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"# 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_full_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 \"Time | temperature (deg C) | A1 | A2 | A3 | A4 | A5 | A6 | A7 | A8 | A9 | A10 | A11 | A12 | B1 | B2 | B3 | B4 | B5 | B6 | B7 | B8 | B9 | B10 | B11 | B12 | C1 | C2 | C3 | C4 | C5 | C6 | C7 | C8 | C9 | C10 | C11 | … | F2 | F3 | F4 | F5 | F6 | F7 | F8 | F9 | F10 | F11 | F12 | G1 | G2 | G3 | G4 | G5 | G6 | G7 | G8 | G9 | G10 | G11 | G12 | H1 | H2 | H3 | H4 | H5 | H6 | H7 | H8 | H9 | H10 | H11 | H12 | time (s) | time (hr) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
str | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | … | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 | f64 |
"0:05:10" | 37.0 | 0.08 | 0.083 | 0.086 | 0.118 | 0.122 | 0.121 | 0.097 | 0.089 | 0.086 | 0.113 | 0.117 | 0.117 | 0.111 | 0.116 | 0.085 | 0.115 | 0.125 | 0.133 | 0.101 | 0.113 | 0.111 | 0.102 | 0.112 | 0.111 | 0.112 | 0.13 | 0.108 | 0.111 | 0.107 | 0.127 | 0.114 | 0.115 | 0.124 | 0.109 | 0.125 | … | 0.107 | 0.106 | 0.115 | 0.111 | 0.116 | 0.109 | 0.113 | 0.127 | 0.115 | 0.11 | 0.111 | 0.11 | 0.107 | 0.121 | 0.12 | 0.11 | 0.11 | 0.111 | 0.118 | 0.115 | 0.111 | 0.107 | 0.095 | 0.202 | 0.214 | 0.134 | 0.131 | 0.108 | 0.11 | 0.159 | 0.239 | 0.218 | 0.189 | 0.115 | 0.13 | 0.0 | 0.0 |
"0:11:10" | 37.1 | 0.081 | 0.083 | 0.086 | 0.119 | 0.122 | 0.122 | 0.097 | 0.089 | 0.086 | 0.112 | 0.116 | 0.117 | 0.118 | 0.12 | 0.086 | 0.113 | 0.122 | 0.143 | 0.101 | 0.113 | 0.117 | 0.103 | 0.112 | 0.11 | 0.113 | 0.122 | 0.11 | 0.112 | 0.108 | 0.124 | 0.116 | 0.116 | 0.126 | 0.107 | 0.124 | … | 0.106 | 0.105 | 0.114 | 0.111 | 0.118 | 0.109 | 0.112 | 0.121 | 0.115 | 0.11 | 0.111 | 0.108 | 0.107 | 0.12 | 0.124 | 0.108 | 0.106 | 0.11 | 0.116 | 0.123 | 0.11 | 0.108 | 0.098 | 0.202 | 0.211 | 0.133 | 0.13 | 0.109 | 0.111 | 0.161 | 0.215 | 0.231 | 0.189 | 0.114 | 0.119 | 360.0 | 0.1 |
"0:17:10" | 37.0 | 0.083 | 0.083 | 0.086 | 0.121 | 0.123 | 0.123 | 0.097 | 0.089 | 0.086 | 0.113 | 0.116 | 0.115 | 0.101 | 0.118 | 0.086 | 0.114 | 0.122 | 0.121 | 0.102 | 0.114 | 0.112 | 0.104 | 0.113 | 0.111 | 0.113 | 0.12 | 0.114 | 0.112 | 0.11 | 0.125 | 0.12 | 0.111 | 0.124 | 0.112 | 0.126 | … | 0.105 | 0.105 | 0.114 | 0.111 | 0.118 | 0.109 | 0.113 | 0.12 | 0.116 | 0.111 | 0.113 | 0.11 | 0.107 | 0.119 | 0.12 | 0.11 | 0.106 | 0.111 | 0.12 | 0.127 | 0.104 | 0.115 | 0.101 | 0.202 | 0.215 | 0.133 | 0.13 | 0.109 | 0.112 | 0.164 | 0.215 | 0.224 | 0.187 | 0.114 | 0.113 | 720.0 | 0.2 |
