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Group: compneur - library [175 articles]

Recent papers posted by members of the compneur group
  • Petriweb: A Repository for Petri Nets
    Petri Nets and Other Models of Concurrency - ICATPN 2006 (2006), pp. 411-420.
    by R Goud, Kees van Hee, R Post, J van der Werf
    posted to model_repository petrinets by dagmar to the group compneur on 2008-08-31 12:56:13 as *****
  • Fusing and Composing Macromolecular Regulatory Network Models
    (March 2007), pp. 337-344.
    by R Randhawa, CA Shaffer, JJ Tyson
    posted to model model_components by dagmar to the group compneur on 2008-04-18 14:26:54 as ***** along with 1 group dIEMoSIRIS
  • SBML Extensions for Level 3: Experiments, Simulation, Parameters, Results and Plots
    (March 2008)
    by Fedor Kopalov
    posted to biouml miase sbml by dagmar to the group compneur on 2008-03-25 13:04:51 as read
  • A New Algorithm for Monte Carlo Simulation of Ising Spin Systems
    Journal of Computational Physics, Vol. 17 (January 1975), 10.
    by AB Bortz, MH Kalos, JL Lebowitz
    posted to monte_carlo simulation_algorithms by dagmar to the group compneur on 2007-11-28 16:39:59 as **
  • Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems
    Biotechnol. Prog. (26 September 2007)
    by H Li, Y Cao, LR Petzold, DT Gillespie
    posted to simulation_algorithms stochastic by dagmar to the group compneur on 2007-11-26 17:02:53 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Family tree of Markov models in systems biology
    Systems Biology, IET, Vol. 1, No. 4. (2007), pp. 247-254.
    by M Ullah, O Wolkenhauer
    posted to simulation_algorithms by dagmar to the group compneur on 2007-11-26 16:57:49 as **
  • Some general implicit processes for the numerical solution of differential equations
    The Computer Journal, Vol. 5, No. 4. (1 April 1963), pp. 329-330.
    by HH Rosenbrock
    posted to deterministic kisao simulation_algorithms by dagmar to the group compneur on 2007-11-20 11:25:03 as **
  • An Automatic Method for Finding the Greatest or Least Value of a Function
    The Computer Journal, Vol. 3, No. 3. (1 March 1960), pp. 175-184.
    by HH Rosenbrock
    posted to deterministic kisao simulation_algorithms by dagmar to the group compneur on 2007-11-12 19:07:20 as **
  • The Numerical Analysis of Ordinary Differential Equations: Runge-Kutta and General Linear Methods
    (28 January 1987)
    by JC Butcher
    posted to kisao runge-kutta deterministic by dagmar to the group compneur on 2007-11-12 11:19:25 as **
  • CSA
    posted to deterministic kisao rnuge-kutta by dagmar to the group compneur on 2007-11-12 11:13:28 as **
  • Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.
    OMICS, Vol. 7, No. 4. (2003), pp. 355-372.
    by HM Sauro, M Hucka, A Finney, C Wellock, H Bolouri, J Doyle, H Kitano
    posted to miase sbw simulation_tools by dagmar to the group compneur on 2007-11-06 11:02:14 as ** along with 1 person bootsy
  • Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations
    SIAM Journal on Scientific and Statistical Computing, Vol. 4, No. 1. (1983), pp. 136-148.
    by Linda Petzold
    posted to copasi kisao ode simulation_algorithms by dagmar to the group compneur on 2007-10-30 17:32:57 as ** along with 2 people muraken pmendes
  • Stochastic simulation of chemical reactions with spatial resolution and single molecule detail.
    Phys Biol, Vol. 1, No. 3-4. (December 2004), pp. 137-151.
    by SS Andrews, D Bray
    posted to kisao simulation_algorithms smoldyn by dagmar to the group compneur on 2007-10-29 15:36:49 as ** along with 6 people and 2 groups roland_ewald csanford lenov m_j gabe_rosser arjunan dIEMoSIRIS MoSi-Rostock
  • PVODE, an ODE Solver for Parallel Computers
    International Journal of High Performance Computing Applications, Vol. 13, No. 4. (1 November 1999), pp. 354-365.
    by George D Byrne, Alan C Hindmarsh
    posted to deterministic simulation_algorithms by dagmar to the group compneur on 2007-10-28 19:52:02 as **
  • Stochastic reaction-diffusion simulation with MesoRD
    Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2923-2924.
