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CADLIVE: Comprehensive Dynamic Simulation Software

CADLIVE automatically converts biochemical network maps to dynamic models, offering abstract and concrete modeling levels with JAVA Client-Server System for simulations. It facilitates forward and reverse engineering of mathematical models based on network maps, optimizing parameter values for accurate biological behavior reproduction. CADLIVE is equipped with GUI Network Constructor and permits direct map-to-model connections. Available for free download at www.cadlive.jp.

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CADLIVE: Comprehensive Dynamic Simulation Software

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  1. Computer-Aided Design of LIVing systEms CADLIVE automatically converts a biochemical network map to a dynamic model. JAVA application Client-Server System

  2. Dynamic simulation by CADLIVE Very abstract model (Boolean model) INTERMEDIATE LEVEL in CADLIVE Very concrete model (Experimentally measured kinetics model)

  3. Forward Engineering Mathematical model construction based on a biochemical network map Direct link of a network map to a math model Reverse Engineering Parameter values are tuned to reproduce biological behaviors

  4. CADLIVE (Computer-Aided Design of LIVing systEms) A comprehensive software suite for directly connecting biochemical network maps to dynamic simulations CADLIVE Dynamic Simulator CADLIVE GUI Network Constructor CADLIVE is freely available at http://www.cadlive.jp/

  5. From a Biochemical Map to Simulation GUI Network Constructor Biochemical Map Automatic conversion Dynamic Simulator Regulator-Reaction Equations Automatic conversion Mathematical Model Simulation

  6. Three Layers and Two Stages

  7. Gene Layer Transcription and Translation (TT) Equations

  8. Protein Layer CMA: Conventional Mass Action Problems: Stiff Differential equations

  9. Metabolic layer MM Type GMA: General Mass Action

  10. DAEs are Converted from CMA By Two-Phase Partition Method (TPP) Binding Phase Reaction Phase Rapid-equilibrium approximation

  11. Advantage of TPP Reducing the number of kinetic parameters Generating non-stiff DAEs

  12. PROCESS FLOW Runge-Kutta based algorithms NDF (similar to matlab ode15s) Simulation Optimization on a GRID system Sensitivity and stability analysis

  13. An Example for Automatic Simulation An ammonia assimilation system map The E. coli ammonia assimilation system consists of three layers: gene, protein, and metabolic layers and multiple feedback loops.

  14. Demonstration CADLIVE GUI Network Constructor Regulator-reaction equations were automatically generated.

  15. Export to XML file Regulator-Reaction Equations written in the XML format

  16. Automatic Conversion Client- Server System XML file sent to CADLIVE Simulator CADLIVE Dynamic Simulator automatically converts Regulator-Reaction Equations into a mathematical model.

  17. Automatic Conversion The gene and protein layers are converted into differential and algebraic equations (DAEs) through CMA with ordinary transcription-translation equations (TT). The metabolic layer was converted into simplified Michaelis-Menten type equations (MM).

  18. Mathematical simulation and optimization The simulated time course appears.

  19. Conclusion The CADLIVE Simulator is demonstrated to handle gene regulatory and metabolic networks at an intermediate level without going all the way down to exact biochemical reactions.

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