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    Wyświetlanie 1-9 z 9
    Tytuł:
    Tabu search for the RNA partial degradation problem
    Autorzy:
    Rybarczyk, A.
    Hertz, A.
    Kasprzak, M.
    Blazewicz, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/330324.pdf
    Data publikacji:
    2017
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    RNA degradation
    tabu search
    bioinformatics
    rozkład RNA
    algorytm tabu search
    bioinformatyka
    Opis:
    In recent years, a growing interest has been observed in research on RNA (ribonucleic acid), primarily due to the discovery of the role of RNA molecules in biological systems. They not only serve as templates in protein synthesis or as adapters in the translation process, but also influence and are involved in the regulation of gene expression. The RNA degradation process is now heavily studied as a potential source of such riboregulators. In this paper, we consider the so-called RNA partial degradation problem (RNA PDP). By solving this combinatorial problem, one can reconstruct a given RNA molecule, having as input the results of the biochemical analysis of its degradation, which possibly contain errors (false negatives or false positives). From the computational point of view the RNA PDP is strongly NP-hard. Hence, there is a need for developing algorithms that construct good suboptimal solutions. We propose a heuristic approach, in which two tabu search algorithms cooperate, in order to reconstruct an RNA molecule. Computational tests clearly demonstrate that the proposed approach fits well the biological problem and allows to achieve near-optimal results. The algorithm is freely available at http://www.cs.put.poznan.pl/arybarczyk/tabusearch.php.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2017, 27, 2; 401-415
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    G-PAS 2.0 - an improved version of protein alignment tool with an efficient backtracking routine on multiple GPUs
    Autorzy:
    Frohmberg, W.
    Kierzynka, M.
    Blazewicz, J.
    Wojciechowski, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/201593.pdf
    Data publikacji:
    2012
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    pairwise alignment
    GPU computing
    alignment with backtracking procedure
    Opis:
    Several highly efficient alignment tools have been released over the past few years, including those taking advantage of GPUs (Graphics Processing Units). G-PAS (GPU-based Pairwise Alignment Software) was one of them, however, with a couple of interesting features that made it unique. Nevertheless, in order to adapt it to a new computational architecture some changes had to be introduced. In this paper we present G-PAS 2.0 - a new version of the software for performing high-throughput alignment. Results show, that the new version is faster nearly by a fourth on the same hardware, reaching over 20 GCUPS (Giga Cell Updates Per Second).
    Źródło:
    Bulletin of the Polish Academy of Sciences. Technical Sciences; 2012, 60, 3; 491-494
    0239-7528
    Pojawia się w:
    Bulletin of the Polish Academy of Sciences. Technical Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    A note on the complexity of scheduling of communication-aware directed acyclic graph
    Autorzy:
    Musial, J.
    Guzek, M.
    Bouvry, P.
    Blazewicz, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/202127.pdf
    Data publikacji:
    2018
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    computational complexity
    cloud computing
    communication-aware cloud computing
    directed acyclic graph
    NP-hardness in cloud computing
    złożoność obliczeniowa
    chmura obliczeniowa
    skierowany graf acykliczny
    Opis:
    The most recent incarnation of distributed paradigm is cloud computing. It can be seen as the first widely accepted business model of mass consumption of the distributed computing resources. Despite the differences in business models and technical details regarding cloud platforms, the distributed computing underlies cloud. Communications in cloud systems include transmissions of the results of cloud applications, users interactions, and exchange of data between different services that compose applications. The latter becomes more critical as applications become richer as well as more complex, and may consist of services operated by various providers. The effective communication between components of cloud systems is thus critical to the end user satisfaction and to the success of cloud services. We will discuss different cloud computing models (communication aware and unaware). Main focus will be placed on communication-aware directed acyclic graph (CA-DAG), which extends the classical DAG model by explicitly modeling communication tasks. Moreover, we will analyze and consult computational complexity of this innovative distributed computation model inspired by the characteristics of cloud computing. Providing a proof of strong NP-hardness of the problem allows for a future implementation and evolution of the communication-aware DAG models.
    Źródło:
    Bulletin of the Polish Academy of Sciences. Technical Sciences; 2018, 66, 2; 187-191
    0239-7528
    Pojawia się w:
    Bulletin of the Polish Academy of Sciences. Technical Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    G-DNA – a highly efficient multi-GPU/MPI tool for aligning nucleotide reads
    Autorzy:
    Frohmberg, W.
    Kierzynka, M.
    Blazewicz, J.
    Gawron, P.
    Wojciechowski, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/200827.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    DNA assembly preprocessing
    sequence alignment
    GPU computing
    Opis:
    DNA/RNA sequencing has recently become a primary way researchers generate biological data for further analysis. Assembling algorithms are an integral part of this process. However, some of them require pairwise alignment to be applied to a great deal of reads. Although several efficient alignment tools have been released over the past few years, including those taking advantage of GPUs (Graphics Processing Units), none of them directly targets high-throughput sequencing data. As a result, a need arose to create software that could handle such data as effectively as possible. G-DNA (GPU-based DNA aligner) is the first highly parallel solution that has been optimized to process nucleotide reads (DNA/RNA) from modern sequencing machines. Results show that the software reaches up to 89 GCUPS (Giga Cell Updates Per Second) on a single GPU and as a result it is the fastest tool in its class. Moreover, it scales up well on multiple GPUs systems, including MPI-based computational clusters, where its performance is counted in TCUPS (Tera CUPS).
