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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

 

Region Graphing

Region graphing is used to highlight a specific region in the simulation to focus on when we do spatial graphing. Since Spatial Graphing is column based, selecting regions will be column based as well. What we mean by this is that if a graph is 50 rows by 50 columns, then the simulation is split up into 50 columns, each recording the number of molecules in each column. Note that region graphing is only available for "Spatial vs. # Molecules" graphs, and not "Time vs. # Molecules" type graphs.

Step 1

When we start the simulator, a similar screen to the following will appear:

Step 2

To enable a specific region to focus on, rather than all the simulation columns (which happens when we do not specify a region to focus on), we first press the furthest button to the right, the "Select ..." button(this will pause the current simulation, and disable the "Run", "Record ...", "Pause" and "Graph ..."), click and drag with the mouse on a selected portion of the simulation. After doing so, the furthest right button will change it's button name from "Select ..." to "Done" and the region will be highlighted as indicated with a light grayish background as shown below:

Step 3

   After we have finished selecting our region(s), we must notify the simulator that we have finished with highlighting. To do this, we simply depress the "Done" button on the far right. This will then re-enable the "Run", "Record ...", "Pause" and "Graph ..." buttons, allowing us normally functionality. Also the "Done" button will now change itself to a "Clear" button as shown below:

Step 4

To resume the simulation, we simply press the "Run" button and the simulation will continue its operation while the area(s) we selected will be reflected on the current simulation. To get rid of the selected region(s), simply press the "Clear" button on the far right. This will clear any highlighted regions on the simulation and the "Clear" button itself will change into a "Select ..." button again, like the one shown in Step 1 while the simulation is still going on.

When we are ready to graph, we press the "Graph ..." button and select the "Spatial vs. # Molecules" graph type and specify a directory to save to. Then continue with the "OK" button. This will then launch the spatial graphs as seen in the "Spatial vs. Number of Molecules" of the Graph Movie help section.