Sortostat/Notebook - Revision history

Jason R. Kelly: /* Analytical model */

2007-12-23T16:20:19Z

Analytical model

←Older revision		Revision as of 16:20, 23 December 2007
Line 45:		Line 45:
	*put the cleaning period / dilution rate formula derivations on the wiki.		*put the cleaning period / dilution rate formula derivations on the wiki.
	*write up the chemostat equations as they relate to the SS cell concentration (e.g. limiting substrate? Should we reduce the concentration of glycerol?)		*write up the chemostat equations as they relate to the SS cell concentration (e.g. limiting substrate? Should we reduce the concentration of glycerol?)
		+	*These come from the SortostatTiming.m matlab model:
	**12.5 min between cleaning (doubling time = 0.55)		**12.5 min between cleaning (doubling time = 0.55)
	**13.6 min between cleaning (doubling time = 0.60)		**13.6 min between cleaning (doubling time = 0.60)
Line 51:		Line 52:
	**17min between cleaning (doubling time = 0.75)		**17min between cleaning (doubling time = 0.75)
	**18.2min between cleaning (doubling time = 0.8)		**18.2min between cleaning (doubling time = 0.8)
-	**19.~~2min~~ between cleaning (doubling time = 0.85hr)	+	**19.3min between cleaning (doubling time = 0.85hr)
		+	**20.5min between cleaning (doubling time = 0.9hr)
		+	**21.6min between cleaning (doubling time = 0.95hr)
		+	**22.7min between cleaning (doubling time = 1hr)
		+	**23.9min between cleaning (doubling time = 1.5hr)

	==LabView==		==LabView==

Jason R. Kelly: /* Experiments */

2007-12-21T14:25:48Z

Experiments

←Older revision		Revision as of 14:25, 21 December 2007
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	==Experiments==		==Experiments==
	*[[Sortostat/Experiments/Two reactor chip]]		*[[Sortostat/Experiments/Two reactor chip]]
		+	*[[Sortostat/Troubleshooting]]
	===Future Experiments===		===Future Experiments===
	'''replace bulb before these experiments'''		'''replace bulb before these experiments'''

Jason R. Kelly: /* To Do List */

2007-10-05T20:10:40Z

To Do List

←Older revision		Revision as of 20:10, 5 October 2007
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	**Does the leak influence the timing of the events, by making the image processing take too long? (e.g. why does the timing graph get noisy after awhile?)		**Does the leak influence the timing of the events, by making the image processing take too long? (e.g. why does the timing graph get noisy after awhile?)
	**Is it the MATLAB thread that blows up or the LabView? it's MATLAB.		**Is it the MATLAB thread that blows up or the LabView? it's MATLAB.
		+	**[http://www.mathworks.com/support/tech-notes/1100/1106.html MATLAB help page here might be useful.]
	*output the direction of sorting to the output file		*output the direction of sorting to the output file
-	*Clean up the Image Processing MATLAB scripts	+	*Clean up the Image Processing MATLAB scripts

	==Done==		==Done==

Jason R. Kelly at 18:03, 17 September 2007

2007-09-17T18:03:46Z

←Older revision		Revision as of 18:03, 17 September 2007
Line 1:		Line 1:
		+	==To Do List==
		+	*Figure out the MATLAB memory leak
		+	**I suspect this is because I'm not closing the image files properly in the MATLAB script that runs, or it could be something more annoying.
		+	**Does the leak influence the timing of the events, by making the image processing take too long? (e.g. why does the timing graph get noisy after awhile?)
		+	**Is it the MATLAB thread that blows up or the LabView? it's MATLAB.
		+	*output the direction of sorting to the output file
		+	*Clean up the Image Processing MATLAB scripts
		+
		+	==Done==
		+	*Why do I see any variability in the timing? Timing between cleaning events is rock solid, the timing between sorts is influenced by the time it takes to process the image.
		+	*Change the code so that when flipping based on the CFP it is the moving average that is used, rather than a single image.
		+	*Make the list of experiments to evaluate the device performance limits.
		+	**Sorting at various dilution rates, followed by a sort to extinction.
		+
	==Experiments==		==Experiments==
-	*[[Sortostat/Methods/Receiving chips]]
	*[[Sortostat/Experiments/Two reactor chip]]		*[[Sortostat/Experiments/Two reactor chip]]
	===Future Experiments===		===Future Experiments===
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	*why do we need to initialize the load paraemters array?		*why do we need to initialize the load paraemters array?

-	==~~To Do List~~==	+	==Methods==
-	*~~Figure out the MATLAB memory leak~~	+	*[[Sortostat/Methods/Receiving chips]]
-	**I suspect this is because I'm not closing the image files properly in the MATLAB script that runs, or it could be something more annoying.	+
-	**Does the leak influence the timing of the events, by making the image processing take too long? (e.g. why does the timing graph get noisy after awhile?)	+
-	**Is it the MATLAB thread that blows up or the LabView? it's MATLAB.	+
-	*output the direction of sorting to the output file	+
-	*Clean up the Image Processing MATLAB scripts	+

-	~~==Done==~~
-	*Why do I see any variability in the timing? Timing between cleaning events is rock solid, the timing between sorts is influenced by the time it takes to process the image.
-	*Change the code so that when flipping based on the CFP it is the moving average that is used, rather than a single image.
-	*Make the list of experiments to evaluate the device performance limits.
-	**Sorting at various dilution rates, followed by a sort to extinction.
	==References==		==References==
	*[[Sortostat/Foundry report card]] - post notes on each chip fabricated so can document common failure points in fabrication to better avoid them.		*[[Sortostat/Foundry report card]] - post notes on each chip fabricated so can document common failure points in fabrication to better avoid them.

