Calculate Growth Rate from Cell Numbers

[mcnaughtonadm]

We have:

1. Cell number data for each condition
2. Growth Rates for the bioreactor (1/h units) $\frac{g_{biomass} }{ (g_{biomass} \cdot hr)}$

We will need to add this data to raw_data and the build.py

We need to create linear regression
Train Set - cell number to growth rates
Eval Set - cell number (predict growth rate)

[JamesPino]

I volunteer. Just need the data.

[JamesPino]

Growth rates in Growth_rates_WT_Ad.xlsx

Where are the cell numbers per condition?

[JamesPino]

There seem to be varying rates of growth that depend on what time point you focus on. Early ones are large expansion phase, while later is some form of confluency, which probably explains the negative values towards the end?
Thoughts?

[JamesPino]

Based on link, we might be hitting a few phases of growth with the axenic culture. The ox-stress data, for WT cells, provides a single point to compare with, but we need to convert from cells/ml/hr to /hr. Need Pavlo input. Real question is where will this data be used, and which data to use for constraining? Especially if we are measuring multiple phases of growth.

• lag phase, the delay before the start of exponential growth;
• exponential or log phase, where cells divide at a constant rate;
• stationary phase, when conditions become unfavourable for growth and bacteria stop replicating;
• death phase, when cells lose viability.

[djinnome]

@JamesPino is this branch ready to be merged into main?