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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

 

Menu

There are 4 Menus - File, Edit, Run and Help

File has the following items:

New - Creates a new SimCell Application
Open - Opens a previously saved SimCell File or Opens a SimCell Animation
Save - Saves the current objects on Canvas to the current file opened
Save As - Saves the current objects on Canvas to a user specified file
Print - Prints an image of the Canvas
Export JPG - Exports an image of the Canvas to a user specified jpg file
Close - Closes this SimCell Application
Exit - Closes all SimCell Applications that are opened
 


Edit has the following items:

Undo - Undo a create, erase or clear action
Clear - Clears the Canvas
Preferences - Set Simulation Preferences
Notepad - For saving header notes (Non-Canvas)
Text Labels - Remove and Shows the names of the Object on the Canvas
 


Run has the following items:

Run - Run the Simulation based on the current Objects on the Draw Pad
Object Information - Information on each type of Object and Interactions
 


Help has the following items:

Help - Opens the Help Page
 


File

New
Use this to create another SimCell Application.

Open
Use this to open a SimCell file, a SimCell file can be any of the 3

.SCF
.SCM
.SCGM

An .SCF file is a file that consists of Objects from a previously saved Canvas along with Notes and Preferences.

An .SCM file is Animation file listing the image files involved in the Simulation animation and the animation options involved, opening this file will open up an Animation Window.



For More Information See: Screenshots

An .SCGM file is Animation file much like an .SCM file. The difference is an .SCM file consists of Screenshots of the Simulation whereas an .SCGM file consists of Screenshots of the Graphs generated from Spatial data gathered during the Simulation.



For More Information See: Graph

Save and Save As
Use this to save the current objects on the DrawPad to a file as an .SCF file, this will prompt the user to specify a file if no filename is currently loaded.

Print
Use this to print the image on the DrawPad. This will open a generic Print Command Window. Press Print to begin printing.

Export JPG
Use this to save the image on the DrawPad as a JPG. This will prompt the user for a name. Press OK to save the Image.

Close and Exit
Close will close the current SimCell Application. Exit will close all SimCell Applications that were created as well as the current SimCell Application.
 


Edit

Undo
Use this to Undo Actions the user has done, it allows the user to undo a move, undo a sequence of creates, undo a sequence of erases, and undo a clear screen. To undo, just select the undo menu item under Menu Edit.

Clear
Use this to clear the whole Draw Pad.


Preferences
Use this to preset preferences for the simulation. The following field are editable:
 

Properties Description
Grid Size: Width This is the number of columns that the Simulator will consist of
Grid Size: Height This is the number of rows that the Simulator will consist of
Random Number Seed This is the Random Number Seed Generator, this number represents a single random sequence the simulator will use to generate object movements. Leave this at 0 if you want one generated for you


Interval Length is currently hardcoded as 100 iterations at the moment, this field is used for the graphing - where every Interval represents when the graph is saved for the Spatial Graph and represents each x column at a certain time for the Number of Molecules Graph.



Notepad
Use this to Save Notes to a file as a header. Notes will be visible if we opened a previously saved file. To be able to save notes, we must have a working filename to save to, to issue a working filename, just save the canvas.

Text Labels
Use to show or hide objects names on the Draw Pad.
 


Run

Run
Use this to start the Simulation based on the Objects that are present in the Draw Pad.

For more Information See: Simulator

Object Information
Use this to see tabled information regarding each object and Interactions present on the Draw Pad. Each Item on the Menu will be selected if there is at least one Object of that type on the Canvas. Example of a generated Table is shown below:



 


Help

Help
Use this open the Help Page. Help Page opens up this page.