Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

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High-performance computing for next-generation DNA sequencing

2011/01/B/ST6/07021

Keywords:

parallel algorithms high-performance computing DNA sequencing

Descriptors:

  • ST6_12: Scientific computing, simulation and modelling tools
  • ST6_9: Human computer interaction, speech recognition and synthesis, natural language processing

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

Host institution :

Instytut Chemii Bioorganicznej, Polskiej Akademii Nauk

woj. wielkopolskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Aleksandra Świercz 

Number of co-investigators in the project: 15

Call: OPUS 1 - announced on 2011-03-15

Amount awarded: 260 000 PLN

Project start date (Y-m-d): 2011-12-08

Project end date (Y-m-d): 2013-12-07

Project duration:: 24 months (the same as in the proposal)

Project status: Project settled

Information in the final report

  • Publication in academic press/journals (11)
  • Book publications / chapters in book publications (1)
  1. Complexity issues in computational biology
    Authors:
    J. Blazewicz, M. Kasprzak
    Academic press:
    Fundamenta Informaticae (rok: 2012, tom: 118, strony: 385-401), Wydawca: IOS Press
    Status:
    Published
    DOI:
    10.3233/FI-2012-721 - link to the publication
  2. GeVaDSs - decision support system for novel Genetic Vaccine development process
    Authors:
    J. Błażewicz, M. Borowski, W. Chaara, P. Kędziora, D. Klatzmann, P. Łukasiak, A. Six, P. Wojciechowski,
    Academic press:
    BMC Bioinformatics (rok: 2012, tom: 13, strony: 91), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/1471-2105-13-91 - link to the publication
  3. Reduced-by-matching graphs: toward simplifying Hamiltonian circuit problem
    Authors:
    J. Blazewicz, M. Kasprzak
    Academic press:
    Fundamenta Informaticae (rok: 2012, tom: 118, strony: 225-244), Wydawca: IOS Press
    Status:
    Published
    DOI:
    10.3233/FI-2012-711 - link to the publication
  4. DNA Sequence Assembly Involving an Acyclic Graph Model
    Authors:
    J. Blazewicz, W. Frohmberg, P. Gawron, M. Kasprzak, M. Kierzynka, A. Swiercz, P. Wojciechowski
    Academic press:
    Foundations of Computing and Decision Sciences (rok: 2013, tom: 38, strony: 25-34), Wydawca: Poznań University of Technology
    Status:
    Published
    DOI:
    10.2478/v10209-011-0019-4 - link to the publication
  5. Highly efficient parallel approach to the next-generation DNA sequencing
    Authors:
    J. Blazewicz, B. Bosak, P. Gawron, M. Kasprzak, K. Kurowski, T. Piontek, A. Swiercz
    Academic press:
    Lecture Notes in Computer Science (rok: 2012, tom: 7204, strony: 262-271), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/978-3-642-31500-8_27 - link to the publication
  6. Preprocessing and storing high-throughput sequencing data
    Authors:
    A. Swiercz, B. Bosak, M. Chlopkowski, A. Hoffa, M. Kasprzak, K. Kurowski, T. Piontek, J. Blazewicz
    Academic press:
    Computational Methods in Science and Technology (rok: 2014, tom: 20, strony: 45555), Wydawca: Poznan Supercomputing and Networking Center
    Status:
    Published
    DOI:
    10.12921/cmst.2014.20.01.9-20 - link to the publication
  7. Unified encoding for hyper-heuristics with application to bioinformatics
    Authors:
    A. Swiercz, E.K. Burke, M. Cicheński, G. Pawlak, S. Petrovic, T. Zurkowski, J. Blazewicz
    Academic press:
    Central European Journal of Operations Research (rok: 2014, tom: 22, strony: 567-589), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s10100-013-0321-8 - link to the publication
  8. A General Purpose Lossless Data Compression Method for GPU
    Authors:
    M Chłopkowski, R. Walkowiak
    Academic press:
    Journal of Parallel and Distributed Computing (rok: 2015, tom: 75, strony: 40-52), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jpdc.2014.09.016 - link to the publication
  9. Characterization of Sus scrofa Small RNA Sequences Present in Both Female and Male Gonads
    Authors:
    D. Kowalczykiewicz, A. Świercz, L. Handschuh, K. Wiechetek, M. Figlerowicz, J. Wrzesinski
    Academic press:
    PLOS One (rok: 2014, tom: -, strony: -), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0113249 - link to the publication
  10. G-DNA – a highly efficient multi-GPU/MPI tool for aligning nucleotide reads
    Authors:
    W. Frohmberg, M. Kierzynka, J. Blazewicz, P. Gawron, P. Wojciechowski
    Academic press:
    Bulletin of the Polish Academy of Sciences Technical Sciences (rok: 2013, tom: 61, strony: 989-992), Wydawca: Division IV Technical Sciences of the Polish Academy of Sciences
    Status:
    Published
    DOI:
    10.2478/bpasts-2013-0106 - link to the publication
  11. G-PAS 2.0 – an improved version of protein alignment tool with an efficient backtracking routine on multiple GPUs
    Authors:
    W. Frohmberg, M. Kierzynka, J. Blazewicz, P. Wojciechowski
    Academic press:
    Bulletin of the Polish Academy of Sciences: Technical Sciences (rok: 2012, tom: 60, strony: 491-494), Wydawca: IV Division of the Polish Academy of Sciences
    Status:
    Published
    DOI:
    10.2478/v10175-012-0062-1 - link to the publication
  1. Ties between Graph Theory and Biology
    Authors:
    J. Blazewicz, M. Kasprzak, N. Vlassis
    Book:
    Handbook of Graph Theory (second edition) (rok: 2013, ), Wydawca: Chapman and Hall/CRC
    Status:
    Published

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