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SimCell Help

1. Introduction
2. Create
    2.1 Objects
  2.1.1 Membrane
  2.1.2 DNA
  2.1.3 Gene
  2.1.4 Protein
  2.1.5 Membrane Protein
  2.1.6 Small Molecule
    2.2 Interactions
  2.2.1 Transport
  2.2.2 Bind and Stick
  2.2.3 Touch and Go
    2.3 Others
3. Menu
  2.1.1 File
  2.1.2 Edit
  2.1.3 Run
  2.1.4 Help
4. Simulator
    4.1 Screenshot
    4.2 Graph
    4.3 Region Graphing

 

Graph

Step 1

When the user depresses the Graph button in the Simulator Window, the following Window will appear

 

Graph Types

The user can choose between a Time vs. Number of Molecules type of graph or a Spatial vs. Number of Molecules type of graph   

    Time vs. Number of Molecules

   

    This type of graph places the Number of Molecules on the Y axis and the Amount of Time Elapsed on the X axis. Time is based on the number of Intervals that has passed. The default Interval Length is every 100 Iterations.
 

    Spatial vs. Number of Molecules

   

    This type of graph places the Number of Molecules on the Y axis and each cell column on the X axis. Each cell column is calculated to determine the amount of each molecule that resides in that column. Each graph image is an interval, every interval is 100 Iterations.

 

Filename

This is where the user specifies the name of the header file and the path where the screenshot images and the screenshot header file will be saved to

Step 2

  

   Clicking on the "Save As" button will result in the exporting JPG images of the graphs.

      Time vs. Number of Molecules

          If displaying this type of graph, the "Save As" will export a single jpg file that represents the exact graph shown.

      Spatial vs. Number of Molecules

          If displaying this type of graph, the "Save As" will export a series of jpgs at each interval as well as a .SCGM file, this File is the header file for the images and can be used to view the graphs as an animation when the user opens the .SCGM file under the SimCell User Interface Open Graphs Menu Item.