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"source": [
"# Analysis of E. coli growth data\n",
"\n",
"(c) 2024 Justin Bois. This work is licensed under a [Creative Commons Attribution License CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/). All code contained herein is licensed under an [MIT license](https://opensource.org/licenses/MIT).\n",
"\n",
"This document was prepared at [Caltech](http://www.caltech.edu) with support financial support from the [Donna and Benjamin M. Rosen Bioengineering Center](http://rosen.caltech.edu).\n",
"\n",
"\n",
"\n",
"*This tutorial was generated from an Jupyter notebook. You can download the notebook [here](ecoli_growth_plate_reader_analysis.ipynb).*\n",
"\n",
"
\\n\"+\n", " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"
\\n\"+\n", " \"\\n\"+\n",
" \"from bokeh.resources import INLINE\\n\"+\n",
" \"output_notebook(resources=INLINE)\\n\"+\n",
" \"
\\n\"+\n",
" \"\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"
\\n\"+\n \"\n", " | Time | \n", "temperature (deg C) | \n", "A1 | \n", "A2 | \n", "A3 | \n", "A4 | \n", "A5 | \n", "A6 | \n", "A7 | \n", "A8 | \n", "... | \n", "H5 | \n", "H6 | \n", "H7 | \n", "H8 | \n", "H9 | \n", "H10 | \n", "H11 | \n", "H12 | \n", "time (s) | \n", "time (hr) | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "0:05:10 | \n", "29.8 | \n", "0.083 | \n", "0.084 | \n", "0.085 | \n", "0.085 | \n", "0.084 | \n", "0.086 | \n", "0.087 | \n", "0.085 | \n", "... | \n", "0.085 | \n", "0.085 | \n", "0.085 | \n", "0.085 | \n", "0.085 | \n", "0.088 | \n", "0.083 | \n", "0.084 | \n", "0.0 | \n", "0.0 | \n", "
1 | \n", "0:11:10 | \n", "33.9 | \n", "0.083 | \n", "0.084 | \n", "0.085 | \n", "0.085 | \n", "0.084 | \n", "0.086 | \n", "0.087 | \n", "0.085 | \n", "... | \n", "0.085 | \n", "0.085 | \n", "0.085 | \n", "0.085 | \n", "0.085 | \n", "0.088 | \n", "0.083 | \n", "0.084 | \n", "360.0 | \n", "0.1 | \n", "
2 | \n", "0:17:10 | \n", "36.9 | \n", "0.083 | \n", "0.084 | \n", "0.085 | \n", "0.085 | \n", "0.084 | \n", "0.086 | \n", "0.086 | \n", "0.085 | \n", "... | \n", "0.085 | \n", "0.085 | \n", "0.085 | \n", "0.085 | \n", "0.085 | \n", "0.088 | \n", "0.083 | \n", "0.084 | \n", "720.0 | \n", "0.2 | \n", "
3 | \n", "0:23:10 | \n", "37.0 | \n", "0.083 | \n", "0.084 | \n", "0.085 | \n", "0.085 | \n", "0.083 | \n", "0.086 | \n", "0.086 | \n", "0.085 | \n", "... | \n", "0.085 | \n", "0.084 | \n", "0.084 | \n", "0.085 | \n", "0.085 | \n", "0.088 | \n", "0.083 | \n", "0.084 | \n", "1080.0 | \n", "0.3 | \n", "
4 | \n", "0:29:10 | \n", "37.0 | \n", "0.082 | \n", "0.084 | \n", "0.085 | \n", "0.085 | \n", "0.083 | \n", "0.086 | \n", "0.088 | \n", "0.085 | \n", "... | \n", "0.085 | \n", "0.084 | \n", "0.085 | \n", "0.085 | \n", "0.085 | \n", "0.088 | \n", "0.083 | \n", "0.084 | \n", "1440.0 | \n", "0.4 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
236 | \n", "23:41:10 | \n", "37.0 | \n", "0.082 | \n", "0.083 | \n", "0.084 | \n", "0.085 | \n", "0.083 | \n", "0.086 | \n", "0.087 | \n", "0.084 | \n", "... | \n", "0.084 | \n", "0.084 | \n", "0.084 | \n", "0.086 | \n", "0.085 | \n", "0.088 | \n", "0.082 | \n", "0.084 | \n", "84960.0 | \n", "23.6 | \n", "
