Endy:Notebook/Sortostat Paper

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Current Issues

  1. What is the story of the paper? Or, how are we packaging the paper?
    • Continuous culture is important, to both science and biotech. Screening, selection, and directed evolution are important too, again across science and technology. Coupling between the two has been limited (be careful to define this existing coupling fairly, precisely, and constructively). Bringing continuous culture, with programmable screens and selections is an important next step, again impacting both science and technology. Thus, the sortostat.
  2. What statistical tests should be used to evaluate the PDFs?
  3. What would a user of the sortostat want to know in choosing to use the device (or not), or in configuring a run?
    • What is the strongest selective pressure that can be applied to a mixed population with equal growth rates?
    • What is the biggest disadvantaged growth difference that can be promoted / maintained?
  4. Look at related papers?
  5. Is the sortostat, as implemented, an instance of a larger family of devices? Is this issues specific to the modeling? This seems like a big project.

Goals for June 4 meeting

  • Statistical tests for distributions
    • Chi-squared goodness of fit for binomial distributions
  • Regenerate all data plots
    • Done. Feeling good with the data in Jason's hands (and now it is backed up too). Noticed that 4/21 run, at the end of the run, the stupid memory leak in Lab View flooded, resulting in image acquisition continuing, but acquisition halting, so another 40 hours of data acquired, but no directed sorting. Data needs to be analyzed.
  • Sketch modeling plan to answer two classes of "user" questions
    • No time, yet. Remember to use the simplest, most first-order model to answer these questions, noting assumptions. Consider two things. What is the average and variance of the cells showing up in the reactor. What is the current make-up of the cells (50:50, 80:20, 99:1)? How does available selective pressure vary as a function of these two variables?
  • Make a paragraph-level outline

Goals for June 19 meeting

  • Complete processing and analysis of remaining 4/21 data
  • Figure out Chi-square for distributions
  • Implemented model and answered question(s)
  • Paragraph level outline

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