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Python-based tools and utilities for NUFEB simulations

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Documentation Status pypi Tox testing status DOI

Description

Python-based tools and utilities for NUFEB simulations

Getting Started

Install via pip:

pip install nufeb-tools

Generate NUFEB simulations from the CLI:

nufeb-seed

Remove old runs:

nufeb-clean

Get data from a simulation for analysis

from nufeb_tools import utils
x = utils.get_data(test=True)

Plot the overall growth

from nufeb_tools import plot
import matplotlib.pyplot as plt
f, ax = plt.subplots()
plot.overall_growth(x.biomass,ax=ax)
/docs/_static/images/total_biomass_vs_time.png

Plot colonies based on initial seed cells

from nufeb_tools import utils, plot
import matplotlib.pyplot as plt
x = utils.get_data(directory=r'E:\sucrose\runs\Run_50_50_1.00e+00_1_2022-01-11_48525')
f,ax = plt.subplots()
plot.colony(x,25900,colors,ax=ax)
plt.show()
/docs/_static/images/colonies.png

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