    Źródło:
    Bulletin of the Polish Academy of Sciences. Technical Sciences; 2013, 61, 4; 989-992
    0239-7528
    Pojawia się w:
    Bulletin of the Polish Academy of Sciences. Technical Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Wpływ frakcjonowania i czasu słodowania ziarna jęczmienia na liczbę Kolbacha słodów oraz zawartość wolnego azotu alfa-aminokwasowego w brzeczkach
    Effect of malting time and fractionation of barley grain on malt Kolbach index and content of free amino nitrogen in worts
    Autorzy:
    Szwed, L.
    Blazewicz, J.
    Zembold-Gula, A.
    Pelak, M.
    Dawidowicz, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/827775.pdf
    Data publikacji:
    2009
    Wydawca:
    Polskie Towarzystwo Technologów Żywności
    Tematy:
    azot alfa-aminokwasowy
    browarnictwo
    brzeczka
    frakcjonowanie
    jeczmien
    liczba Kolbacha
    slod
    slodowanie
    ziarno
    zawartosc azotu
    Opis:
    Celem badań było określenie wpływu czasu słodowania i dodatkowego frakcjonowania ziarna jęczmienia browarnego na zasobność słodów i otrzymanych z nich brzeczek pod względem produktów hydrolizy enzymatycznej białek. Materiał badawczy stanowiło ziarno jęczmienia browarnego odmian: Lailla, Jersey, Hanka oraz Brenda, pochodzące z sezonu wegetacyjnego 2004, z rejonu Dolnego Śląska, rozsortowane pod względem grubości na 3 frakcje: standardową (ziarno o grubości > 2,5 mm), frakcję 2,5-2,8 mm oraz frakcję >2,8mm, które poddano słodowaniu 5-, 6- i 7-dniowemu. W otrzymanych ze słodów brzeczkach laboratoryjnych oznaczono zawartość azotu alfa-aminokwasowego oraz obliczono liczbę Kolbacha. Otrzymane wyniki przeanalizowano programem Statistica. Analiza statystyczna wykazała, że zarówno czas słodowania 5-, 6- i 7-dniowy, jak i dodatkowe frakcjonowanie nie zróżnicowały w istotny sposób wartości liczby Kolbacha. Oba czynniki nie wpłynęły również w sposób istotny na zawartość wolnego azotu alfa-aminokwasowego w brzeczkach. Słody charakteryzowały się wysokim stopniem rozluźnienia. Zasadne wydaje się więc stwierdzenie, że proces słodowania można skrócić nawet poniżej 5 dni, co poprawi ekonomikę produkcji zarówno przez skrócenie czasu trwania procesu, jak i ograniczenie ubytków naturalnych związanych z rozwojem korzonków i kiełków liścieniowych. Dodatkowe frakcjonowanie ziarna nie różnicowało liczby Kolbacha i zawartości azotu alfa-aminokwasowego. Wprowadzanie zatem frakcjonowania, jako dodatkowego procesu, nie ma uzasadnienia technologicznego przy rozpatrywaniu ilości produktów hydrolizy enzymatycznej białek.
    The objective of the investigations was to determine the effect of malting time and additional fractionation of brewing barley grain on the affluence of malt and worts produced thereof as regards the products of enzymatic hydrolisation of proteins. The investigation material were brewing barley grains of Lailla, Jersey, Hanka, and Brenda cultivars originating from the vegetation season in 2004, from the Lower Silesia region. All the grains analyzed were classified by their thickness into 3 fractions: standard grain fraction (grains larger than 2.5 mm), fraction of grains ranging from 2.5 to 2.8 mm, and fraction with grains larger than 2. 8 mm. The grains of the three fractions were then malted for 5, 6, and 7 days. In the laboratory worts obtained from these malts, the content of free amino nitrogen was determined, and the Kolbach index was calculated. The results obtained were analyzed using a Statistica software. Based on the statistical analysis performed, it was shown that neither the malting time of 5, 6, and 7 days nor the additional fractionation considerably impacted the value of Kolbach index. Those two factors did not considerably impact the content of free amino nitrogen in worts analyzed. The malts were characterized by a high loosening level. Thus, it seems justified to assume that when shortening the malting process period to less than 5 days, the economics of production could be improved owing to the shorter process duration and to the reduced natural malting losses related with the development of rootlets and acrospires. The additional grain fractionation affected neither the Kolbach index, nor the content of free amino nitrogen. Therefore, no technological justification exists of introducing the fractionation as an additional process when considering the product quantities of enzymatic hydrolisation of proteins.
