Vincenzo Manca, Alberto Castellini, Giuditta Franco, et al., “Metabolic PSystems:A Discrete Model for Biological Dynamics,” Chinese Journal of Electronics, vol. 22, no. 4, pp. 717-723, 2013,
Citation: Vincenzo Manca, Alberto Castellini, Giuditta Franco, et al., “Metabolic PSystems:A Discrete Model for Biological Dynamics,” Chinese Journal of Electronics, vol. 22, no. 4, pp. 717-723, 2013,

Metabolic PSystems:A Discrete Model for Biological Dynamics

More Information
  • Corresponding author: Giuditta Franco
  • Received Date: 2013-01-01
  • Rev Recd Date: 2013-02-01
  • Publish Date: 2013-09-25
  • A recent methodology to model biochemical systems is here presented. It is based on a conceptual framework rooted in membrane computing and developed with concepts typical of discrete dynamical systems. According to our approach, from data observed at suitable macroscopic temporal scales, one can deduce, by means of algebraic and algorithmic procedures, a discrete model (calledMetabolic Psystem) which accounts for the experimental data, and opens the possibility to understand the systemic logic of the investigated phenomenon. The procedures of such a method have been implemented within a computational platform, a Java software called MetaPlab, processing data and simulating behaviors of metabolic models. In the paper, we briefly describe the theory underlying the modeling of biochemical systems by Metabolic Psystems, along with its development stages and the related extensive literature.
  • loading
  • J. Fisher and T.A. Henzinger, “Executable cell biology”, Nat Biotech, Vol.25, No.11, pp.1239-1249, 2007.
    H. Kitano, “Computational systems biology”, Nature, Vol.420,p p.206-210, 2002.
    V. Manca, L. Bianco, and F. Fontana, “Evolutions and oscillations of Psystems: Applications to biochemical phenomena”,in Gh. P. ăun and G. Rozenberg, editors, LNCS 3365, Springer,p p.63-84, 2005.
    G. Păun, “Computing with membranes”, Journal of Computer and System Sciences, Vol.61, No.1, pp.108-143, 2000.
    V. Manca, “The metabolic algorithm: Principles and applications”,T heoretical Computer Science, Vol.404, No.1-2, pp.142-1 55, 2008.
    V. Manca, “Log-gain principles for metabolic Psystems”, in A. Condon et al., editor, Algorithmic Bioprocesses, Natural ComputingS eries, Springer, chapter 28, 2009.
    V. Manca, “Fundamentals of metabolic Psystems”, in G. Păun,G . Rozenberg, and A. Salomaa, editors, Handbook of Membrane Computing, Oxford University Press, chapter 19, pp.475-498,2 009.
    A. Goldbeter, “A minimal cascade model for the mitotic oscillatori nvolving cyclin and cdc2 kinase”, PNAS, Vol.88, No.20,p p.9107-9111, 1991.
    V. Manca, “M Psystems approaches to biochemical dynamics:B iological rhythms and oscillations”, in LNCS 4361, Springer,p p.86-99, 2006.
    V. Manca, “Metabolic Pdynamics”, in G. Păun, G. Rozenberg, and A. Salomaa, editors, Handbook of Membrane Computing.O xford University Press, chapter 20, pp.499-528, 2009.
    V. Manca, R. Pagliarini and S. Zorzan, “A photosynthetic processm odelled by a metabolic Psystem”, Natural Computing,D OI 10.1007/s11047-008-9104-x, 2009.
    A. Castellini and V. Manca, “MetaPlab: A computationalf ramework for metabolic Psystems”, in D.W. Corne, P. Frisco,G h. Paun, G. Rozenberg, and A. Salomaa, editors, LNCS,S pringer-Verlag, Vol.5391, pp.157-168, 2009.
    V. Manca and L. Bianco, “Biological networks in metabolic Ps ystems”, BioSystems, Vol.372, No.2-3, pp.165-182, 2007.
    L. Von Bertalanffy, General Systems Theory: Foundations, Developments,A pplications. 1st edition, George Braziller Inc.,1 967.
