Sortostat/Notebook

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

 * 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?
 * 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

 * Sortostat/Methods/Receiving chips