The HCV Multiscale Model 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.

Virus Multiscale Model Equations Solver and Fitter Java source code and executable jar file:

 click here to download

How to use the Multiscale Model Virus Equations Solver and Fitter

1) Extract the file "SolverAndFitter.zip"
2) Enter the folder "SolverAndFitter"
3) Run "Simulator.jar" file.

Modeling by the simulator


Initial Modeling 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.
6) Upload data - with this option it is possible to add data points to the plots.
- 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 "SolverAndFitter" folder.

Example of parameters file:


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

Fitting by the simulator

Initial Fiting window (with default parameters):


Available options:
1) In order to start fitting:
- please upload the data to the plot by using the "Upload data" button.
- choose the fitting method: Least square fitter (Gauss-Newton) or Cobyla fitter.
- choose which parameters to estimate and their constraints (min and max paremetr values - optional) in "Fitting parameters" section.
- fill in the fixed parameters values as well as the initial guesses fot fitting parameters.
- press "Fit" button and wait until the fitting is finished.
- after the fitting is finished the error value displayed at the bottom of the window. Press "Draw Fitting" to generate the fit line on the plot.
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) Save parameters - with this option it is possible to save to file the parameters currently available in the GUI fields.


Example of uploaded data from the file:


Example of the fitting of parameter gamma using least square fitter:


Fitting of gamma finished:


Adding the line of the fit to the plot: