{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Growth media VMH high fat low carb diet\n", "\n", "Similar to the western-style diet we will again start by loading the diet and depleting components absorbed by the host. In this case we have no manual annotation for which components should be diluted so we will use a generic human metabolic model to find those.\n", "The growth medium supllied here was created the following way:\n", "\n", "Let's start by reading the diet which was downloaded from https://www.vmh.life/#diet/High%20fat,%20low%20carb. Flux is in mmol/human/day. This has to be adjusted to 1 hour. Also the VMH site has a bug where it will clip fluxes after 4 digits, so we will set values like 0.0000 to 0.0001. " ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | reaction | \n", "flux | \n", "
---|---|---|
0 | \n", "EX_etoh | \n", "0.000004 | \n", "
1 | \n", "EX_h2o | \n", "6608.413339 | \n", "
2 | \n", "EX_caro | \n", "0.000068 | \n", "
3 | \n", "EX_retinol | \n", "0.129458 | \n", "
4 | \n", "EX_thm | \n", "0.075371 | \n", "
... | \n", "... | \n", "... | \n", "
86 | \n", "EX_lgnc | \n", "0.008570 | \n", "
87 | \n", "EX_fol | \n", "0.000005 | \n", "
88 | \n", "EX_strch1 | \n", "0.002862 | \n", "
89 | \n", "EX_i | \n", "0.000320 | \n", "
90 | \n", "EX_starch1200 | \n", "0.000026 | \n", "
91 rows × 2 columns
\n", "\n", " | reaction | \n", "flux | \n", "dilution | \n", "metabolite | \n", "global_id | \n", "
---|---|---|---|---|---|
0 | \n", "EX_etoh_m | \n", "0.000100 | \n", "0.1 | \n", "etoh_m | \n", "EX_etoh(e) | \n", "
1 | \n", "EX_h2o_m | \n", "6608.413339 | \n", "0.1 | \n", "h2o_m | \n", "EX_h2o(e) | \n", "
2 | \n", "EX_caro_m | \n", "0.000100 | \n", "0.1 | \n", "caro_m | \n", "EX_caro(e) | \n", "
3 | \n", "EX_retinol_m | \n", "0.129458 | \n", "0.1 | \n", "retinol_m | \n", "EX_retinol(e) | \n", "
4 | \n", "EX_thm_m | \n", "0.075371 | \n", "0.1 | \n", "thm_m | \n", "EX_thm(e) | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
86 | \n", "EX_lgnc_m | \n", "0.008570 | \n", "0.1 | \n", "lgnc_m | \n", "EX_lgnc(e) | \n", "
87 | \n", "EX_fol_m | \n", "0.000100 | \n", "0.1 | \n", "fol_m | \n", "EX_fol(e) | \n", "
88 | \n", "EX_strch1_m | \n", "0.002862 | \n", "0.1 | \n", "strch1_m | \n", "EX_strch1(e) | \n", "
89 | \n", "EX_i_m | \n", "0.000320 | \n", "0.1 | \n", "i_m | \n", "EX_i(e) | \n", "
90 | \n", "EX_starch1200_m | \n", "0.000100 | \n", "1.0 | \n", "starch1200_m | \n", "EX_starch1200(e) | \n", "
91 rows × 5 columns
\n", "