    K. Dhar, M.T. Chee, S. Sandeep, Y. Li, S. Kishore, K. Arun,B .M. Ridwan, W.S.H. Wah, C. Mandar and H. Zhu, “Grid cellware:T he first grid-enabled tool for modelling and simulatingc ellular processes”, Bioinformatics, Vol.21, No.7, pp.1284-1287,2 005.
    P. Dhar, T.C. Meng, S. Somani, L. Ye, A. Sairam, M. Chitre, Z.H ao and K. Sakharkar, “Cellware-a multi-algorithmic softwaref or computational systems biology”, Bioinformatics, Vol.20,N o.8, pp.1319-1321, 2004.
    H. Li, Y. Cao, L.R. Petzold and D.T. Gillespie, “Algorithms and software for stochastic simulation of biochemical reactings ystems”, Biotechnology Progress, Vol.24, No.1, pp.56-61, 2008.
    N. Le Novere and S.T. Shimizu, “Stochsim: M0odelling of stochastic biomolecular processes”, Bioinformatics, Vol.17,N o.6, pp.575-576, 2001.
    D.T. Gillespie, “Exact stochastic simulation of coupled chemicalr eactions”, The Journal of Physical Chemistry, Vol.81, No.25,p p.2340-2361, 1977.
    D.T. Gillespie, “Approximate accelerated stochastic simulation of chemically reacting systems”, The Journal of Chemical Physics, Vol.115, No.4, pp.1716-1733, 2001.
    S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus,M . Singhal, L. Xu, P. Mendes, and U. Kummer, “COPASI a COmplex PAthway SImulator”, Bioinformatics, Vol.22, No.24,p p.3067-3074, 2006.
    M. Nagasaki, A. Doi, H. Matsuno, and S. Miyano, “Genomico bjectnet: I. A platform for modelling and simulating biopathways”,A pplied Bioinformatics, Vol.2, No.3, pp.181-184, 2004.
    K. Takahashi, N. Ishikawa, Y. Sadamoto, H. Sasamoto, S.O hta, A. Shiozawa, F. Miyoshi, Y. Naito, Y. Nakayama andM . Tomita, “E-cell2: Multi-platform e-cell simulation system”,B ioinformatics, Vol.19, No.13, pp.1727-1729, 2003.
    M. Tomita, K. Hashimoto, K. Takahashi, T.S. Shimizu, Y. Matsuzaki,F . Miyoshi, K. Saito, S. Tanida, K.Yugi, J.C. Venter and C.A. Hutchison, “E-CELL: Software environment for whole-cells imulation”, Bioinformatics, Vol.15, No.1, pp.72-84, 1999.
    T.R. Kiehl, R.M. Mattheyses and M.K. Simmons, “Hybrids imulation of cellular behavior”, Bioinformatics, Vol.20, No.3,p p.316-322, 2004.
    H. Matsuno, Y. Tanaka, H. Aoshima, A. Doi, M. Matsui andS . Miyano, “Biopath-ways representation and simulation on hybridf unctional petri nets”, Silico Biology, Vol.3, No.3, pp.389-4 04, 2003.
    A. Castellini, G. Franco and V. Manca, “Hybrid functional petrin ets as M Psystems”, Natural Computing, Vol.9, No.1, pp.61-8 1, 2010.
    Alberto Castellini, Vincenzo Manca and Luca Marchetti, “MPs ystems and hybrid petri nets”, Studies in Computational Intelligence( SCI), Vol.129, pp.53-62, 2008.
    S. Klamt, J. Stelling, M. Ginkel and E.D. Gilles, “Fluxanalyzer:E xploring structure, pathways, and flux distributions inm etabolic networks on interactive flux maps”, Bioinformatics,Vol.19, No.2, pp.261-269, 2003.
    E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay and M. Ozturk, “PATIKA: An integrated visuale nvironment for collaborative construction and analysis of cellularp athways”, Bioinformatics, Vol.18, No.7, pp.996-1003, 2002.
    H.M. Sauro, M. Hucka, A. Finney, C. Wellock, H. Bolouri, J.D oyle and H. Kitano, “Next generation simulation tools: Thes ystems biology workbench and biospice integration”, OMICS,Vol.7, No.4, pp.355-372, 2003.
    L. Bianco, V. Manca, L. Marchetti and M. Petterlini, PSim:A simulator for biomolecular dynamics based on Psystems”, Proceedings of the IEEE CE C2007, pp.883-887, 2007.
    A. Castellini, G. Franco and R. Pagliarini, “Data analysisp ipeline from laboratory to M Pmodels”, Natural Computing,Vol.10, No.1, pp.55-76, 2011.
    V. Manca and L. Marchetti, “Metabolic approximation of realp eriodical functions”, The Journal of Logic and Algebraic Programming,Vol,179, No.6, pp.363-373, 2010.
