Sortostat/Notebook
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==To Do List== | ==To Do List== | ||
*Figure out the MATLAB memory leak | *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. | **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?) | **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. |
| + | **[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. | ||
| - | * | + | **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? | ||
| - | * | + | *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== | ||
| + | *[[Sortostat/Methods/Receiving chips]] | ||
| + | |||
==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
- Sortostat/Foundry report card - post notes on each chip fabricated so can document common failure points in fabrication to better avoid them.
