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  • This topic has 3 replies, 2 voices, and was last updated 3 days ago by GabiM.
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  • March 12, 2025 at 12:39 pm #1908
    GabiM
    Participant

    Hello.
    I wat to perform a experiment similar with the one shown in the Fig 3C of the following paper: Initial Paper: H. Steel, R. Habgood, C. Kelly, A Papachristodoulou, In situ characterisation and manipulation of biological systems with Chi.Bio, PLoS Biology, 2020. Accoding to what i read, that growth rate curve was construcute with the growt rate data collected from the csv file, right? But in order to have growth rate calculated, i have to use the turbidostat mode, is that right?
    Can you give me more details on how this experiment was performed?

    Thanks

    March 23, 2025 at 11:46 am #1909
    harrison
    Keymaster

    Hello!

    Yes, indeed, this was run in turbidostat mode, and using the “zigzag” function in the software.
    You could set it up to do things differently. For example you could calculate approximate/rough growth rates from the pump rate data – i.e. doing a time average of this (and assuming OD is approxiamtely constant over time i.e. population is not net increasing/decreasing) you can get a rate of population growth.
    Or you could even do a series of standard growth curves (without dilution) and fit exponential growth rates to these using any method of your choice (e.g. entirely separate to the Chi.BIo software, such as with R)

    March 27, 2025 at 10:19 am #1910
    GabiM
    Participant

    Hi Harrison.

    So I tried to reproduce the experiment, but I’ve failed again 🙁

    Here’s what I did: set target OD to 0,4 in UI and in the app.py, line 64, I changed the parameter “zig” with 0,1. So that, I imagined my OD shoul have fluctuated between 0,3 and 0,5. Instead, what I got was a graph with OD fluctuating between 0,38 and 0,44. Also, the growth rate was not calculated (the “growth_rate” column of the csv output file is 0).

    What else I have to do to make this work? Can you please give me a detailed explanation?

    Thanks in advance,
    Gabriella

    • This reply was modified 4 days, 2 hours ago by GabiM.
    • This reply was modified 4 days, 2 hours ago by GabiM.
    March 28, 2025 at 11:50 am #1913
    GabiM
    Participant

    Hi Harrison,

    Just wanted to let you know that I’ve managed to get it working. I’m really sorry to have bothered you with so many questions. This is the first time Chi.bio has been used in our department, and understanding it, particularly the code changes necessary to adapt to our aim, has been quite difficult.

    Thanks again for your patience and assistance

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