    V. Manca and L. Marchetti, “Log-gain stoichiometic stepwiser egression for M Psystems”, Int. Journal of Foundations of Computer Science, Vol.22, No.1, pp.97-106, 2011.
    V. Manca and L. Marchetti, “Solving dynamical inverse problemsb y means of metabolic Psystems”, BioSystems, Vol.109,N o.1, pp.78-86, 2012.
    V. Manca and L. Marchetti, “Goldbeter's mitotic oscillator entirelym odeled by M Psystems”, LNCS, Vol.6501, pp.273-284,2 010.
    V. Manca, L. Marchetti and R. Pagliarini, “M Pmodelling ofg lucose-insulin interactions in the intravenous Glucose tolerancet est”, International Journal of Natural Computing Research,Vol.2, No.3, pp.13-24, 2011.
    L. Marchetti and V. Manca, “A methodology based on MPt heory for gene expression analysis”, CM C2011, LNCS 7184,p p.300-313, 2012.
    V. Manca and L. Marchetti, “XML representation of MPs ystems”, In IEEE Congress on Evolutionary Computation( CEC2009), Trondheim, Norway, pp.3103-3110, 2009.
    J.J. Mandel, H. Fuss, N.M. Palfreyman and W. Dubitzky,“Modeling biochemical transformation processes and informationp rocessing with narrator”, BM CBioinformatics, Vol.8,N o.3, pp.103-119, 2007.
    A. Goldbeter, “Computational approaches to cellular rhythms”,N ature, Vol.420, pp.238-245, 2002.
    T. Maiwald and J. Timmer, “Dynamical modeling and multiexperimentf itting with Potters Wheel”, Bioinformatics, Vol.24,N o.18, pp.2037-2043, 2008.
    V. Manca, Infobiotics, Springer, 2013.
    I.C. Chou and E.O. Voit, “Recent developments in parametere stimation and structure identification of biochemical and genomic systems”, Mathematical Biosciences, Vol.219, No.2,p p.57-83, 2009.
    J. Decraene and T. Hinze, “A multidisciplinary survey of computationalt echniques for the modelling, simulation and analysis of biochemical networks”, Journal of Universal Computer Science,Vol.16, No.9, pp.1152-1175, 2010.
    M. Gheorghe, V. Manca, and F.J. Romero-Campero, “Deterministic and stochastic Psystems for modelling cellular processes”,N atural Computing, Vol.9, pp.457-473, 2010.
    F.J. Romero-Campero, J. Twycross, M. Cámara, M. Bennett,M . Gheorghe and N. Krasnogor, “Modular assembly of cell systemsb iology models using Psystems”, International Journal of Foundations of Computer Science, Vol.20, No.3, pp.427-442,2 009.
    D. Pescini, D. Besozzi, G. Mauri and C. Zandron, “Dynamicalp robabilistic Psystems”, International Journal of Foundations of Computer Science, Vol.17, pp.183-204, 2006.
    F.J. Romero-Campero, H. Cao, M. Cámara and N. Krasnogor,“Structure and parameter estimation for cell systems biologym odels”, in Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2008, ACM Publisher, pp.331-3 38, 2008.
    V. Manca, “Discrete simulations of biochemical dynamics”,in M.H. Garzon and H. Yan, editors, DNA 13, LNCS 4848,S pringer, pp.231-235, 2008.
    G. Franco, P.H. Guzzi, V. Manca and T. Mazza, “Mitotic oscillatorsas M Pgraphs”, in H.J. Hoogeboom, Gh. Păun, G. Rozenberg, and A. Salomaa, editors, LNCS 4361, Springer, pp.382-3 94, 2006.
    L. Bianco, F. Fontana, G. Franco and V. Manca, “ Psystemsf or biological dynamics”, in G. Ciobanu, G. Păun, and M.J. Pérez-Jiménez, editors, Applications of Membrane Computing,N atural Computing Series, Springer, Berlin, pp.81-126, 2006.
    V. Manca, “Metabolic Psystems for biochemical dynamics', Progress in Natural Sciences, Vol.17, No.4, pp.384-391, 2007.
    F. Fontana and V. Manca, “Discrete solutions to differentiale quations by metabolic Psystems”, Theoretical Computer Science,Vol.372, No.2-3, pp.165-182, 2007.
  • 加载中


    通讯作者: 陈斌,
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Article Metrics

    Article views (472) PDF downloads(1228) Cited by()
    Proportional views


    DownLoad:  Full-Size Img  PowerPoint