{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Growth vs. Yield" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Load a few packages." ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false }, "outputs": [], "source": [ "import pandas\n", "pandas.options.display.max_rows = 12\n", "from cameo import models, phenotypic_phase_plane" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Load a model _E. coli_ central carbon metabolism." ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": true }, "outputs": [], "source": [ "model = models.bigg.e_coli_core.copy()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Compute the phenotypic phase plane for growth and acetate secretion." ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": true }, "outputs": [], "source": [ "result = phenotypic_phase_plane(model,\n", " variables=[model.reactions.BIOMASS_Ecoli_core_w_GAM],\n", " objective=model.reactions.EX_ac_e)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Look at the result in a tabular view." ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
\n", " | BIOMASS_Ecoli_core_w_GAM | \n", "objective_lower_bound | \n", "objective_upper_bound | \n", "
---|---|---|---|
0 | \n", "0.000000 | \n", "0.0 | \n", "2.000000e+01 | \n", "
1 | \n", "0.045996 | \n", "0.0 | \n", "1.930093e+01 | \n", "
2 | \n", "0.091992 | \n", "0.0 | \n", "1.860186e+01 | \n", "
3 | \n", "0.137988 | \n", "0.0 | \n", "1.790280e+01 | \n", "
4 | \n", "0.183983 | \n", "0.0 | \n", "1.720373e+01 | \n", "
5 | \n", "0.229979 | \n", "0.0 | \n", "1.650466e+01 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "
14 | \n", "0.643942 | \n", "0.0 | \n", "9.619970e+00 | \n", "
15 | \n", "0.689938 | \n", "0.0 | \n", "7.906992e+00 | \n", "
16 | \n", "0.735934 | \n", "0.0 | \n", "6.021404e+00 | \n", "
17 | \n", "0.781930 | \n", "0.0 | \n", "4.014269e+00 | \n", "
18 | \n", "0.827926 | \n", "0.0 | \n", "2.007135e+00 | \n", "
19 | \n", "0.873922 | \n", "0.0 | \n", "-5.664869e-15 | \n", "
20 rows × 3 columns
\n", "\n", " | EX_ac_e | \n", "EX_o2_e | \n", "objective_lower_bound | \n", "objective_upper_bound | \n", "
---|---|---|---|---|
0 | \n", "0.0 | \n", "-6.000000e+01 | \n", "0.0 | \n", "-4.842084e-17 | \n", "
1 | \n", "0.0 | \n", "-5.877551e+01 | \n", "0.0 | \n", "2.801293e-02 | \n", "
2 | \n", "0.0 | \n", "-5.755102e+01 | \n", "0.0 | \n", "5.602585e-02 | \n", "
3 | \n", "0.0 | \n", "-5.632653e+01 | \n", "0.0 | \n", "8.403878e-02 | \n", "
4 | \n", "0.0 | \n", "-5.510204e+01 | \n", "0.0 | \n", "1.120517e-01 | \n", "
5 | \n", "0.0 | \n", "-5.387755e+01 | \n", "0.0 | \n", "1.400646e-01 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
2494 | \n", "20.0 | \n", "-6.122449e+00 | \n", "0.0 | \n", "0.000000e+00 | \n", "
2495 | \n", "20.0 | \n", "-4.897959e+00 | \n", "0.0 | \n", "0.000000e+00 | \n", "
2496 | \n", "20.0 | \n", "-3.673469e+00 | \n", "0.0 | \n", "0.000000e+00 | \n", "
2497 | \n", "20.0 | \n", "-2.448980e+00 | \n", "0.0 | \n", "0.000000e+00 | \n", "
2498 | \n", "20.0 | \n", "-1.224490e+00 | \n", "0.0 | \n", "0.000000e+00 | \n", "
2499 | \n", "20.0 | \n", "-2.160206e-30 | \n", "0.0 | \n", "0.000000e+00 | \n", "
2500 rows × 4 columns
\n", "