    Źródło:
    Żywność Nauka Technologia Jakość; 2009, 16, 6
    1425-6959
    Pojawia się w:
    Żywność Nauka Technologia Jakość
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Building the library of RNA 3D nucleotide conformations using the clustering approach
    Autorzy:
    Zok, T.
    Antczak, M.
    Riedel, M.
    Nebel, D.
    Villmann, T.
    Lukasiak, P.
    Blazewicz, J.
    Szachniuk, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/329744.pdf
    Data publikacji:
    2015
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    RNA nucleotides
    conformer library
    torsion angles
    clustering
    neural gas
    Opis:
    An increasing number of known RNA 3D structures contributes to the recognition of various RNA families and identification of their features. These tasks are based on an analysis of RNA conformations conducted at different levels of detail. On the other hand, the knowledge of native nucleotide conformations is crucial for structure prediction and understanding of RNA folding. However, this knowledge is stored in structural databases in a rather distributed form. Therefore, only automated methods for sampling the space of RNA structures can reveal plausible conformational representatives useful for further analysis. Here, we present a machine learning-based approach to inspect the dataset of RNA three-dimensional structures and to create a library of nucleotide conformers. A median neural gas algorithm is applied to cluster nucleotide structures upon their trigonometric description. The clustering procedure is two-stage: (i) backbone- and (ii) ribose-driven. We show the resulting library that contains RNA nucleotide representatives over the entire data, and we evaluate its quality by computing normal distribution measures and average RMSD between data points as well as the prototype within each cluster.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2015, 25, 3; 689-700
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    A method for analysis and interpretation of data from field and brewery trials
    Autorzy:
    Mejza, I.
    Ambrozy-Deregowska, K.
    Bocianowski, J.
    Blazewicz, J.
    Liszewski, M.
    Nowosad, K.
    Powiązania:
    https://bibliotekanauki.pl/articles/9595.pdf
    Data publikacji:
    2018
    Wydawca:
    Uniwersytet Przyrodniczy w Lublinie. Katedra Zastosowań Matematyki i Informatyki
    Źródło:
    Colloquium Biometricum; 2018, 48
    1896-7701
    Pojawia się w:
    Colloquium Biometricum
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Exact and heuristic approaches to solve the Internet shopping optimization problem with delivery costs
    Autorzy:
    Lopez-Loces, M. C.
    Musial, J.
    Pecero, J. E.
    Fraire-Huacuja, H. J.
    Blazewicz, J.
    Bouvry, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/330508.pdf
    Data publikacji:
    2016
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    internet shopping optimization
    integer linear programming
    cellular processing algorithm
    heuristic algorithms
    optimization in e-commerce
    zakupy internetowe
    programowanie liniowe
    algorytm heurystyczny
    handel elektroniczny
    Opis:
    Internet shopping has been one of the most common online activities, carried out by millions of users every day. As the number of available offers grows, the difficulty in getting the best one among all the shops increases as well. In this paper we propose an integer linear programming (ILP) model and two heuristic solutions, the MinMin algorithm and the cellular processing algorithm, to tackle the Internet shopping optimization problem with delivery costs. The obtained results improve those achieved by the state-of-the-art heuristics, and for small real case scenarios ILP delivers exact solutions in a reasonable amount of time.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2016, 26, 2; 391-406
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Algorithms solving the Internet shopping optimization problem with price discounts
    Autorzy:
    Musial, J.
    Pecero, J. E.
    Lopez-Loces, M. C.
    Fraire-Huacuja, H. J.
    Bouvry, P.
    Blazewicz, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/200209.pdf
    Data publikacji:
    2016
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    e-commerce
    Internet shopping
    applications of operations research
    approximations
    algorithms
    heuristics
    combinatorial optimization
    zakupy przez Internet
    wnioski z badań operacyjnych
    aproksymacje
    algorytmy
    heurystyki
    optymalizacja kombinatoryczna
    Opis:
    The Internet shopping optimization problem arises when a customer aims to purchase a list of goods from a set of web-stores with a minimum total cost. This problem is NP-hard in the strong sense. We are interested in solving the Internet shopping optimization problem with additional delivery costs associated to the web-stores where the goods are bought. It is of interest to extend the model including price discounts of goods. The aim of this paper is to present a set of optimization algorithms to solve the problem. Our purpose is to find a compromise solution between computational time and results close to the optimum value. The performance of the set of algorithms is evaluated through simulations using real world data collected from 32 web-stores. The quality of the results provided by the set of algorithms is compared to the optimal solutions for small-size instances of the problem. The optimization algorithms are also evaluated regarding scalability when the size of the instances increases. The set of results revealed that the algorithms are able to compute good quality solutions close to the optimum in a reasonable time with very good scalability demonstrating their practicability.
    Źródło:
    Bulletin of the Polish Academy of Sciences. Technical Sciences; 2016, 64, 3; 505-516
    0239-7528
    Pojawia się w:
    Bulletin of the Polish Academy of Sciences. Technical Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-9 z 9

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