"0:23:10" | 37.0 | 0.083 | 0.083 | 0.086 | 0.123 | 0.126 | 0.126 | 0.097 | 0.089 | 0.086 | 0.114 | 0.118 | 0.117 | 0.102 | 0.117 | 0.085 | 0.114 | 0.123 | 0.136 | 0.102 | 0.114 | 0.112 | 0.102 | 0.115 | 0.112 | 0.116 | 0.117 | 0.112 | 0.113 | 0.111 | 0.127 | 0.116 | 0.113 | 0.126 | 0.113 | 0.126 | … | 0.106 | 0.105 | 0.116 | 0.112 | 0.119 | 0.11 | 0.113 | 0.126 | 0.117 | 0.113 | 0.117 | 0.11 | 0.107 | 0.119 | 0.123 | 0.108 | 0.106 | 0.112 | 0.131 | 0.129 | 0.103 | 0.111 | 0.104 | 0.202 | 0.209 | 0.134 | 0.133 | 0.111 | 0.113 | 0.158 | 0.214 | 0.224 | 0.17 | 0.114 | 0.115 | 1080.0 | 0.3 |
"0:29:10" | 37.1 | 0.081 | 0.082 | 0.086 | 0.126 | 0.129 | 0.129 | 0.097 | 0.089 | 0.086 | 0.115 | 0.119 | 0.118 | 0.102 | 0.141 | 0.085 | 0.116 | 0.125 | 0.144 | 0.103 | 0.116 | 0.113 | 0.103 | 0.115 | 0.114 | 0.115 | 0.118 | 0.113 | 0.115 | 0.113 | 0.128 | 0.117 | 0.123 | 0.128 | 0.11 | 0.128 | … | 0.105 | 0.106 | 0.122 | 0.113 | 0.116 | 0.111 | 0.115 | 0.127 | 0.118 | 0.113 | 0.111 | 0.11 | 0.107 | 0.119 | 0.124 | 0.11 | 0.106 | 0.113 | 0.133 | 0.132 | 0.103 | 0.112 | 0.105 | 0.203 | 0.211 | 0.135 | 0.13 | 0.112 | 0.114 | 0.16 | 0.215 | 0.22 | 0.167 | 0.114 | 0.115 | 1440.0 | 0.4 |
… | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … | … |
"23:41:10" | 37.1 | 1.691 | 0.083 | 0.085 | 1.771 | 1.774 | 1.777 | 0.097 | 0.088 | 0.086 | 0.9 | 1.121 | 1.124 | 0.922 | 0.913 | 0.085 | 1.206 | 1.236 | 1.026 | 0.991 | 1.116 | 1.048 | 1.086 | 1.132 | 1.149 | 1.17 | 1.09 | 1.088 | 1.064 | 1.059 | 1.068 | 1.066 | 1.087 | 1.081 | 1.095 | 1.116 | … | 0.919 | 0.903 | 1.025 | 1.035 | 1.026 | 0.995 | 1.024 | 1.04 | 0.99 | 0.984 | 1.04 | 0.679 | 0.618 | 0.63 | 1.032 | 0.942 | 0.82 | 1.082 | 1.155 | 0.79 | 0.887 | 1.09 | 1.037 | 0.293 | 0.299 | 0.147 | 0.488 | 1.056 | 1.077 | 0.763 | 0.963 | 0.297 | 0.254 | 1.065 | 1.106 | 84960.0 | 23.6 |
"23:47:10" | 37.1 | 1.69 | 0.082 | 0.085 | 1.77 | 1.773 | 1.776 | 0.097 | 0.088 | 0.086 | 0.9 | 1.119 | 1.122 | 0.92 | 0.913 | 0.085 | 1.204 | 1.228 | 1.026 | 0.99 | 1.114 | 1.047 | 1.086 | 1.131 | 1.147 | 1.169 | 1.089 | 1.087 | 1.062 | 1.057 | 1.067 | 1.065 | 1.087 | 1.08 | 1.093 | 1.115 | … | 0.918 | 0.902 | 1.024 | 1.035 | 1.025 | 0.995 | 1.023 | 1.039 | 0.99 | 0.983 | 1.04 | 0.679 | 0.618 | 0.631 | 1.032 | 0.941 | 0.825 | 1.082 | 1.155 | 0.79 | 0.887 | 1.089 | 1.035 | 0.293 | 0.299 | 0.145 | 0.488 | 1.055 | 1.075 | 0.762 | 0.964 | 0.282 | 0.254 | 1.064 | 1.105 | 85320.0 | 23.7 |
"23:53:10" | 37.0 | 1.688 | 0.083 | 0.085 | 1.77 | 1.773 | 1.775 | 0.097 | 0.088 | 0.086 | 0.899 | 1.118 | 1.121 | 0.92 | 0.912 | 0.085 | 1.203 | 1.228 | 1.036 | 0.99 | 1.114 | 1.046 | 1.087 | 1.13 | 1.147 | 1.17 | 1.089 | 1.086 | 1.061 | 1.056 | 1.066 | 1.064 | 1.085 | 1.079 | 1.092 | 1.115 | … | 0.917 | 0.902 | 1.025 | 1.035 | 1.025 | 0.995 | 1.024 | 1.04 | 0.989 | 0.984 | 1.04 | 0.678 | 0.618 | 0.63 | 1.032 | 0.942 | 0.819 | 1.082 | 1.155 | 0.79 | 0.888 | 1.093 | 1.036 | 0.324 | 0.3 | 0.144 | 0.485 | 1.054 | 1.076 | 0.764 | 0.963 | 0.3 | 0.254 | 1.064 | 1.109 | 85680.0 | 23.8 |
