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Improve flexibility of screen design #62

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tlnagy opened this issue Apr 21, 2023 · 0 comments
Open

Improve flexibility of screen design #62

tlnagy opened this issue Apr 21, 2023 · 0 comments

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@tlnagy
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tlnagy commented Apr 21, 2023

Crispulator could benefit from some refactoring to improve its handling of custom screen designs, particularly for growth screens. The current structure is:

  1. transfect = transfection + growth to bottleneck representation
  2. select = growth, subsample to bottleneck representation, repeat for num_bottlenecks
  3. sequencing

The mixture of growth in with the other steps isn't intuitive and with #60 merged, select doesn't require subsampling every step after grow!. In these cases, num_bottlenecks can now refer to the number of doublings (because now there isn't subsampling, only growth). That's confusing! Additionally, having to bump the bottleneck_representation to prevent the subsampling in select is an ugly workaround.

The better solution would be expose grow!, allow it to handle multiple doublings, and redefine select for growth screens to only refer to the subsampling step.

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