Accession Number : ADA480737


Title :   Stochastic Simulations of Cellular Biological Processes


Descriptive Note : Conference paper


Corporate Author : AIR FORCE RESEARCH LAB WRIGHT-PATTERSON AFB OH


Personal Author(s) : Chushak, Yaroslav ; Foy, Brent ; Frazier, John


Full Text : http://www.dtic.mil/dtic/tr/fulltext/u2/a480737.pdf


Report Date : Jun 2007


Pagination or Media Count : 10


Abstract : INTRODUCTION: From a systems engineering point of view, cells consist of a complex set of nested, nonlinear control systems dominated by feed-back and feed-forward loops. The more complex the system is, the more important are the issues concerning the robustness and parameter optimization, therefore modeling and simulations are important for both engineering and reverse-engineering of biosystems. OBJECTIVE: At the functional level, all biological processes in cells can be represented as a series of biochemical reactions. Since such reactions are stochastic in nature, the user must run thousands of simulations to characterize the ensemble behavior of biological systems. We developed a software package called Biomolecular Network Simulator (BNS) to model and simulate complex biomolecular reaction networks using High Performance Computing (HPC). METHODOLOGY: The Biomolecular Network Simulator uses the Gillespie stochastic algorithm to simulate the evolution of a system of biochemical reactions. The BNS code is a combination of MATLAB and C-coded modules. This combination allows one to use the interactive features and visualization tools of MATLAB, while achieving high speed for the computationally intensive part of the software. The software is parallelized with the MPI library to run on multiprocessor architectures. RESULT: The Biomolecular Network Simulator consists of two sets of tools: for simulations of the system and for the analysis of simulation results. The Graphical User Interface of BNS allows users to easily set parameters for the model and simulations and to select analysis method. Multiple types of post-simulation analyses are available. SIGNIFICANCE TO DoD: The Developed software allows DoD scientists to build, simulate and analyze complex cellular biomolecular networks utilizing the capacities of HPC. It provides the foundational capability to design and integrate biological constructs into a new generation of biotechnology products.


Descriptors :   *SIMULATION , *STOCHASTIC PROCESSES , *BIOMOLECULES , *BIOTECHNOLOGY , ALGORITHMS , NETWORK ARCHITECTURE , SOFTWARE TOOLS , GRAPHICAL USER INTERFACE , CELLS(BIOLOGY) , BIOCHEMISTRY , SYMPOSIA


Subject Categories : Biochemistry
      Statistics and Probability
      Computer Programming and Software


Distribution Statement : APPROVED FOR PUBLIC RELEASE