    by Johan Hattne, David Fange, Johan Elf
    posted to simulation_algorithms simulation_tools stochastic by dagmar to the group compneur on 2007-10-26 17:27:43 as ** along with 8 people and 3 groups jberro balabu jiyu roland_ewald mattis23 lenov csanford arjunan Projet_ENSIMAG dIEMoSIRIS MoSi-Rostock
  • A practical guide to stochastic simulations of reaction-diffusion processes
    (15 Apr 2007)
    by Radek Erban, Jonathan Chapman, Philip Maini
    posted to simulation_algorithms stochastic by dagmar to the group compneur on 2007-10-26 16:16:44 as ***** along with 3 people and 2 groups cottrell roland_ewald csgillespie dIEMoSIRIS MoSi-Rostock
  • Green's-function reaction dynamics: A particle-based approach for simulating biochemical networks in time and space.
    J Chem Phys, Vol. 123, No. 23. (15 December 2005)
    by JS van Zon, PR Ten Wolde
    posted to simulation_algorithms stochastic by dagmar to the group compneur on 2007-10-25 22:15:13 as ** along with 1 person madhadron
  • Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
    The Journal of Chemical Physics, Vol. 118, No. 11. (2003), pp. 4999-5010.
    by Christopher V Rao, Adam P Arkin
    posted to kisao simulation_algorithms by dagmar to the group compneur on 2007-10-23 15:06:12 as **
  • The numerical stability of leaping methods for stochastic simulation of chemically reacting systems.
    J Chem Phys, Vol. 121, No. 24. (22 December 2004), pp. 12169-12178.
    by Y Cao, LR Petzold, M Rathinam, DT Gillespie
    posted to kisao simulation_algorithms tau by dagmar to the group compneur on 2007-10-23 14:08:22 as **
  • Avoiding negative populations in explicit Poisson tau-leaping
    J. Chem. Phys., Vol. 123 (August 2005), 4104.
    by Y Cao, DT Gillespie, LR Petzold
    posted to gillespie kisao simulation_algorithms tau by dagmar to the group compneur on 2007-10-22 16:14:37 as **
  • Improved leap-size selection for accelerated stochastic simulation
    J. Chem. Phys., Vol. 119 (October 2003), pp. 8229-8234.
    by DT Gillespie, LR Petzold
    posted to gillespie simulation_algorithms tau by dagmar to the group compneur on 2007-10-19 14:44:44 as **
  • Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
    The Journal of Chemical Physics, Vol. 117, No. 15. (2002), pp. 6959-6969.
    by Eric L Haseltine, James B Rawlings
    posted to simulation_algorithms stochastic by dagmar to the group compneur on 2007-10-19 09:15:36 as ** along with 3 people jstajic jjray ner25
  • Modeling and simulation of genetic regulatory systems: a literature review.
    J Comput Biol, Vol. 9, No. 1. (2002), pp. 67-103.
    by H de Jong
    posted to kisao modelling simulation_algorithms by dagmar to the group compneur on 2007-10-18 17:28:28 as ** along with 14 people and 2 groups eldan tmmurali bayesian balicea Happybene wnpx kengg noano sstoma josepe jo_davies roys maburkitt phoenixzxl VirtualPlants Plantandetc
  • Stochastic simulation of coupled reaction-diffusion processes
    J. Comput. Phys., Vol. 127, No. 1. (August 1996), pp. 196-207.
    by Audrius B Stundzia, Charles J Lumsden
    posted to simulation_algorithms stochastic by dagmar to the group compneur on 2007-10-18 14:14:01 as ** along with 1 person and 1 group jberro Projet_ENSIMAG
  • Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli
    Bioinformatics, Vol. 22, No. 15. (1 August 2006), pp. 1895-1901.
    by Vidal J Rodriguez, Jaap A Kaandorp, Maciej Dobrzynski, Joke G Blom
    posted to simulation_algorithms spatial by dagmar to the group compneur on 2007-10-17 14:50:04 as **
  • Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics
    The Journal of Chemical Physics, Vol. 127, No. 10. (2007)
    by Tatiana, Kevin Burrage
    posted to gillespie simulation_algorithms tau by dagmar to the group compneur on 2007-10-16 17:23:00 as **
  • Binomial leap methods for simulating stochastic chemical kinetics
    The Journal of Chemical Physics, Vol. 121, No. 21. (2004), pp. 10356-10364.
