RedicGUI - Revision history

Bradley Monk: Adding image note: These items will be used as the baseline parameters for the PSD-95 clusters. If ''Homeostatic Scaling'' is turned ON, these values will r

2013-09-08T01:30:17Z

Adding image note: These items will be used as the baseline parameters for the PSD-95 clusters. If ''Homeostatic Scaling'' is turned ON, these values will r

← Older revision		Revision as of 18:30, 7 September 2013
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	This run item will delete all particles in PSD1 at exactly 950 steps into the simulation. I will soon add more control over this function from the GUI.		This run item will delete all particles in PSD1 at exactly 950 steps into the simulation. I will soon add more control over this function from the GUI.
	{{ImageNoteEnd\|id=14}}		{{ImageNoteEnd\|id=14}}
			{{ImageNote\|id=15\|x=536\|y=453\|w=199\|h=138\|dimx=871\|dimy=644\|style=2}}
			These items will be used as the baseline parameters for the PSD-95 clusters. If ''Homeostatic Scaling'' is turned ON, these values will remain the baseline values while the total number of AMPAR particles in PSDs is within the range of high and low ''Homeostatic tolerance' values specified by the user. When the total AMPAR particles in PSDs is outside of this range, the Cluster parameters will be adjusted allowing for growth or shrinking. When the total number of AMPAR particles in PSDs returns to a value within the tolerance range, the values set here will be restored.
			{{ImageNoteEnd\|id=15}}
	</div>		</div>

Bradley Monk: Adding image note: This run item will delete all particles in PSD1 at exactly 950 steps into the simulation. I will soon add more control over this function

2013-09-08T01:25:41Z

Adding image note: This run item will delete all particles in PSD1 at exactly 950 steps into the simulation. I will soon add more control over this function

← Older revision		Revision as of 18:25, 7 September 2013
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	This run item will trace one particle over the specified number of steps drawing the particle path as it moves.		This run item will trace one particle over the specified number of steps drawing the particle path as it moves.
	{{ImageNoteEnd\|id=13}}		{{ImageNoteEnd\|id=13}}
			{{ImageNote\|id=14\|x=545\|y=370\|w=61\|h=28\|dimx=871\|dimy=644\|style=2}}
			This run item will delete all particles in PSD1 at exactly 950 steps into the simulation. I will soon add more control over this function from the GUI.
			{{ImageNoteEnd\|id=14}}
	</div>		</div>

Bradley Monk: Adding image note: This run item will trace one particle over the specified number of steps drawing the particle path as it moves.

2013-09-08T01:24:23Z

Adding image note: This run item will trace one particle over the specified number of steps drawing the particle path as it moves.

← Older revision		Revision as of 18:24, 7 September 2013
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	This will cause a burst of 100 Calcium-representing particles to appear in PSD2. This will influence several parameters related to the cluster simulation, briefly giving the cluster a higher potential for growth. The effects of this function are the most dramatic when homeostatic scaling is turned on, and when a burst happens during a "scaling-down" period. I will be adding several fields to the GUI providing more control over this run item directly from the GUI.		This will cause a burst of 100 Calcium-representing particles to appear in PSD2. This will influence several parameters related to the cluster simulation, briefly giving the cluster a higher potential for growth. The effects of this function are the most dramatic when homeostatic scaling is turned on, and when a burst happens during a "scaling-down" period. I will be adding several fields to the GUI providing more control over this run item directly from the GUI.
	{{ImageNoteEnd\|id=12}}		{{ImageNoteEnd\|id=12}}
			{{ImageNote\|id=13\|x=545\|y=343\|w=124\|h=24\|dimx=871\|dimy=644\|style=2}}
			This run item will trace one particle over the specified number of steps drawing the particle path as it moves.
			{{ImageNoteEnd\|id=13}}
	</div>		</div>

Bradley Monk: Adding image note: This will cause a burst of 100 Calcium-representing particles to appear in PSD2. This will influence several parameters related to the cl

2013-09-08T01:23:04Z

Adding image note: This will cause a burst of 100 Calcium-representing particles to appear in PSD2. This will influence several parameters related to the cl

← Older revision		Revision as of 18:23, 7 September 2013
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	psd.D = 3 / 49 = .05		psd.D = 3 / 49 = .05
	{{ImageNoteEnd\|id=11}}		{{ImageNoteEnd\|id=11}}
			{{ImageNote\|id=12\|x=547\|y=317\|w=106\|h=21\|dimx=871\|dimy=644\|style=2}}
			This will cause a burst of 100 Calcium-representing particles to appear in PSD2. This will influence several parameters related to the cluster simulation, briefly giving the cluster a higher potential for growth. The effects of this function are the most dramatic when homeostatic scaling is turned on, and when a burst happens during a "scaling-down" period. I will be adding several fields to the GUI providing more control over this run item directly from the GUI.
			{{ImageNoteEnd\|id=12}}
	</div>		</div>