237 | \n", "23:47:10 | \n", "37.0 | \n", "0.082 | \n", "0.083 | \n", "0.084 | \n", "0.085 | \n", "0.083 | \n", "0.086 | \n", "0.086 | \n", "0.084 | \n", "... | \n", "0.085 | \n", "0.084 | \n", "0.084 | \n", "0.086 | \n", "0.085 | \n", "0.088 | \n", "0.083 | \n", "0.084 | \n", "85320.0 | \n", "23.7 | \n", "
238 | \n", "23:53:10 | \n", "37.0 | \n", "0.082 | \n", "0.083 | \n", "0.084 | \n", "0.085 | \n", "0.083 | \n", "0.086 | \n", "0.084 | \n", "0.084 | \n", "... | \n", "0.085 | \n", "0.084 | \n", "0.084 | \n", "0.086 | \n", "0.085 | \n", "0.088 | \n", "0.083 | \n", "0.084 | \n", "85680.0 | \n", "23.8 | \n", "
239 | \n", "23:59:10 | \n", "37.0 | \n", "0.082 | \n", "0.083 | \n", "0.084 | \n", "0.085 | \n", "0.083 | \n", "0.086 | \n", "0.084 | \n", "0.084 | \n", "... | \n", "0.085 | \n", "0.084 | \n", "0.084 | \n", "0.086 | \n", "0.085 | \n", "0.088 | \n", "0.083 | \n", "0.084 | \n", "86040.0 | \n", "23.9 | \n", "
240 | \n", "24:05:10 | \n", "37.0 | \n", "0.082 | \n", "0.083 | \n", "0.084 | \n", "0.085 | \n", "0.083 | \n", "0.086 | \n", "0.084 | \n", "0.084 | \n", "... | \n", "0.085 | \n", "0.084 | \n", "0.084 | \n", "0.086 | \n", "0.085 | \n", "0.088 | \n", "0.083 | \n", "0.084 | \n", "86400.0 | \n", "24.0 | \n", "
241 rows × 100 columns
\n", "\n", " | sugar | \n", "trial | \n", "A0 | \n", "r | \n", "
---|---|---|---|---|
0 | \n", "glucose | \n", "0 | \n", "0.006727 | \n", "0.667060 | \n", "
1 | \n", "glucose | \n", "1 | \n", "0.006275 | \n", "0.683410 | \n", "
2 | \n", "galactose | \n", "0 | \n", "0.010666 | \n", "0.158853 | \n", "
3 | \n", "galactose | \n", "1 | \n", "0.011758 | \n", "0.158613 | \n", "
4 | \n", "sorbitol | \n", "0 | \n", "0.006524 | \n", "0.459459 | \n", "
5 | \n", "sorbitol | \n", "1 | \n", "0.006654 | \n", "0.462238 | \n", "
6 | \n", "xylose | \n", "0 | \n", "0.004304 | \n", "0.486919 | \n", "
7 | \n", "xylose | \n", "1 | \n", "0.004488 | \n", "0.485660 | \n", "
\n", " | condition | \n", "trial | \n", "diaux_phase | \n", "A0 | \n", "r | \n", "
---|---|---|---|---|---|
0 | \n", "glucose | \n", "0 | \n", "0 | \n", "0.006727 | \n", "0.667060 | \n", "
1 | \n", "glucose | \n", "1 | \n", "0 | \n", "0.006275 | \n", "0.683410 | \n", "
2 | \n", "sorbitol | \n", "0 | \n", "0 | \n", "0.006524 | \n", "0.459459 | \n", "
3 | \n", "sorbitol | \n", "1 | \n", "0 | \n", "0.006654 | \n", "0.462238 | \n", "
4 | \n", "sorbitol:glucose 1:4 | \n", "0 | \n", "0 | \n", "0.007230 | \n", "0.651689 | \n", "
5 | \n", "sorbitol:glucose 1:4 | \n", "0 | \n", "1 | \n", "0.025639 | \n", "0.367873 | \n", "
6 | \n", "sorbitol:glucose 1:4 | \n", "1 | \n", "0 | \n", "0.006049 | \n", "0.672106 | \n", "
7 | \n", "sorbitol:glucose 1:4 | \n", "1 | \n", "1 | \n", "0.019600 | \n", "0.403852 | \n", "
8 | \n", "sorbitol:glucose 1:1 | \n", "0 | \n", "0 | \n", "0.005685 | \n", "0.684604 | \n", "
9 | \n", "sorbitol:glucose 1:1 | \n", "0 | \n", "1 | \n", "0.012195 | \n", "0.471591 | \n", "
10 | \n", "sorbitol:glucose 1:1 | \n", "1 | \n", "0 | \n", "0.005655 | \n", "0.703265 | \n", "
11 | \n", "sorbitol:glucose 1:1 | \n", "1 | \n", "1 | \n", "0.012643 | \n", "0.471652 | \n", "
12 | \n", "sorbitol:glucose 4:1 | \n", "0 | \n", "0 | \n", "0.007424 | \n", "0.619212 | \n", "
13 | \n", "sorbitol:glucose 4:1 | \n", "0 | \n", "1 | \n", "0.011168 | \n", "0.480342 | \n", "
14 | \n", "sorbitol:glucose 4:1 | \n", "1 | \n", "0 | \n", "0.007000 | \n", "0.631984 | \n", "
15 | \n", "sorbitol:glucose 4:1 | \n", "1 | \n", "1 | \n", "0.010908 | \n", "0.481002 | \n", "