# Sortostat/Notebook

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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=== | ||

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*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== |

## Revision as of 14:01, 17 September 2007

## Contents |

## 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?)

## LabView

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

## 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.

## References

- Sortostat/Foundry report card - post notes on each chip fabricated so can document common failure points in fabrication to better avoid them.