{ "cells": [ { "cell_type": "markdown", "metadata": { "deletable": true, "editable": true }, "source": [ "# Analyzing models\n", "\n", "**cameo** uses and extends the model data structures defined by [cobrapy](https://opencobra.github.io/cobrapy/), our favorite **CO**nstraints-**B**ased **R**econstruction and **A**nalysis tool for **Py**thon. **cameo** is thus 100% compatible with **cobrapy**. For efficiency reasons though **cameo** implements its own analysis methods that take advantage of a more advanced solver interface." ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false, "deletable": true, "editable": true }, "outputs": [ { "data": { "text/html": [] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "(function(global) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var force = \"1\";\n", "\n", " if (typeof (window._bokeh_onload_callbacks) === \"undefined\" || force !== \"\") {\n", " window._bokeh_onload_callbacks = [];\n", " window._bokeh_is_loading = undefined;\n", " }\n", "\n", "\n", " \n", " if (typeof (window._bokeh_timeout) === \"undefined\" || force !== \"\") {\n", " window._bokeh_timeout = Date.now() + 5000;\n", " window._bokeh_failed_load = false;\n", " }\n", "\n", " var NB_LOAD_WARNING = {'data': {'text/html':\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", " \"
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" \"from bokeh.resources import INLINE\\n\"+\n",
" \"output_notebook(resources=INLINE)\\n\"+\n",
" \"
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" \"\\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",
" \"
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" \"\n", " | upper_bound | \n", "lower_bound | \n", "
---|---|---|
ACALD | \n", "0.00 | \n", "-20.000000 | \n", "
ACALDt | \n", "0.00 | \n", "-20.000000 | \n", "
ACKr | \n", "0.00 | \n", "-20.000000 | \n", "
ACONTa | \n", "20.00 | \n", "0.000000 | \n", "
... | \n", "... | \n", "... | \n", "
THD2 | \n", "333.22 | \n", "0.000000 | \n", "
TKT1 | \n", "20.00 | \n", "-0.154536 | \n", "
TKT2 | \n", "20.00 | \n", "-0.466373 | \n", "
TPI | \n", "10.00 | \n", "-10.000000 | \n", "
95 rows × 2 columns
\n", "\n", " | upper_bound | \n", "lower_bound | \n", "
---|---|---|
ACALD | \n", "0.000000 | \n", "-12.602453 | \n", "
ACALDt | \n", "0.000000 | \n", "-12.602453 | \n", "
ACKr | \n", "0.000000 | \n", "-13.358852 | \n", "
ACONTa | \n", "13.830289 | \n", "0.471437 | \n", "
... | \n", "... | \n", "... | \n", "
THD2 | \n", "168.676660 | \n", "0.000000 | \n", "
TKT1 | \n", "13.280680 | \n", "-0.154536 | \n", "
TKT2 | \n", "13.122937 | \n", "-0.466373 | \n", "
TPI | \n", "9.565355 | \n", "-3.793497 | \n", "
95 rows × 2 columns
\n", "\n", " | BIOMASS_Ecoli_core_w_GAM | \n", "objective_lower_bound | \n", "objective_upper_bound | \n", "c_yield_lower_bound | \n", "c_yield_upper_bound | \n", "mass_yield_lower_bound | \n", "mass_yield_upper_bound | \n", "
---|---|---|---|---|---|---|---|
0 | \n", "0.559051 | \n", "9.90568 | \n", "11.503269 | \n", "0.330189 | \n", "0.383442 | \n", "0.324647 | \n", "0.377006 | \n", "
1 | \n", "0.529627 | \n", "2.62796 | \n", "11.950466 | \n", "0.087599 | \n", "0.398349 | \n", "0.086128 | \n", "0.391663 | \n", "
2 | \n", "0.500203 | \n", "0.00000 | \n", "12.397662 | \n", "0.000000 | \n", "0.413255 | \n", "0.000000 | \n", "0.406319 | \n", "
3 | \n", "0.470779 | \n", "0.00000 | \n", "12.844858 | \n", "0.000000 | \n", "0.428162 | \n", "0.000000 | \n", "0.420975 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
16 | \n", "0.088271 | \n", "0.00000 | \n", "18.658411 | \n", "0.000000 | \n", "0.621947 | \n", "0.000000 | \n", "0.611508 | \n", "
17 | \n", "0.058847 | \n", "0.00000 | \n", "19.105607 | \n", "0.000000 | \n", "0.636854 | \n", "0.000000 | \n", "0.626164 | \n", "
18 | \n", "0.029424 | \n", "0.00000 | \n", "19.552804 | \n", "0.000000 | \n", "0.651760 | \n", "0.000000 | \n", "0.640821 | \n", "
19 | \n", "0.000000 | \n", "0.00000 | \n", "20.000000 | \n", "0.000000 | \n", "0.666667 | \n", "0.000000 | \n", "0.655477 | \n", "
20 rows × 7 columns
\n", "\n", " | BIOMASS_Ecoli_core_w_GAM | \n", "objective_lower_bound | \n", "objective_upper_bound | \n", "c_yield_lower_bound | \n", "c_yield_upper_bound | \n", "mass_yield_lower_bound | \n", "mass_yield_upper_bound | \n", "
---|---|---|---|---|---|---|---|
0 | \n", "0.559051 | \n", "9.90568 | \n", "11.503269 | \n", "0.330189 | \n", "0.383442 | \n", "0.324647 | \n", "0.377006 | \n", "
1 | \n", "0.529627 | \n", "2.62796 | \n", "11.950466 | \n", "0.087599 | \n", "0.398349 | \n", "0.086128 | \n", "0.391663 | \n", "
2 | \n", "0.500203 | \n", "0.00000 | \n", "12.397662 | \n", "0.000000 | \n", "0.413255 | \n", "0.000000 | \n", "0.406319 | \n", "
3 | \n", "0.470779 | \n", "0.00000 | \n", "12.844858 | \n", "0.000000 | \n", "0.428162 | \n", "0.000000 | \n", "0.420975 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
16 | \n", "0.088271 | \n", "0.00000 | \n", "18.658411 | \n", "0.000000 | \n", "0.621947 | \n", "0.000000 | \n", "0.611508 | \n", "
17 | \n", "0.058847 | \n", "0.00000 | \n", "19.105607 | \n", "0.000000 | \n", "0.636854 | \n", "0.000000 | \n", "0.626164 | \n", "
18 | \n", "0.029424 | \n", "0.00000 | \n", "19.552804 | \n", "0.000000 | \n", "0.651760 | \n", "0.000000 | \n", "0.640821 | \n", "
19 | \n", "0.000000 | \n", "0.00000 | \n", "20.000000 | \n", "0.000000 | \n", "0.666667 | \n", "0.000000 | \n", "0.655477 | \n", "
20 rows × 7 columns
\n", "\n", " | perturbed | \n", "
---|---|
ACALD | \n", "False | \n", "
ACALDt | \n", "False | \n", "
ACKr | \n", "False | \n", "
ACt2r | \n", "False | \n", "
... | \n", "... | \n", "
SUCCt3 | \n", "False | \n", "
SUCDi | \n", "False | \n", "
THD2 | \n", "False | \n", "
TPI | \n", "False | \n", "
62 rows × 1 columns
\n", "