    by Tianhai Tian, Kevin Burrage
    posted to simulation_algorithms by dagmar to the group compneur on 2007-10-16 15:53:35 as ** along with 1 person and 2 groups roland_ewald dIEMoSIRIS MoSi-Rostock
  • Description and Use of LSODE, the Livermore Solver for Ordinary Differential Equations
    Lawrence Livermore National Laboratory Report, Vol. UCRL-ID-113855 (1993)
    by Krishnan Radhakrishnan, Alan C Hindmarsh
    posted to lsode lsodi simulation_algorithms by dagmar to the group compneur on 2007-10-16 14:32:37 as **
  • Mathematical simulation and analysis of cellular metabolism and regulation.
    Bioinformatics, Vol. 15, No. 9. (September 1999), pp. 749-758.
    by I Goryanin, TC Hodgman, E Selkov
    posted to dbsolve simulation_tools by dagmar to the group compneur on 2007-10-16 11:50:25 as ** along with 1 person chrn
  • Predicting temporal fluctuations in an intracellular signalling pathway.
    J Theor Biol, Vol. 192, No. 1. (7 May 1998), pp. 117-128.
    by CJ Morton-Firth, D Bray
    posted to cellular_automata simulation_algorithms by dagmar to the group compneur on 2007-10-16 10:56:04 as ** along with 3 people and 1 group chrn jberro lenov Projet_ENSIMAG
  • Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation
    Bioinformatics, Vol. 14, No. 10. (1 November 1998), pp. 869-883.
    by P Mendes, D Kell
    posted to gepasi simulation_algorithms simulation_tools by dagmar to the group compneur on 2007-10-16 10:51:12 as ** along with 3 people dullhunk csgillespie pmendes
  • Modeling and simulation of intracellular dynamics: choosing an appropriate framework
    NanoBioscience, IEEE Transactions on, Vol. 3, No. 3. (2004), pp. 200-207.
    by O Wolkenhauer, M Ullah, W Kolch, Kwang-Hyun Cho
    posted to kisao simulation_algorithms by dagmar to the group compneur on 2007-10-15 14:13:50 as ****
  • A multi-algorithm, multi-timescale method for cell simulation.
    Bioinformatics, Vol. 20, No. 4. (1 March 2004), pp. 538-546.
    by K Takahashi, K Kaizu, B Hu, M Tomita
    posted to simulation_algorithms by dagmar to the group compneur on 2007-10-15 09:41:10 as ** along with 4 people and 2 groups chrn carmaus lenov csanford dIEMoSIRIS MoSi-Rostock
  • INTRODUCTION TO THE KINETIC MONTE CARLO METHOD
    Radiation Effects in Solids (2007), pp. 1-23.
    by Arthur Voter
    posted to kisao monte_carlo simulation_algorithms by dagmar to the group compneur on 2007-10-13 12:41:24 as ** along with 1 person softsimu
  • Trapezoidal tau-leaping formula for the stochastic simulation of biochemical systems
    (2005), pp. 149-152.
    by Y Cao, L Petzold
    posted to gillespie simulation_algorithms stochastic by dagmar to the group compneur on 2007-10-11 15:01:39 as **
  • Adaptive explicit-implicit tau-leaping method with automatic tau selection
    The Journal of Chemical Physics, Vol. 126, No. 22. (2007)
    by Yang Cao, Daniel T Gillespie, Linda R Petzold
    posted to gillespie simulation_algorithms by dagmar to the group compneur on 2007-10-11 14:50:44 as ** along with 1 person khachsar
  • Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method
    The Journal of Chemical Physics, Vol. 119, No. 24. (2003), pp. 12784-12794.
    by Muruhan Rathinam, Linda R Petzold, Yang Cao, Daniel T Gillespie
    posted to gillespie simulation_algorithms stochastic by dagmar to the group compneur on 2007-10-11 14:43:41 as **
  • The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
    Computational Biology and Chemistry, Vol. 30, No. 1. (February 2006), pp. 39-49.
    by James M Mccollum, Gregory D Peterson, Chris D Cox, Michael L Simpson, Nagiza F Samatova
    posted to gillespie simulation_algorithms by dagmar to the group compneur on 2007-10-11 13:55:16 as **
  • Exact Stochastic Simulation of Coupled Chemical Reactions
    The Journal of Physical Chemistry, Vol. 81, No. 25. (1977), pp. 2340-2361.
    by DT Gillespie
    posted to gillespie simulation_algorithms by dagmar to the group compneur on 2007-10-11 11:09:02 as ** along with 1 person pmendes
  • The slow-scale stochastic simulation algorithm.