Bradley Monk: Adding image note: When checked, the diffusion rate of the PSDs will be set by a PSD-95 cluster simulation instead of the manually entered value. I did this

2013-09-08T01:17:32Z

Adding image note: When checked, the diffusion rate of the PSDs will be set by a PSD-95 cluster simulation instead of the manually entered value. I did this

← Older revision		Revision as of 18:17, 7 September 2013
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	When this is checked (ON), when the total number of particles in PSD areas falls outside of the ''Homeostatic tolerance' range specified, this function will make adjustments to several parameters controlling Cluster growth and stability.		When this is checked (ON), when the total number of particles in PSD areas falls outside of the ''Homeostatic tolerance' range specified, this function will make adjustments to several parameters controlling Cluster growth and stability.
	{{ImageNoteEnd\|id=10}}		{{ImageNoteEnd\|id=10}}
			{{ImageNote\|id=11\|x=546\|y=288\|w=110\|h=24\|dimx=871\|dimy=644\|style=2}}
			When checked, the diffusion rate of the PSDs will be set by a PSD-95 cluster simulation instead of the manually entered value. I did this because there's no reason to have both a manually set PSD diffusion rate and the cluster simulation running at the same time (since the clusters would be having no influence on anything happening in the diffusion simulation -- essentially you'd just be running two independent simulations).

			Because the default starting cluster size is 7x7, or 49 total cluster molecules, and diffusion is scaled as a function of both the extrasynaptic diffusion rate (you do specify this) in the following way:

			psd.D = D.es / N.cluster

			psd.D = 3 / 49 = .05
			{{ImageNoteEnd\|id=11}}
	</div>		</div>

Bradley Monk: Adding image note: When this is checked (ON), when the total number of particles in PSD areas falls outside of the ''Homeostatic tolerance' range specified,

2013-09-08T01:04:28Z

Adding image note: When this is checked (ON), when the total number of particles in PSD areas falls outside of the ''Homeostatic tolerance' range specified,

← Older revision		Revision as of 18:04, 7 September 2013
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	This is a short sanity check of diffusion rate values. When this is checked, it overrides the values for all other Parameters and Run Items except for ''Particle Diffusion Rates (D)''. It will generate 100 particles and run them through 100 steps at the diffusion rate for the item specified in the dropdown menu. It will then track the paths of those molecules and compute the MSD and D for those paths. It can be used as a check to make sure the diffusion rate specified is actually producing particle diffusion at the desired rate.		This is a short sanity check of diffusion rate values. When this is checked, it overrides the values for all other Parameters and Run Items except for ''Particle Diffusion Rates (D)''. It will generate 100 particles and run them through 100 steps at the diffusion rate for the item specified in the dropdown menu. It will then track the paths of those molecules and compute the MSD and D for those paths. It can be used as a check to make sure the diffusion rate specified is actually producing particle diffusion at the desired rate.
	{{ImageNoteEnd\|id=9}}		{{ImageNoteEnd\|id=9}}
			{{ImageNote\|id=10\|x=544\|y=256\|w=141\|h=28\|dimx=871\|dimy=644\|style=2}}
			When this is checked (ON), when the total number of particles in PSD areas falls outside of the ''Homeostatic tolerance' range specified, this function will make adjustments to several parameters controlling Cluster growth and stability.
			{{ImageNoteEnd\|id=10}}
	</div>		</div>

Bradley Monk: Adding image note: This is a short sanity check of diffusion rate values. When this is checked, it overrides the values for all other Parameters and Run Ite

2013-09-08T00:59:15Z

Adding image note: This is a short sanity check of diffusion rate values. When this is checked, it overrides the values for all other Parameters and Run Ite

