Pioreactor development log #2

⭐️ This week, we added some updates to the user-interface, a new data-viz, and did our first tests comparing heated and non-heated effects on growth rates.

Doubling time

An alternative way to think about culture growth is to consider how long it takes for the culture to double - called the doubling time. The doubling time has a real-world interpretation, unlike the traditional growth rate measure. Compare the following "The growth rate is 0.4 per hour" vs "The doubling time is 1.7 hours." The latter is much easier to understand, and to make predictions from (ex: culture will be 4x in 3.4 hours). However, the relationship between growth rate and doubling time is trivial: doubling_time = ln(2) / growth_rate.

We've added an configuration option to change the "Implied Growth Rate" chart to "Implied Doubling Time" in the Experiment Overview. We left the default to be "Implied Growth Rate", however, for two reasons:

1. The Pioreactor system internally uses growth rate for inference, and uses growth rate for set points on automations.

2. There are some problems with doubling time when growth rate is negative, or near 0. In Pioreactor, the growth rate can be negative, or near 0, either due to cultures dying, or due to noise. What does a negative doubling time mean? Furthermore, the scale of the doubling time is much larger. A culture's growth rate starts at near 0/h, and maybe gets to 0.5/h. The doubling time goes from near infinity to about 1 over the same time frame. This makes the scale of the graph of the doubling time look ridiculous. A simple solution is to "cap" the graph, but then the user has periods where they see no relevant data. Below we've added this cap, but you can see that it doesn't provide much information.




For now, we've left the option in to change to doubling time, but we turn to the community to see if they have any solutions to how to best graph it! Leave a comment below!

Make your yeast happy with a heated blanket

We've had heating available for a few weeks, but we finally got around to comparing yeast cultures with and without a heated environment. Below are our tests. (We are using some old Kalman Filter parameters, which is why the curves seems a bit wonky - that's been fixed).



Though the absolute yeast mass at the end was pretty close (heated culture just slightly ahead), the maximum observed growth rates were very different. The max growth rate for the heated culture was about 0.685 (doubling time ~1 hour), and the max growth rate for the room temperature culture was 0.385 (doubling time ~1.8h).