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The Virtual Cell Page

Key Value
Tool Name: Virtual Cell
Author(s): Schaff
Simulator Type: Multiple methods
User Interface: Graphical
Function (s): View Models , Change Values , Change Topology , Create Models , Export Models , Import Models , SBML , VCML
URL: http://vcell.org
  Includes Spatial Modeling

-- RaquellHolmes - 02 Oct 2007

Some Questions You May Have

You will find here some answers to your questions and information about the Virtual Cell. Please refer to the User Guide for any other questions at www.vcell.org or http://vcell.org/userdocs/Rel/user_guide.pdf

How do you get the VCell application client?

Go to www.vcell.org and click on the tab "VCell software." Click on "Run VCell (Release)" to download the application. (In some cases, you will need to click Open VCell.) Any first-time user has to create an account. Once this is done, the VCML files when clicked should open your VCell application. Note: You must save the model as your own in order to run a simulation.

How do you open a model?

There are multiple ways:
1. In Vcell, look for the Education folder as follows: File > Open > BioModel or MathModel > Shared Models>Education > double click on the model you want to view.
2. Click the VCML file on Twiki site to open the model.
3. Save the VCML file to your desktop (right click> save target as> name_of_model.VCML). In some cases you will need to change the file extension from .xml to .vcml. Once saved you can either double click the file to open the associated application (VCell) or open VCell and import the file.

How do you create a VCML file to load on the Teaching Modules? Instructions coming soon

What is the difference between a BioModel, MathModel, and Geometry?

Click on the topic links for definitions or refer to Page 1 in the User Guide

Geometry: Is a representation of a spatial structure, which a BioModel or a MathModel application uses for spatially resolved simulations.

What is the most important Vcell resource for me as a student or faculty?

Most of your questions should be answered in the VCell User Guide It is a very helpful, detailed, precise, and elaborate resource for you to learn about the Virtual Cell and get familiar with its various functions and unique capabilities. It is improved by a dedicated development team at the Center for Cell Modeling and Analysis at UConn Health Center, CT. On the same page, you can find tutorials that show you how to model, step-by-step, and what you need to fill (and some optional tools) in order to run a simulation.

For any more questions on VCell you'd like to see appear on this Twiki collaboration site, you can email Raquell Holmes at rholmes@uchc.edu

-- KhanhNguyen - 10 Jun 2009

Topic revision: r14 - 2011-03-27 - 15:18:16 - RaquellHolmes
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