← Older revision		Revision as of 17:59, 7 September 2013
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	When checked (ON) this will make half of the AMPAR dots perform like GluR1 particles. The only major difference between GluR1 and the default (GluR2) particle, is that GluR1 particles have a faster diffusion rate in the PSD (center) region compared to the periPSD (periphery) region. Currently, this diffusion rate differences is scaled such that, for GluR2 only, the periPSD diffusion rate is 2x the PSD (center) diffusion rate		When checked (ON) this will make half of the AMPAR dots perform like GluR1 particles. The only major difference between GluR1 and the default (GluR2) particle, is that GluR1 particles have a faster diffusion rate in the PSD (center) region compared to the periPSD (periphery) region. Currently, this diffusion rate differences is scaled such that, for GluR2 only, the periPSD diffusion rate is 2x the PSD (center) diffusion rate
	{{ImageNoteEnd\|id=8}}		{{ImageNoteEnd\|id=8}}
			{{ImageNote\|id=9\|x=544\|y=227\|w=213\|h=27\|dimx=871\|dimy=644\|style=2}}
			This is a short sanity check of diffusion rate values. When this is checked, it overrides the values for all other Parameters and Run Items except for ''Particle Diffusion Rates (D)''. It will generate 100 particles and run them through 100 steps at the diffusion rate for the item specified in the dropdown menu. It will then track the paths of those molecules and compute the MSD and D for those paths. It can be used as a check to make sure the diffusion rate specified is actually producing particle diffusion at the desired rate.
			{{ImageNoteEnd\|id=9}}
	</div>		</div>

Bradley Monk: Adding image note: When checked (ON) this will make half of the AMPAR dots perform like GluR1 particles. The only major difference between GluR1 and the def

2013-09-08T00:54:23Z

Adding image note: When checked (ON) this will make half of the AMPAR dots perform like GluR1 particles. The only major difference between GluR1 and the def

← Older revision		Revision as of 17:54, 7 September 2013
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	When checked (ON), these will provide visuals for a live 2D or 3D simulation. Keep in mind, these both require a high amount of processor time to render, which can significantly slow down the simulation. If you are only interested in the final output, turn them off.		When checked (ON), these will provide visuals for a live 2D or 3D simulation. Keep in mind, these both require a high amount of processor time to render, which can significantly slow down the simulation. If you are only interested in the final output, turn them off.
	{{ImageNoteEnd\|id=7}}		{{ImageNoteEnd\|id=7}}
			{{ImageNote\|id=8\|x=544\|y=198\|w=130\|h=26\|dimx=871\|dimy=644\|style=2}}
			When checked (ON) this will make half of the AMPAR dots perform like GluR1 particles. The only major difference between GluR1 and the default (GluR2) particle, is that GluR1 particles have a faster diffusion rate in the PSD (center) region compared to the periPSD (periphery) region. Currently, this diffusion rate differences is scaled such that, for GluR2 only, the periPSD diffusion rate is 2x the PSD (center) diffusion rate
			{{ImageNoteEnd\|id=8}}
	</div>		</div>

Bradley Monk: Adding image note: When checked (ON), these will provide visuals for a live 2D or 3D simulation. Keep in mind, these both require a high amount of processor

2013-09-08T00:49:49Z

Adding image note: When checked (ON), these will provide visuals for a live 2D or 3D simulation. Keep in mind, these both require a high amount of processor

← Older revision		Revision as of 17:49, 7 September 2013
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	Keep these unchecked (OFF). These are experimental items, and may cause the simulation to produce odd behavior.		Keep these unchecked (OFF). These are experimental items, and may cause the simulation to produce odd behavior.
	{{ImageNoteEnd\|id=6}}		{{ImageNoteEnd\|id=6}}
			{{ImageNote\|id=7\|x=545\|y=144\|w=119\|h=53\|dimx=871\|dimy=644\|style=2}}
			When checked (ON), these will provide visuals for a live 2D or 3D simulation. Keep in mind, these both require a high amount of processor time to render, which can significantly slow down the simulation. If you are only interested in the final output, turn them off.
			{{ImageNoteEnd\|id=7}}
	</div>		</div>

Bradley Monk: Adding image note: Keep these unchecked (OFF). These are experimental items, and may cause the simulation to produce odd behavior.

2013-09-08T00:47:16Z

Adding image note: Keep these unchecked (OFF). These are experimental items, and may cause the simulation to produce odd behavior.

← Older revision		Revision as of 17:47, 7 September 2013
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	** Homeostatic Regulation (ON)		** Homeostatic Regulation (ON)
	{{ImageNoteEnd\|id=5}}		{{ImageNoteEnd\|id=5}}
			{{ImageNote\|id=6\|x=546\|y=89\|w=132\|h=50\|dimx=871\|dimy=644\|style=2}}
			Keep these unchecked (OFF). These are experimental items, and may cause the simulation to produce odd behavior.
			{{ImageNoteEnd\|id=6}}
	</div>		</div>