"23:59:10" | 37.0 | 1.687 | 0.083 | 0.085 | 1.769 | 1.772 | 1.774 | 0.097 | 0.088 | 0.086 | 0.899 | 1.119 | 1.122 | 0.919 | 0.912 | 0.085 | 1.204 | 1.233 | 1.025 | 0.99 | 1.114 | 1.045 | 1.087 | 1.13 | 1.147 | 1.168 | 1.087 | 1.085 | 1.06 | 1.057 | 1.065 | 1.063 | 1.084 | 1.079 | 1.092 | 1.114 | … | 0.916 | 0.901 | 1.026 | 1.034 | 1.025 | 0.995 | 1.023 | 1.039 | 0.988 | 0.983 | 1.039 | 0.678 | 0.617 | 0.63 | 1.033 | 0.943 | 0.82 | 1.082 | 1.155 | 0.79 | 0.889 | 1.094 | 1.036 | 0.294 | 0.299 | 0.145 | 0.487 | 1.054 | 1.076 | 0.762 | 0.963 | 0.296 | 0.254 | 1.063 | 1.104 | 86040.0 | 23.9 |
"24:05:10" | 37.0 | 1.687 | 0.083 | 0.085 | 1.768 | 1.771 | 1.773 | 0.097 | 0.089 | 0.086 | 0.898 | 1.118 | 1.121 | 0.918 | 0.912 | 0.085 | 1.203 | 1.226 | 1.024 | 0.99 | 1.113 | 1.045 | 1.087 | 1.129 | 1.146 | 1.168 | 1.087 | 1.084 | 1.06 | 1.056 | 1.064 | 1.062 | 1.084 | 1.078 | 1.091 | 1.114 | … | 0.915 | 0.899 | 1.025 | 1.034 | 1.025 | 0.994 | 1.022 | 1.038 | 0.988 | 0.982 | 1.046 | 0.676 | 0.617 | 0.63 | 1.032 | 0.942 | 0.82 | 1.083 | 1.156 | 0.789 | 0.888 | 1.09 | 1.038 | 0.293 | 0.301 | 0.144 | 0.485 | 1.053 | 1.074 | 0.761 | 0.964 | 0.3 | 0.254 | 1.062 | 1.104 | 86400.0 | 24.0 |
sugar | trial | OD_low | OD_high | A0 | r |
---|---|---|---|---|---|
str | i64 | f64 | f64 | f64 | f64 |
"glucose" | 0 | 0.1 | 0.4 | 0.024282 | 0.593354 |
"glucose" | 1 | 0.1 | 0.4 | 0.025689 | 0.60446 |
"glucose" | 2 | 0.1 | 0.4 | 0.02751 | 0.594018 |
"galactose" | 0 | 0.1 | 0.4 | 0.027992 | 0.229443 |
"galactose" | 1 | 0.1 | 0.4 | 0.026537 | 0.253469 |
… | … | … | … | … | … |
"sorbitol" | 0 | 0.1 | 0.6 | 0.027545 | 0.392449 |
"sorbitol" | 1 | 0.1 | 0.6 | 0.026191 | 0.400065 |
"sorbitol" | 2 | 0.1 | 0.6 | 0.024077 | 0.412325 |
"xylose" | 0 | 0.1 | 0.4 | 0.014733 | 0.442673 |
"xylose" | 1 | 0.1 | 0.4 | 0.010956 | 0.449941 |
condition | trial | diaux_phase | OD_low | OD_high | A0 | r |
---|---|---|---|---|---|---|
str | i64 | i64 | f64 | f64 | f64 | f64 |
"glucose" | 0 | 0 | 0.1 | 0.4 | 0.024282 | 0.593354 |
"glucose" | 1 | 0 | 0.1 | 0.4 | 0.025689 | 0.60446 |
"glucose" | 2 | 0 | 0.1 | 0.4 | 0.02751 | 0.594018 |
"sorbitol" | 0 | 0 | 0.1 | 0.6 | 0.027545 | 0.392449 |
"sorbitol" | 1 | 0 | 0.1 | 0.6 | 0.026191 | 0.400065 |
… | … | … | … | … | … | … |
"sorbitol:glucose 1:1" | 0 | 1 | 0.65 | 0.8 | 0.101014 | 0.281996 |
"sorbitol:glucose 1:1" | 1 | 0 | 0.1 | 0.3 | 0.026459 | 0.597242 |
"sorbitol:glucose 1:1" | 1 | 1 | 0.65 | 0.8 | 0.101654 | 0.298754 |
"sorbitol:glucose 1:1" | 2 | 0 | 0.1 | 0.3 | 0.026599 | 0.561807 |
"sorbitol:glucose 1:1" | 2 | 1 | 0.65 | 0.8 | 0.105969 | 0.278731 |