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[65] W Sandmann Stochastic simulation of biochemical systems via discrete-time conversion In Proceedings of the 2nd Conference on Foundations of Systems Biology in Engineering, pp 267 272 Fraunhofer IRB Verlag, Stuttgart, 2007 [66] W Sandmann Discrete-time stochastic modeling and simulation of biochemical networks Computational Biology and Chemistry, 32(4): 292 297, 2008 [67] W Sandmann and V Wolf Computational probability for systems biology In Proceedings of the Workshop on Formal Methods in Systems Biology, Lecture Notes in Computer Science 5054, pp 33 47 Springer, Stuttgart, 2008 [68] M Schauer and R Heinrich Analysis of the quasi-steady state approximation for an enzymatic one-substrate reaction Journal of Theoretical Biology, 79: 425 442, 1979 [69] L A Segel On the validity of the steady-state assumption of enzyme kinetics Bulletin of Mathematical Biology, 50: 579 593, 1988 [70] L A Segel and M Slemrod The quasi-steady state assumption: A case study in perturbation SIAM Review , 31(3): 446 477, 1989 [71] E Seneta Non-Negative Matrices and Markov Chains Springer, New York, 1981 [72] K Singer Application of the theory of stochastic processes to the study of irreproducible chemical reactions and nucleation processes Journal of the Royal Statistical Society, Series B , 15(1): 92 106, 1953 [73] W J Stewart Introduction to the Numerical Solution of Markov Chains Princeton University Press, Princeton, NJ, 1994 [74] Z Szallasi, J Stelling, and V Periwal, eds System Modeling in Cellular Biology MIT Press, Cambridge, MA, 2006 [75] T E Turner, S Schnell, and K Burrage Stochastic approaches for modelling in vivo reactions Computational Biology and Chemistry, 28: 165 178, 2004 [76] C Valeriani, R J Allen, M J Morelli, D Frenkel, and P R ten Wolde Computing stationary distributions in equilibrium and nonequilibrium systems with forward ux sampling Journal of Chemical Physics, 127(11): 114109/1 114109/11, 2007 [77] N van Kampen Stochastic Processes in Physics and Chemistry Elsevier, Amsterdam, 1992 [78] K Vasudeva and U S Bhalla Adaptive stochastic-deterministic chemical kinetics simulation Bioinformatics, 20(1): 78 84, 2004 [79] D J Wilkinson Stochastic Modelling for Systems Biology Taylor & Francis, Boca Raton, FL, 2006 [80] O Wolkenhauer, M Ullah, W Kolch, and K-H Cho Modelling and simulation of intracellular dynamics: Choosing an appropriate framework IEEE Transactions on NanoBioscience, 3(3): 200 207, 2004 [81] Z Xu and W Cai Unbiased tau-leaping methods for stochastic simulation of chemically reacting systems Journal of Chemical Physics, 128(15): 154112, 2008.

java data matrix barcode reader

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From the flow in Figure 5-10, we can see that the initial state of the managed heap includes five objects starting with Obj A at address 0x02000000 At a certain point, a platform invocation call to an asynchronous native API is required Furthermore, the address of Obj C (0x02000090) needs to be passed to the API Upon successfully calling the asynchronous native API, a garbage collection occurs causing Obj A and Obj B to be collected This leaves a gap of two free objects on the managed heap and the garbage collector dutifully rectifies the problem by compacting the managed heap and therefore moving Obj C to address 0x02000000 It also coalesces the two free blocks and places them at the end of the heap After the garbage collection has finished, the asynchronous API call we made earlier decides to write to the address initially passed to it (0x02000090), which originally held Obj C As you can see, with the asynchronous API writing to that address, we will experience a managed heap corruption as the memory is no longer occupied by Obj C Because the invocation of native code is such a common task, a solution had to be devised that allowed for safe invocation in light of a compacting garbage collector The solution is called pinning and refers to the capability to pin specific objects on the managed heap When an object is pinned, the garbage collector will not move the object for any reason until the object is unpinned If Obj C in Figure 5-10 was pinned prior to invoking the asynchronous native API, the managed heap corruption would not have occurred due to the garbage collector not moving Obj C during the compaction phase Let s take a look at an example of a simple application that performs pinning and see what it looks like in the debugger Listing 5-6 shows the source code of the application Listing 5-6 Sample application using pinning.

java data matrix barcode reader

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java data matrix reader

java data matrix reader

java data matrix barcode reader

java data matrix barcode reader

java data matrix barcode reader

java data matrix barcode reader

java data matrix reader

java data matrix barcode reader

java data matrix reader

java data matrix barcode reader

java data matrix reader

java data matrix barcode reader

java data matrix reader