The general command to execute the VC is as follows:

Command line options:

  C: Calibrate
  D: Debug mode
  F: Figure of Merit (FOM) calculation
  H: Help (this screen)
  K: Print cell and damage-repair kinetics
  N: Add noise to output
  S: Silent execution (echo off)
  X: Print extra bio-dose information (e.g., RBD and BED)

Examples:

  VC [interactive program input]
  VC -h [request help]
  VC cell.inp -d -s [debug mode, silent execution]
  VC cell.inp -n [generate a synthetic dataset]
  VC cell.inp s1.radx -k [run using exposure scenarios in s1.radx]
  VC cell.inp s1.xdat -c [calibrate model]
  VC cell.inp electron.mcer [Load MCDS/MCER data from electron.mcer]

RADX Files (see also the RIO computer code)

Random access (binary) files are used to store detailed information about the temporal delivery of radiation (i.e., to specify one or more instantaneous dose rate functions).  The RADX file is also be used to store some microdosimetric quantities such as the frequency-mean specific energy per radiation event.  The VC, RIO, and XIO applications automatically recognize files with the .radx filename extension as a RADX binary file (see above examples).  However if the name of a RADX file is not specified on the command line, the VC application uses information from the primary ASCII input file to construct the exposure scenarios and to create a new RADX file.

XDAT Files (see also the XIO computer code)

The VC application includes two different non-linear optimization algorithms to adjust biophysical inputs to reflect the characteristics of specific cell types (i.e., generate a model calibration).  The VC software uses a pair of XDAT and RADX binary files to access the experimental results in a standardized way.  The XDAT file stores information on biological endpoints (e.g., cell killing), and the RADX file contains a detailed description of the dose and dose rate information associated with the experiment.  At present, the VC application can only tune model inputs based on cell survival data for any type of dose rate function that can be specified via the RADX module (single dose at various dose rates, split-dose exposures, multi-fraction exposures, exponentially decreasing dose rate, etc., etc.).  A future version will include the ability to tune model inputs using additional endpoints (e.g., the DSB rejoining rate or neoplastic transformation).