Calculating doubling times from dilution volume over time

[harrison]

Hello,

Indeed this is possible. There are two approaches
1) (Best approach) use the In-built “zigzag” function (labelled as “Dither OD” in the UI) which will allow the cells to grow in a zig-zag shape that can yield an accurate calculation of growth rate over time. To do this it would (for example) grow cells from OD 0.45 to 0.55, then rapidly dilute back to 0.45, then repeat. That is, it doesn’t keep them EXACTLY at your OD set point, but dithers the value of OD by a small amount about this point so you can more accurately estimate growth. You can adjust the size of the dither by editing the parameters that drive it in the software (see function ZigZag(M) in app.py)

2) (Worse approach) as you suggested, the system does record the input pump rate over time, which you can then use to crudely estimate growth rate and how this changes over time. All pump behaviour is logged when running an experiment in the output .csv file. The problem with this approach is that the pumps are not paticularly accurate, and the pump rate (i.e. how much liquid ACTUALLY flows when pump set to 0.01) varies significantly between different pumps. So, to use this approach you would need to spend a lot of time calibrating individual pumps so you know how each performs. As I said, approach (1) above is much better..

Harrison

[hludewig]

Thank you very much for answering my question. This has been very helpful!

[mpatterson]

Could you be a little more specific about which line(s) to change if we wanted to grow between, say, an OD of 0.4 and 0.6? Is it in line 61 when creating the sysdata structure, or later on in the Zigzag function itself?

[harrison]

You need to set the OD to 0.5, and thet set the value of the “zig” parameter to 0.1, Then it would go from 0.5-0.1=0.4 up to 0.5+0.1=0.6. This can be done in the sysData structure. Or you could re-code it (i.e. re-write) the zigzag function itself if you prefer.

[mpatterson]

Great, thank you!

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