Sortostat/Notebook

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Current revision (12:20, 23 December 2007) (view source)
(Analytical model)
 
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==Experiments==
 
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*[[Sortostat/Experiments/Two reactor chip]]
 
-
 
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==Modeling==
 
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*[[Sortostat/Model]]
 
-
 
==To Do List==
==To Do List==
*Figure out the MATLAB memory leak
*Figure out the MATLAB memory leak
Line 10: Line 4:
**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
 +
 +
==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.
*Make the list of experiments to evaluate the device performance limits.
-
*Work on the model and compare to experimental results.
+
**Sorting at various dilution rates, followed by a sort to extinction.
 +
 
 +
==Experiments==
 +
*[[Sortostat/Experiments/Two reactor chip]]
 +
*[[Sortostat/Troubleshooting]]
 +
===Future 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.
 +
*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".
 +
**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).
 +
*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==
 +
*[[Sortostat/Model]]
*How much faster can we drive it given the timing?
*How much faster can we drive it given the timing?
*Are there more or less cells in a sort vs a screen?
*Are there more or less cells in a sort vs a screen?
**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?
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*Move all the pictures from the last run to the same HD (back up the ones from the long zigzag run).
+
*2/18/06 lab notebook page has some information about the appropriate sorting volume to use in the model, move this to the wiki
-
**Waiting for the new drive to come in.
+
 
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*Clean up the MATLAB scripts (particularly the image processing, have lots of old versions lying around).
+
===Output===
-
*Why do I see any variability in the timing?
+
*Sortostat mFiles doc - list of all the mfiles that matter (except the image processing).  These are all commented and cleaned up at this point.  
-
*Update MATLAB since the license is running out.
+
*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.
 +
 
 +
===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?)
 +
*These come from the SortostatTiming.m matlab model:
 +
**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)
 +
**19.3min 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==
 +
*why do we need to initialize the load paraemters array?
 +
 
 +
==Methods==
 +
*[[Sortostat/Methods/Receiving chips]]
-
==Done==
 
-
*Change the code so that when flipping based on the CFP it is the moving average that is used, rather than a single image.
 
==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.

Current revision

Contents

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.
    • MATLAB help page here might be useful.
  • 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

Future 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.
  • 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".
    • 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).
  • 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

  • Sortostat/Model
  • How much faster can we drive it given the timing?
  • Are there more or less cells in a sort vs a screen?
    • No, looked at this before last lab meeting, but should write it up.
  • 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

  • Sortostat mFiles doc - list of all the mfiles that matter (except the image processing). These are all commented and cleaned up at this point.
  • 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.

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?)
  • These come from the SortostatTiming.m matlab model:
    • 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)
    • 19.3min 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

  • why do we need to initialize the load paraemters array?

Methods


References

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