Objects
In this version, you may create 6 types of Objects, the Objects are the
Following:
The Membrane, DNA, Small Molecule and Protein can be created without rule
restrictions. In order to create a Gene Object, you will need to first create a DNA
Object and then create the Gene object on top of the DNA Object, likewise for
creating a Membrane Protein Object, you will need to first create a Membrane and
then create the Membrane Protein Object on top of the Membrane Object.
Membrane
To create a Membrane Object, select the Membrane Button.
On the Drawing Panel, with the Mouse, click and drag towards the SouthEast and
Release. Upon release, a Properties Window should appear querying the user for
their preferences.
On the left side are the data properties, and on the Right side is the allowable
colors. The Following are the Properties of the Membrane:
| Properties |
Description |
| Height |
The Height of the Membrane as a percentage of the total
Simulator/Screen Size |
| Width |
The Width of the Membrane as a percentage of the total
Simulator/Screen Size |
The preview is available if the user presses "enter" after typing in the value in the
text box (This is different from pressing the button "OK").
Once the user is done, press the "OK" button and the membrane should appear on
the DrawPad.
Troubleshooting: If the membrane Object doesn't not appear then just press
another button, this should refresh the DrawPad Panel and
reveal the membrane Object. If doing the above does not solve it, then you will
have to create another Membrane
Object as it appears the previous Membrane Object was not created properly.
DNA
To create a DNA Object, select the DNA Button.
On the Drawing Panel, with the Mouse, much like the Membrane Object, click and
drag towards the SouthEast and Release. Upon release, a DNA Properties Window
should appear querying the user for their preferences. NOTE: The DNA is a fixed
size.
On the left side are the data properties, and on the Right side is the allowable
colors. The Following are the Properties of the DNA:
| Properties |
Description |
| Name |
The name of this particular Object |
| # of Molecules |
The number of objects this particular object will represent in the
simulator |
Once the user is done, press the "OK" button and the DNA should appear on
the DrawPad.
Troubleshooting: If the DNA Object doesn't not appear then just press another
button, this should refresh the DrawPad Panel and
reveal the DNA Object. If doing the above does not solve it, then you will have
to create another DNA
Object as it appears the previous DNA Object was not created properly.
Gene
To create a Gene Object, you first need to create a DNA Object, once the DNA has
been created, then select the Gene Button
On the Drawing Panel, with the Mouse, click somewhere along the DNA. Upon
release, a Gene Properties Window should appear querying the user for their
preferences. NOTE: If you click somewhere that is not deemed to be on the DNA
Object, an error message will arise, if you click on somewhere that looks to be
on the DNA and the error message still appears, just keep trying towards the
lower area of the DNA.
On the left side are the data properties, and on the Right side is the allowable
colors. The Following are the Properties of the Gene:
| Properties |
Description |
| Name |
The name of this particular Object |
| # of Genes |
The number of Genes this particular object will represent in the
simulator |
| Transcription Rate |
The rate at which this Gene will produce proteins |
| Protein Table |
The proteins this Gene will create |
Once the user is done, press the "OK" button and the Gene should appear on the DrawPad.
Troubleshooting: If the Gene Object doesn't not appear then just press another
button, this should refresh the DrawPad Panel and
reveal the Gene Object. If doing the above does not solve it, then you will have
to create another Gene
Object as it appears the previous Gene Object was not created properly.
Protein
To create a Protein Object, select the Protein Button.
On the Drawing Panel, with the Mouse, click somewhere in the DrawPad. Upon
release, a Protein Properties Window should appear querying the user for their
preferences.
On the left side are the data properties, and on the Right side is the allowable
colors. The Following are the Properties of the Protein:
| Properties |
Description |
| Name |
The name of this particular Object |
| # of Molecules |
The number of objects this particular object will represent in the
simulator |
| Velocity |
The speed at which these Object(s) will be moving at |
| Membrane Permeability |
The ability of this Object to penetrate a Membrane |
| Distribution |
The area on the canvas where the Object will be dispersed |
| Location |
(Not Shown) This appears when a Membrane is created. Specifies where
the Object is relative to the Membrane. |
| Decay Rate |
The rate at which the Object diffuses |
| Creation Rate |
The rate at which the Object is created |
Once the user is done, press the "OK" button and the Protein should appear on
the DrawPad.
Troubleshooting: If the Protein Object doesn't not appear then just press
another button, this should refresh the DrawPad Panel and
reveal the Protein Object. If doing the above does not solve it, then you will
have to create another Protein
Object as it appears the previous Protein Object was not created properly.
Membrane Protein
To create a Membrane Protein Object, the user will first need to create a Membrane Object.
Once the Membrane has been created, then select the Membrane Protein Button.
On the Drawing Panel, with the Mouse, click somewhere along the Membrane. Upon
release, a Membrane Protein Properties Window should appear querying the user
for their preferences. NOTE: If you click somewhere that is not deemed to be on
the Membrane Object, an error message will arise, if you click on somewhere that
looks to be on the Membrane and the error message still appears, just keep
trying and eventually you should get the Membrane Protein to appear.
On the left side are the data properties, and on the Right side is the allowable
colors. The Following are the Properties of the Membrane Protein:
| Properties |
Description |
| Name |
The name of this particular Object |
| # of Molecules |
The number of objects this particular object will represent in the
simulator |
| Velocity |
The speed at which these Object(s) will be moving at |
| Decay Rate |
The rate at which the Object diffuses |
| Creation Rate |
The rate at which the Object diffuses |
Once the user is done, press the "OK" button and the Gene should appear on the DrawPad.
Troubleshooting: If the Membrane Protein Object doesn't not appear then just
press another button, this should refresh the DrawPad Panel and reveal the
Membrane Protein Object. If doing the above does not solve it, then you will
have to create another Membrane Protein Object as it appears the previous
Membrane Protein Object was not created properly.
Small Molecule
To create a Small Molecule Object, select the Small Molecule Button.
On the Drawing Panel, with the Mouse, click somewhere in the DrawPad. Upon
release, a Small Molecule Properties Window should appear querying the user for
their preferences.
On the left side are the data properties, and on the Right side is the allowable
colors. The Following are the Properties of the Small Molecule:
| Properties |
Description |
| Name |
The name of this particular Object |
| # of Molecules |
The number of objects this particular object will represent in the
simulator |
| Velocity |
The speed at which these Object(s) will be moving at |
| Membrane Permeability |
The ability of this Object to penetrate a Membrane |
| Distribution |
The area on the canvas where the Object will be dispersed |
| Location |
(Not Shown) This appears when a Membrane is created. Specifies where
the Object is relative to the Membrane. |
| Decay Rate |
The rate at which the Object diffuses |
| Creation Rate |
TThe rate at which the Object diffuses |
Once the user is done, press the "OK" button and the Small Molecule should
appear on the DrawPad.
Troubleshooting: If the Small Molecule Object doesn't not appear then just press
another button, this should refresh the DrawPad Panel and reveal the Small
Molecule Object. If doing the above does not solve it, then you will have to
create another Small Molecule Object as it appears the previous Small Molecule
Object was not created properly.
