 1004-1010. ISSN 0167-739X. ScienceDirect info
  • HOLUB, Petr, Eva HLADKÁ a Luděk MATYSKA. Scalability and Robustness of Virtual Multicast for Synchronous Multimedia Distribution. In Pascal Lorenz, Petre Dini. Lecture Notes in Computer Science 3421. Germany: Springer Berlin / Heidelberg, 2005. s. 876-883, 8 s. ISBN 978-3-540-25338-9. doi:10.1007/978-3-540-31957-3_99. SpringerLink info
  • HOLUB, Petr a Eva HLADKÁ. Ubiquitous User-Empowered Networks of Active Elements. In TERENA Networking Conference 2005. Poznan, Poland: TERENA, 2005. s. 1-3, 3 s. Paper. info
  • HOLUB, Petr. High-Definition Video at CESNET. Philadelphia, PA, USA: Internet2, 2005. I2 Fall 2005 Member Meeting. URL URL info
  • HOLUB, Petr. Grid Video Processing: Distributed Approach to Video Processing. Philadelphia, PA, USA: Internet2, 2005. I2 Fall 2005 Member Meeting. URL URL info
  • HOLUB, Petr a Miloš LIŠKA. High-Definition Video Transmissions for Medical Applications and Education. Technology and Health Care, Amsterdam (The Netherlands): IOS Press, 2005, roč. 13, č. 5, s. 398-400. ISSN 0928-7329. info
  • HOLUB, Petr. Network and Grid Support for Multimedia Distribution and Processing. Brno: Masarykova univerzita v Brne, 2005. 117 s. Ph.D. Thesis. info
  • HLADKÁ, Eva, Petr HOLUB a Jiří DENEMARK. User Empowered Virtual Multicast for Multimedia Communication. In Proccedings of 3rd International Conference on Networking. Colmar, France: University of Haute Alsace, 2004. 6 s. ISBN 0-86341-325-0. info
  • HOLUB, Petr, Martin KUBA, Luděk MATYSKA a Miroslav RUDA. Grid Infrastructure Monitoring as Reliable Information Service. In Grid Computing, Second European AcrossGrids Conference, AxGrids 2004, Lecture Notes in Computer Science 3165. Berlin / Heidelberg: Springer-Verlag, 2004. s. 220-229, 10 s. ISBN 3-540-22888-8. SpringerLink info
  • HOLUB, Petr a Lukáš HEJTMÁNEK. Distributed Encoding Environment Based on Grids and IBP Infrastructure. In Selected Papers from TERENA Networking Conference 2004. : TERENA, 2004. 10 s. ISBN 90-77559-04-3. Full paper. TNC2004 Proceedings. info
  • HLADKÁ, Eva, Petr HOLUB a Jiří DENEMARK. User-Empowered Programmable Network Support for Collaborative Environment. In Universal Multiservice Networks: Third European Conference, ECUMN 2004, Porto, Portugal, October 25-27, 2004. Proceedings. Heidelberg, Němeko: Lecture Notes in Computer Science 3262, Springer-Verlag Heidelberg, 2004. s. 367-376, 10 s. ISBN 3-540-23551-5. SpringerLink info

2019/01/17