Jason R. Kelly: /* Experiments */

2007-09-17T18:03:09Z

Experiments

←Older revision		Revision as of 18:03, 17 September 2007
Line 1:		Line 1:
	==Experiments==		==Experiments==
		+	*[[Sortostat/Methods/Receiving chips]]
	*[[Sortostat/Experiments/Two reactor chip]]		*[[Sortostat/Experiments/Two reactor chip]]
	===Future Experiments===		===Future Experiments===

Jason R. Kelly: /* Analytical model */

2007-09-17T18:02:27Z

Analytical model

←Older revision		Revision as of 18:02, 17 September 2007
Line 29:		Line 29:
	*put the cleaning period / dilution rate formula derivations on the wiki.		*put the cleaning period / dilution rate formula derivations on the wiki.
	*write up the chemostat equations as they relate to the SS cell concentration (e.g. limiting substrate? Should we reduce the concentration of glycerol?)		*write up the chemostat equations as they relate to the SS cell concentration (e.g. limiting substrate? Should we reduce the concentration of glycerol?)
		+	**12.5 min between cleaning (doubling time = 0.55)
		+	**13.6 min between cleaning (doubling time = 0.60)
		+	**14.8 min between cleaning (doubling time = 0.65)
		+	**15.9 min between cleaning (doubling time = 0.7)
		+	**17min between cleaning (doubling time = 0.75)
		+	**18.2min between cleaning (doubling time = 0.8)
		+	**19.2min between cleaning (doubling time = 0.85hr)

	==LabView==		==LabView==

Jason R. Kelly at 18:01, 17 September 2007

2007-09-17T18:01:42Z

←Older revision		Revision as of 18:01, 17 September 2007
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	**No, looked at this before last lab meeting, but should write it up.		**No, looked at this before last lab meeting, but should write it up.
	*Do fluctuations in the total cell count correlate with anything?		*Do fluctuations in the total cell count correlate with anything?
		+	*2/18/06 lab notebook page has some information about the appropriate sorting volume to use in the model, move this to the wiki

	===Output===		===Output===
Line 24:		Line 25:
	*Sortostat Modeling Probability Distributions doc - description of the modeling of the probability distributions for the number of cells in the sorting chamber and how many are CFP or YFP.		*Sortostat Modeling Probability Distributions doc - description of the modeling of the probability distributions for the number of cells in the sorting chamber and how many are CFP or YFP.
	*Sortostat Modeling Stochastic Sim doc - description of the stochastic simulation of Sortostat performance.		*Sortostat Modeling Stochastic Sim doc - description of the stochastic simulation of Sortostat performance.
		+
		+	===Analytical model===
		+	*put the cleaning period / dilution rate formula derivations on the wiki.
		+	*write up the chemostat equations as they relate to the SS cell concentration (e.g. limiting substrate? Should we reduce the concentration of glycerol?)
		+
		+	==LabView==
		+	*why do we need to initialize the load paraemters array?

	==To Do List==		==To Do List==

Jason R. Kelly: /* Future Experiments */

2007-08-29T18:41:51Z

Future Experiments

←Older revision		Revision as of 18:41, 29 August 2007
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	*Zig-zag experiment with different dilution rate (e.g. different total number of cells).		*Zig-zag experiment with different dilution rate (e.g. different total number of cells).
	*Get the exact size of sorting chamber by cell counting		*Get the exact size of sorting chamber by cell counting
		+	*F2620 is in MG1655 whose flagella might cause a problem
		+	**Need to co-transform with RFP expression plasmid anyway.
		+	*We already have the zig-zag automated, but should include a "pulse" as well (e.g. /-\_/-\) where it has regions with no selection.

	==Modeling==		==Modeling==

Jason R. Kelly: /* Future Experiments */

2007-08-29T16:06:57Z

Future Experiments

←Older revision		Revision as of 16:06, 29 August 2007
Line 8:		Line 8:
	**Could demonstrate this with a slower growing CFP vs YFP or via something like F2620.		**Could demonstrate this with a slower growing CFP vs YFP or via something like F2620.
	*Zig-zag experiment with different dilution rate (e.g. different total number of cells).		*Zig-zag experiment with different dilution rate (e.g. different total number of cells).
		+	*Get the exact size of sorting chamber by cell counting

	==Modeling==		==Modeling==

Jason R. Kelly at 15:54, 25 August 2007

2007-08-25T15:54:32Z

←Older revision		Revision as of 15:54, 25 August 2007
Line 3:		Line 3:
	===Future Experiments===		===Future Experiments===
	'''replace bulb before these experiments'''		'''replace bulb before these experiments'''
-	**check on pH of the media if we are adding AHL, it needs to be <8 for AHL to be stable.	+	*check on pH of the media if we are adding AHL, it needs to be <8 for AHL to be stable.
	*Zig-zag run where we vary from 0.4 to 0.6 so that we can get more sampling of the selective pressure.		*Zig-zag run where we vary from 0.4 to 0.6 so that we can get more sampling of the selective pressure.
	*Maintenance of a slower growing variant vs. a faster growing "mutant".		*Maintenance of a slower growing variant vs. a faster growing "mutant".