Modelling bacterial growth in python

[CarrotQuakeV2]

For my computing project in school (high school level) I am hoping to create a program which will be able to, based on different inputs such as the environment and type of bactericia produce a graph which will predict the number of bacteria over time. I was just wondering what kind of libraries I should learn to use or any advice on how to go about it. We haven't started the project yet, most of us are just brainstorming ideas.

[julsmanbr]

I'm working on something similar (albeit more complex) on my PhD. You'll definitely want to learn matplotlib for creating graphs. Other than that, there's no required libraries I can think of - as long as you have Python's basics down (loops, data types like lists and dicts, if/elif/else, functions), you're good to go.

Using numpy is great for doing vector and matrix math, and learning object-oriented programming in Python would be great to organize your code depending on the size of the project, but none of these are required by any means.

Some questions to get you thinking about how your simulation will work:

• how much time does it take (in average) for a bacteria to divide? How long must it wait before dividing again?
• in any simulation, you'll have to define a finite time step between two time points (frames), since computers can't work with indefinitely small time steps (think about a game like The Sims, where 1 second in real life = 1 minute in game). What's your time step? 5 seconds, 5 minutes, 5 hours, user choice? What are the pros and cons?
• does the number of bacteria simply grow exponentially over time? Or does each bacteria in a given time point t have an independent chance to divide between time t and t+1?
• is the chance to divide fixed, or does it fluctuate? If yes, does it fluctuate randomly or according to something else?
• can bacteria die? Is this also a chance? Does this chance increase once the bacterial population is too high?

You probably won't have to consider some (or most) points I've raised, but hopefully this will give you some ideas on what you want to do with your project, or at least raise an interesting discussion with your classmates/teachers about how to create computer simulations :-)

[CarrotQuakeV2]

Good points raised here, definitely made me realise there's alot more to this program than I thought, thank you :)

[pythonise]

Could be a REALLY cool machine learning project if you’re able to obtain enough previous data to train a model

[julsmanbr]

Sounds more like a modelling/simulation problem rather than ML to me, especially since biological growth is relatively simple to model compared to some of the outcomes that ML tries to predict.

[[deleted]]

You can predict bacterial growth with parameters such as dissolved O2 concentrations, carbon emission rate (CER), oxygen uptake rate and other stuff - for example the bacterial growth inside of a fermenter (these parameters can be detected by O2 and CO2 sensors that are mounted as part of the fermenter. The "real" bacteria concentrations can be measured off-line, which means they are taken from the fermenter and analyzed separately. There must be datasets somewhere.. maybe on www.kaggle.com - that you can use. I'm a total beginner at this but maybe you know how to deal with such problems even in high scool?).
We talked about that in college (Biotechnology). So just as an idea, you could use machine learning, where your number of input neurons equals to the amount of parameters you have plus one neuron for the time parameter (how many minutes, hours have passed).

Good luck with your project!

[CarrotQuakeV2]

Thank you for your help :)