    J Chem Phys, Vol. 122, No. 1. (1 January 2005)
    by Y Cao, DT Gillespie, LR Petzold
    posted to gillespie simulation_algorithms by dagmar to the group compneur on 2007-10-10 13:15:56 as ** along with 1 person and 2 groups roland_ewald dIEMoSIRIS MoSi-Rostock
  • Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB.
    Syst Biol (Stevenage), Vol. 153, No. 2. (March 2006), pp. 53-60.
    by M Ullah, H Schmidt, KH Cho, O Wolkenhauer
    posted to simulation_algorithms by dagmar to the group compneur on 2007-10-06 20:19:39 as ***** along with 2 people and 3 groups beapen cangiani Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics
  • Space in systems biology of signaling pathways - towards intracellular molecular crowding in silico
    FEBS Letters, Vol. 579, No. 8. (21 March 2005), pp. 1783-1788.
    by Kouichi Takahashi, Satya N Arjunan, Masaru Tomita
    posted to sb simulation_algorithms by dagmar to the group compneur on 2007-09-25 15:31:13 as **** along with 8 people and 2 groups monocyte biplabbose chrn biosv carmaus m_j csanford arjunan dIEMoSIRIS MoSi-Rostock
  • Modelling Cellular Processes Using Membrane Systems with Peripheral and Integral Proteins
    Computational Methods in Systems Biology (2006), pp. 108-126.
    by Matteo Cavaliere, Sean Sedwards
    posted to simulation_tools cytosim by dagmar to the group compneur on 2007-09-21 14:32:31 as **** along with 1 group dIEMoSIRIS
  • Cyto-Sim Example Models: Oscillators
    (December 2006)
    by Sean Sedwards
    posted to simulation_tools miose lotka_volterra cytosim by dagmar to the group compneur on 2007-09-21 13:52:11 as ***** along with 1 group dIEMoSIRIS
  • Diffusion control of protein phosphorylation in signal transduction pathways.
    Biochem J, Vol. 350 Pt 3 (15 September 2000), pp. 901-907.
    by BN Kholodenko, GC Brown, JB Hoek
    posted to spatial signalling modelling mapk cascade by lenov to the group compneur on 2007-09-20 10:59:08 as read
  • Spatial gradients of cellular phospho-proteins.
    FEBS Lett, Vol. 457, No. 3. (3 September 1999), pp. 452-454.
    by GC Brown, BN Kholodenko
    posted to spatial signalling modelling mapk cascade by lenov to the group compneur on 2007-09-20 10:56:48 as read
  • Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors.
    J Exp Biol, Vol. 206, No. Pt 12. (June 2003), pp. 2073-2082.
    by BN Kholodenko
    posted to spatial signalling modelling mapk cascade by lenov to the group compneur on 2007-09-20 10:39:37 as read along with 1 person TGerald
  • Bidirectional synaptic plasticity as a consequence of interdependent Ca2+-controlled phosphorylation and dephosphorylation pathways.
    Eur J Neurosci, Vol. 17, No. 12. (June 2003), pp. 2521-2528.
    by P D'Alcantara, SN Schiffmann, S Swillens
    posted to synapse signalling modelling camkii calmodulin by lenov to the group compneur on 2007-09-17 14:13:56 as read
  • Emergent Properties of Networks of Biological Signaling Pathways
    Science, Vol. 283, No. 5400. (15 January 1999), pp. 381-387.
    by Bhalla
    posted to synapse signalling modelling camkii calmodulin by lenov to the group compneur on 2007-09-17 14:12:36 as read along with 2 people gurkanbebek mattions
  • THE HEMOGLOBIN SYSTEM. VI. THE OXYGEN DISSOCIATION CURVE OF HEMOGLOBIN
    Journal of Biological Chemistry, Vol. 63 (1925), pp. 529-545.
    by Adair
    posted to cooperativity by lenov to the group compneur on 2007-09-17 13:10:53 as read
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