Virtual Cell Virtual Cell WebsiteSchool of Health Sciences WebsitePurdue University Website
About the Virtual CellDownload VCExamplesTheoryUser ManualHelpExecute VC Simulation
Editing input and output files
Getting Started

The Virtual Cell is written in the Fortran 90/95 computer language and does not have a graphical user interface (GUI).  Installation of the VC is (can be) as simple as downloading the distribution and extracting the executables and supporting documentation to a folder on your computer.  Contents of the VC distribution, system requirements, and some tips and tricks that make the VC easier to use are provided below.  Additional “How To” information is available in the Getting Started (all new users should read Getting Started).

The VC software reads (loads) information from one or more ASCII input files (.inp or i. files) and then writes the results of VC simulations back to another series of ASCII output files (.debug, .out and .o files).  An ASCII file is very widely used file format that dates back to the days of the Disk Operating System (DOS).

All input and output files can be viewed and edited (modified) using software readily available under the Microsoft (MS) Windows© and other operating systems.  Programs that are used to open, view and edit ASCII files are commonly called editors.  The Notepad© and Wordpad© programs are two editors included in the MS Windows© family of operating systems.  Do not use MS Word© or WordPerfect© to edit ASCII input files.  These programs use a proprietary file format that the VC software does not understand (cannot read).

The Notepad© and Wordpad© editors can usually be found under the Program Accessories menu of MS Windows.  Alternatively, go to the Start menu and select Run.  When prompted for a file to open, enter Notepad or Wordpad. In order to use Notepad©,

  1. Open the Program Manager (it probably comes up automatically when you turn the computer on).  
  2. Double-click on the Accessories icon. If the Accessories window is already open, skip this step.
  3. Double-click on the Notepad icon. The application will open automatically. After Notepad© is open, you can:

Create a new file

    • Simply begin typing.

Read a file

    • Select File on the menu bar.
    • Click on Open. A screen will appear that allows you to locate the file.
    • When the file is located, click OK.
    • Text will appear with no formatting (cool fonts, bold, etc).

Importing sections from a different file  

    • Left click the mouse and drag over the section needed to copy. The chosen section will highlight (come under shade).
    • Select Edit on the menu bar.
    • Select Copy.
    • Now the file from which contents are copied can be closed (quit) if it is no longer needed.
    • Open the file (now open in an editor, or a new file) and select the position where the contents must be pasted by pointing the mouse-arrow and left clicking.
    • Click on Edit. A screen will appear showing several options.
    • Click on Paste.

Print a file

    • Select File on the menu bar.
    • Click on Print. A screen will appear that allows you to print the document.
    • Click on Print.

Save a file

    • Select Save As... on the menu bar. The Save As dialog box appears.
    • Specify what directory to save the file (location) and choose the file name.
    • Click on Save.

Exit Notepad©

    • Select File on the menu bar.
    • Select Quit.

The Wordpad© editor is used in much the same way as the Notepad editor©.


Tip: The VC software does not have a graphical user interface (GUI).  Instead, VC simulations are executed from the MS Windows command prompt.

School of Health Sciences
Purdue University
Disclaimer

Last updated: 10 June, 2011
Webmaster