The Multiscale Model HCV Simulator

 

The multiscale model of hepatitis C virus (HCV) dynamics has been formulated in recent years in order to study HCV dynamics in patients and decide among various treatment options. It uses the standard viral dynamics model that keeps track of uninfected target cells, productively infected cells, and free virus along with considering the intracellular viral RNA dynamics in an infected cell. The multiscale model with the RNA consideration is considerably more difficult to solve and the governing differential equations are stiff. In one of the differential equations there is also an integral involving RNA that is more accurately computed by considering previous iterations, impeding the use of canned solvers. We present a robust and efficient numerical method that belongs to the family of adaptive stepsize methods and is implicit, a Rosenbrock type method that is highly suited to solve this problem. We provide a friendly Graphical User Interface that applies this method and is useful in realistic simulations of the multiscale model that considers viral RNA replication within the cell.

Virus Equations Solver java source and exacutable jar file:

 click here to download

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How to use Virus Equations Solver

1) Extract file "VirusEquationsSolver.rar"
2) Enter to the folder "VirusEquationsSolver"
3) Run "Solver.jar" file.

Initial GUI window (with default parameters):


Available options:
1) Changing parameters values and running the simulation by pressing the "Start" button.
2) Clear - clears all parameters values and all plots from the graph. May be used before a new set of simulations.
3) Default - puts the default parameters into the GUI fields.
4) Run from file - this option allows to run several simulations from the parameters text file containing several parameters sets.
5) Save parameters - with this option it is possible to save to file the parameters currently available in the GUI fields. Later it is possible to open this file and to run simulation with these parameters, using "Run from file" option.
- In practice it is possible to run any combination of "Run from file" and "Start" using GUI parameters. Each option may be used several times in any order and all plots will be shown on the same plot.
- Example files parameters.txt, parameters_byname.txt (for "Run from file" option) are available in the "VirusEquationsSolver" folder.

Example of parameters file:


Example of using "Run from file" option on file with three different sets of parameters: