{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# High-level interface for users" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
\n", "WARNING: if you're running this notebook on [try.cameo.bio](http://try.cameo.bio), things might run very slow due to our inability to provide access to the [CPLEX](https://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/) solver on a public webserver. Furthermore, Jupyter kernels might crash and restart due to memory limitations on the server.\n", "
" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Users primarily interested in using cameo as a tool\n", "for enumerating metabolic engineering strategies have access to cameo's advanced programming interface via `cameo.api`\n", "that provides access to potential products (`cameo.api.products`), host organisms (`cameo.api.hosts`) and\n", "a configurable design function (`cameo.api.design`). Running `cameo.api.design` requires only minimal input and will run the following workflow.\n", "\"Drawing\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Import the advanced interface." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "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", " function run_callbacks() {\n", " window._bokeh_onload_callbacks.forEach(function(callback) { callback() });\n", " delete window._bokeh_onload_callbacks\n", " console.info(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(js_urls, callback) {\n", " window._bokeh_onload_callbacks.push(callback);\n", " if (window._bokeh_is_loading > 0) {\n", " console.log(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls == null || js_urls.length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " console.log(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " window._bokeh_is_loading = js_urls.length;\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " var s = document.createElement('script');\n", " s.src = url;\n", " s.async = false;\n", " s.onreadystatechange = s.onload = function() {\n", " window._bokeh_is_loading--;\n", " if (window._bokeh_is_loading === 0) {\n", " console.log(\"Bokeh: all BokehJS libraries loaded\");\n", " run_callbacks()\n", " }\n", " };\n", " s.onerror = function() {\n", " console.warn(\"failed to load library \" + url);\n", " };\n", " console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.getElementsByTagName(\"head\")[0].appendChild(s);\n", " }\n", " };\n", "\n", " var js_urls = ['https://cdn.pydata.org/bokeh/release/bokeh-0.12.1.min.js', 'https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.1.min.js', 'https://cdn.pydata.org/bokeh/release/bokeh-compiler-0.12.1.min.js'];\n", "\n", " var inline_js = [\n", " function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", " \n", " function(Bokeh) {\n", " \n", " Bokeh.$(\"#7c78074e-2899-4a24-aa21-47cf71ea70a8\").text(\"BokehJS successfully loaded\");\n", " var kernel = Jupyter.notebook.kernel\n", " if (kernel.execute !== undefined) {\n", " kernel.execute(\"import bokeh.io; bokeh.io._nb_loaded = True\");\n", " }\n", " },\n", " function(Bokeh) {\n", " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-0.12.1.min.css\");\n", " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-0.12.1.min.css\");\n", " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.1.min.css\");\n", " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.1.min.css\");\n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i](window.Bokeh);\n", " }\n", " }\n", "\n", " if (window._bokeh_is_loading === 0) {\n", " console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", " run_inline_js();\n", " } else {\n", " load_libs(js_urls, function() {\n", " console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n", " run_inline_js();\n", " });\n", " }\n", "}(this));" ] }, "metadata": {}, "output_type": "display_data" }, { "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", " function run_callbacks() {\n", " window._bokeh_onload_callbacks.forEach(function(callback) { callback() });\n", " delete window._bokeh_onload_callbacks\n", " console.info(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(js_urls, callback) {\n", " window._bokeh_onload_callbacks.push(callback);\n", " if (window._bokeh_is_loading > 0) {\n", " console.log(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls == null || js_urls.length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " console.log(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " window._bokeh_is_loading = js_urls.length;\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " var s = document.createElement('script');\n", " s.src = url;\n", " s.async = false;\n", " s.onreadystatechange = s.onload = function() {\n", " window._bokeh_is_loading--;\n", " if (window._bokeh_is_loading === 0) {\n", " console.log(\"Bokeh: all BokehJS libraries loaded\");\n", " run_callbacks()\n", " }\n", " };\n", " s.onerror = function() {\n", " console.warn(\"failed to load library \" + url);\n", " };\n", " console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.getElementsByTagName(\"head\")[0].appendChild(s);\n", " }\n", " };\n", "\n", " var js_urls = ['https://cdn.pydata.org/bokeh/release/bokeh-0.12.1.min.js', 'https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.1.min.js', 'https://cdn.pydata.org/bokeh/release/bokeh-compiler-0.12.1.min.js'];\n", "\n", " var inline_js = [\n", " function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", " \n", " function(Bokeh) {\n", " \n", " Bokeh.$(\"#88ebb6fd-3a08-4eae-971e-09baffb76802\").text(\"BokehJS successfully loaded\");\n", " var kernel = Jupyter.notebook.kernel\n", " if (kernel.execute !== undefined) {\n", " kernel.execute(\"import bokeh.io; bokeh.io._nb_loaded = True\");\n", " }\n", " },\n", " function(Bokeh) {\n", " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-0.12.1.min.css\");\n", " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-0.12.1.min.css\");\n", " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.1.min.css\");\n", " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.1.min.css\");\n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i](window.Bokeh);\n", " }\n", " }\n", "\n", " if (window._bokeh_is_loading === 0) {\n", " console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", " run_inline_js();\n", " } else {\n", " load_libs(js_urls, function() {\n", " console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n", " run_inline_js();\n", " });\n", " }\n", "}(this));" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from cameo import api" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Searching for products" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Search by trivial name." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
InChISMILESchargeformulamassnamesourcesearch_rank
MNXM680InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)...CN1C=NC2=C1C(=O)N(C)C(=O)N2C0C8H10N4O2194.1906caffeinechebi:277320
\n", "
" ], "text/plain": [ " InChI \\\n", "MNXM680 InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)... \n", "\n", " SMILES charge formula mass name \\\n", "MNXM680 CN1C=NC2=C1C(=O)N(C)C(=O)N2C 0 C8H10N4O2 194.1906 caffeine \n", "\n", " source search_rank \n", "MNXM680 chebi:27732 0 " ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "api.products.search('caffeine')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Search by ChEBI ID." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
InChISMILESchargeformulamassnamesourcesearch_rank
MNXM680InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)...CN1C=NC2=C1C(=O)N(C)C(=O)N2C0C8H10N4O2194.1906caffeinechebi:277320
\n", "
" ], "text/plain": [ " InChI \\\n", "MNXM680 InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)... \n", "\n", " SMILES charge formula mass name \\\n", "MNXM680 CN1C=NC2=C1C(=O)N(C)C(=O)N2C 0 C8H10N4O2 194.1906 caffeine \n", "\n", " source search_rank \n", "MNXM680 chebi:27732 0 " ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "api.products.search('chebi:27732')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Host organisms" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Currently the following host organisms and respective models are available in cameo. More hosts and models will be added in the future (please get in touch with us if you'd like to get a particular host organism included)." ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Escherichia coli iJO1366\n", "Saccharomyces cerevisiae iMM904\n" ] } ], "source": [ "for host in api.hosts:\n", " for model in host.models:\n", " print(host.name, model.id)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Computing strain engineering strategies" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "For demonstration purposes, we'll set a few options to limit the computational time. Also we'll create a multiprocessing view to take advantage of multicore CPUs (strain design algorithms will be run in parallel for individually predicted heterologous pathways)." ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": true }, "outputs": [], "source": [ "from cameo.parallel import MultiprocessingView\n", "mp_view = MultiprocessingView()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Limit the number of predicted heterlogous pathways to 4." ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": true }, "outputs": [], "source": [ "api.design.options.max_pathway_predictions = 4" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Set a time limit of 30 minutes on individual heuristic optimizations." ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": true }, "outputs": [], "source": [ "api.design.options.heuristic_optimization_timeout = 30" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "scrolled": false }, "outputs": [ { "data": { "text/html": [ "Starting searching for compound vanillin" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "Found 1 compounds that match query 'vanillin'" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
IdNameFormula
MNXM754vanillinC8H8O3
\n", " " ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "Choosing best match (vanillin) ... please interrupt if this is not the desired compound." ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", "

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\n", " " ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", " \n", " " ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "Predicting pathways for product vanillin in Escherichia coli (using model iJO1366)." ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "Pathway 1" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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equationlower_boundupper_bound
MNXR5340H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih...-10001000
MNXR53362.0 H(+) + NADH + vanillate <=> H2O + vanillin...-10001000
MNXR68718H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki...-10001000
MNXR6512.0 H(+) + NADH + formate <=> H2O + formaldehy...-10001000
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" ], "text/plain": [ " equation lower_bound \\\n", "MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 \n", "MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 \n", "MNXR68718 H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... -1000 \n", "MNXR651 2.0 H(+) + NADH + formate <=> H2O + formaldehy... -1000 \n", "\n", " upper_bound \n", "MNXR5340 1000 \n", "MNXR5336 1000 \n", "MNXR68718 1000 \n", "MNXR651 1000 " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Max flux: 7.58479\n" ] }, { "data": { "text/html": [ "Pathway 2" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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equationlower_boundupper_bound
MNXR5340H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih...-10001000
MNXR53362.0 H(+) + NADH + vanillate <=> H2O + vanillin...-10001000
MNXR2795S-adenosyl-L-methionine + glycine <=> H(+) + S...-10001000
MNXR68718H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki...-10001000
\n", "
" ], "text/plain": [ " equation lower_bound \\\n", "MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 \n", "MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 \n", "MNXR2795 S-adenosyl-L-methionine + glycine <=> H(+) + S... -1000 \n", "MNXR68718 H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... -1000 \n", "\n", " upper_bound \n", "MNXR5340 1000 \n", "MNXR5336 1000 \n", "MNXR2795 1000 \n", "MNXR68718 1000 " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Max flux: 4.29196\n" ] }, { "data": { "text/html": [ "Pathway 3" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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equationlower_boundupper_bound
MNXR5340H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih...-10001000
MNXR53362.0 H(+) + NADH + vanillate <=> H2O + vanillin...-10001000
MNXR68718H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki...-10001000
MNXR71473-methyl-2-oxobutanoate + formaldehyde <=> 2-d...-10001000
\n", "
" ], "text/plain": [ " equation lower_bound \\\n", "MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 \n", "MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 \n", "MNXR68718 H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... -1000 \n", "MNXR7147 3-methyl-2-oxobutanoate + formaldehyde <=> 2-d... -1000 \n", "\n", " upper_bound \n", "MNXR5340 1000 \n", "MNXR5336 1000 \n", "MNXR68718 1000 \n", "MNXR7147 1000 " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Max flux: 7.33229\n" ] }, { "data": { "text/html": [ "Pathway 4" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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equationlower_boundupper_bound
MNXR5340H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih...-10001000
MNXR53362.0 H(+) + NADH + vanillate <=> H2O + vanillin...-10001000
MNXR230H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ...-10001000
MNXR640methanol + NAD(+) <=> H(+) + NADH + formaldehyde-10001000
\n", "
" ], "text/plain": [ " equation lower_bound \\\n", "MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 \n", "MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 \n", "MNXR230 H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ... -1000 \n", "MNXR640 methanol + NAD(+) <=> H(+) + NADH + formaldehyde -1000 \n", "\n", " upper_bound \n", "MNXR5340 1000 \n", "MNXR5336 1000 \n", "MNXR230 1000 \n", "MNXR640 1000 " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", " jQuery(\"#ff83d3e2-b1ad-43f0-aa80-a4caed987972\").remove();\n", " " ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", "\n", "
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equationlower_boundupper_bound
MNXR5340H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih...-10001000
MNXR53362.0 H(+) + NADH + vanillate <=> H2O + vanillin...-10001000
MNXR230H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ...-10001000
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" ], "text/plain": [ " equation lower_bound \\\n", "MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 \n", "MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 \n", "MNXR230 H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ... -1000 \n", "\n", " upper_bound \n", "MNXR5340 1000 \n", "MNXR5336 1000 \n", "MNXR230 1000 " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Max flux: 1.90533\n" ] }, { "data": { "text/html": [ "Pathway 2" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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equationlower_boundupper_bound
MNXR5340H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih...-10001000
MNXR53362.0 H(+) + NADH + vanillate <=> H2O + vanillin...-10001000
MNXR68718H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki...-10001000
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" ], "text/plain": [ " equation lower_bound \\\n", "MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 \n", "MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 \n", "MNXR68718 H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... -1000 \n", "\n", " upper_bound \n", "MNXR5340 1000 \n", "MNXR5336 1000 \n", "MNXR68718 1000 " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Max flux: 3.36842\n" ] }, { "data": { "text/html": [ "Pathway 3" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
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equationlower_boundupper_bound
MNXR4008H(+) + 3-oxoadipate <=> H2O + 5-oxo-4,5-dihydr...-10001000
MNXR1843-oxoadipyl-CoA + succinate <=> 3-oxoadipate +...-10001000
MNXR5340H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih...-10001000
MNXR53362.0 H(+) + NADH + vanillate <=> H2O + vanillin...-10001000
MNXR228CO2 + 5-oxo-4,5-dihydro-2-furylacetate <=> H(+...-10001000
MNXR41192.0 H(+) + 3-carboxy-cis,cis-muconate <=> 3,4-...-10001000
MNXR209CoA + 3-oxoadipyl-CoA <=> acetyl-CoA + succiny...-10001000
MNXR36552-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate ...-10001000
\n", "
" ], "text/plain": [ " equation lower_bound \\\n", "MNXR4008 H(+) + 3-oxoadipate <=> H2O + 5-oxo-4,5-dihydr... -1000 \n", "MNXR184 3-oxoadipyl-CoA + succinate <=> 3-oxoadipate +... -1000 \n", "MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 \n", "MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 \n", "MNXR228 CO2 + 5-oxo-4,5-dihydro-2-furylacetate <=> H(+... -1000 \n", "MNXR4119 2.0 H(+) + 3-carboxy-cis,cis-muconate <=> 3,4-... -1000 \n", "MNXR209 CoA + 3-oxoadipyl-CoA <=> acetyl-CoA + succiny... -1000 \n", "MNXR3655 2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate ... -1000 \n", "\n", " upper_bound \n", "MNXR4008 1000 \n", "MNXR184 1000 \n", "MNXR5340 1000 \n", "MNXR5336 1000 \n", "MNXR228 1000 \n", "MNXR4119 1000 \n", "MNXR209 1000 \n", "MNXR3655 1000 " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Max flux: 5.59223\n" ] }, { "data": { "application/javascript": [ "\n", " jQuery(\"#0176ba05-7ebc-4437-b9ef-b24f447b41d3\").remove();\n", " " ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", "\n", "
\n", "
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\n", "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Optimizing 6 pathways\n", "Starting optimization at Wed, 07 Jun 2017 08:50:22\n", "Starting optimization at Wed, 07 Jun 2017 08:51:06\n", "Starting optimization at Wed, 07 Jun 2017 08:51:07\n", "Starting optimization at Wed, 07 Jun 2017 08:51:10\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "ab79595517444853a16a2df4555b264f" } }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "93a8dbbc34b44c779d0709efea5dc452" } }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "fb40da5786294601beba12fe4b769398" } }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "d5e1d2775d3e426aae3db95e07b084fd" } }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Finished after 00:30:13\n", "Finished after 00:30:05\n", "Starting optimization at Wed, 07 Jun 2017 09:21:19\n", "Starting optimization at Wed, 07 Jun 2017 09:22:00\n", "Finished after 00:31:49\n", "Finished after 00:32:06\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "7d304135c6d246e0b00d5020923d7b13" } }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "fd2a4d1cf314475fb35594296b0541c0" } }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Finished after 00:18:19\n", "Finished after 00:30:43\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/Users/niso/Dev/cameo/cameo/strain_design/heuristic/evolutionary/objective_functions.py:289: RuntimeWarning:\n", "\n", "invalid value encountered in double_scalars\n", "\n" ] } ], "source": [ "report = api.design(product='vanillin', view=mp_view)" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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hostmodelmanipulationsheterologous_pathwayfitnessyieldproductbiomassmethod
0Saccharomyces cerevisiaeiMM904(-YOR347C, -YAL038W, -YJL121C, -YPL061W)(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0075290.2128781.282230e-014.715766e-02PathwayPredictor+OptGene
1Saccharomyces cerevisiaeiMM904(-YOR347C, -YAL038W, -YJL121C, -YDL022W)(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0073150.2064741.233825e-014.724036e-02PathwayPredictor+OptGene
2Saccharomyces cerevisiaeiMM904(-YOR347C, -YAL038W, -YJL121C, -YNL111C)(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0073070.2062121.231918e-014.724920e-02PathwayPredictor+OptGene
3Saccharomyces cerevisiaeiMM904(-YOR347C, -YAL038W, -YGR010W, -YJL026W, -YFR0...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0073050.2061151.231222e-014.725242e-02PathwayPredictor+OptGene
4Saccharomyces cerevisiaeiMM904(-YDL021W, -YOR347C, -YAL038W, -YNR001C, -YFR0...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0073050.2061151.231222e-014.725242e-02PathwayPredictor+OptGene
5Saccharomyces cerevisiaeiMM904(-YOR347C, -YAL038W, -YJL121C)(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0073050.2061151.231222e-014.725242e-02PathwayPredictor+OptGene
6Saccharomyces cerevisiaeiMM904(-YOR347C, -YAL038W, -YJL121C, -YIR032C)(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0073050.2061151.231222e-014.725242e-02PathwayPredictor+OptGene
7Escherichia coliiJO1366(-reaction.3OAR140, -reaction.3OAS140, -reacti...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000001.0113057.584790e+000.000000e+00PathwayPredictor+DifferentialFVA
8Escherichia coliiJO1366(+reaction.3OAR140(value=0.008511), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0737360.9007106.755327e+001.091526e-01PathwayPredictor+DifferentialFVA
9Escherichia coliiJO1366(+reaction.3OAR140(value=0.01699), +reaction.3...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.1293650.7901165.925867e+002.183049e-01PathwayPredictor+DifferentialFVA
10Escherichia coliiJO1366(+reaction.3OAR140(value=0.025485), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.1668640.6794345.095758e+003.274573e-01PathwayPredictor+DifferentialFVA
11Escherichia coliiJO1366(+reaction.3OAR140(value=0.033979), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.1855060.5665054.248787e+004.366097e-01PathwayPredictor+DifferentialFVA
12Escherichia coliiJO1366(+reaction.3OAR140(value=0.042474), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.1855810.4533873.400405e+005.457622e-01PathwayPredictor+DifferentialFVA
13Escherichia coliiJO1366(+reaction.3OAR140(value=0.050969), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.1671360.3402702.552028e+006.549146e-01PathwayPredictor+DifferentialFVA
14Escherichia coliiJO1366()(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...-0.0000000.0000000.000000e+009.823718e-01PathwayPredictor+DifferentialFVA
15Escherichia coliiJO1366()(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.0000000.000000e+009.823718e-01PathwayPredictor+DifferentialFVA
16Escherichia coliiJO1366(-reaction.3OAR140, -reaction.3OAS140, -reacti...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.5722624.291964e+000.000000e+00PathwayPredictor+DifferentialFVA
17Escherichia coliiJO1366(+reaction.3OAR140(value=0.008512), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0416470.5087343.815508e+001.091527e-01PathwayPredictor+DifferentialFVA
18Escherichia coliiJO1366(+reaction.3OAR140(value=0.017023), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0728930.4452073.339052e+002.183054e-01PathwayPredictor+DifferentialFVA
19Escherichia coliiJO1366(+reaction.3OAR140(value=0.025534), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0937380.3816802.862597e+003.274579e-01PathwayPredictor+DifferentialFVA
20Escherichia coliiJO1366(+reaction.3OAR140(value=0.034045), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.1041820.3181522.386141e+004.366107e-01PathwayPredictor+DifferentialFVA
21Escherichia coliiJO1366(+reaction.3OAR140(value=0.042474), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.1042230.2546251.909685e+005.457622e-01PathwayPredictor+DifferentialFVA
22Escherichia coliiJO1366(+reaction.3OAR140(value=0.050969), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0938640.1910971.433230e+006.549146e-01PathwayPredictor+DifferentialFVA
23Escherichia coliiJO1366()(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.0000000.000000e+009.823718e-01PathwayPredictor+DifferentialFVA
24Escherichia coliiJO1366()(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.0000000.000000e+009.823718e-01PathwayPredictor+DifferentialFVA
25Escherichia coliiJO1366(-reaction.3OAR140, -reaction.3OAS140, -reacti...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.9776397.332293e+001.052398e-07PathwayPredictor+DifferentialFVA
26Escherichia coliiJO1366(+reaction.3OAR140(value=0.008495), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.8779176.584378e+000.000000e+00PathwayPredictor+DifferentialFVA
27Escherichia coliiJO1366(+reaction.3OAR140(value=0.01699), +reaction.3...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.1253620.7656675.742501e+002.183052e-01PathwayPredictor+DifferentialFVA
28Escherichia coliiJO1366(+reaction.3OAR140(value=0.025485), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.1615170.6576644.932479e+003.274573e-01PathwayPredictor+DifferentialFVA
29Escherichia coliiJO1366(+reaction.3OAR140(value=0.033979), +reaction....(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.1795130.5482014.111511e+004.366097e-01PathwayPredictor+DifferentialFVA
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32Escherichia coliiJO1366()(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.0000000.000000e+009.823718e-01PathwayPredictor+DifferentialFVA
33Escherichia coliiJO1366()(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.0000000.000000e+009.823718e-01PathwayPredictor+DifferentialFVA
34Saccharomyces cerevisiaeiMM904(-reaction.13GS, -reaction.2OXOADPtim, -reacti...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.2540431.905325e+005.018186e-08PathwayPredictor+DifferentialFVA
35Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.036297), +reaction.2OX...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0054380.2266741.700055e+003.198510e-02PathwayPredictor+DifferentialFVA
36Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.072594), +reaction.2OX...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0095620.1993051.494785e+006.397018e-02PathwayPredictor+DifferentialFVA
37Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.10889), +reaction.2OXO...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0123740.1719351.289514e+009.595523e-02PathwayPredictor+DifferentialFVA
38Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.145187), +reaction.2OX...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0138720.1445661.084244e+001.279404e-01PathwayPredictor+DifferentialFVA
39Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.181484), +reaction.2OX...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0140570.1171978.789740e-011.599255e-01PathwayPredictor+DifferentialFVA
40Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.217781), +reaction.2OX...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0127570.0886346.647550e-011.919105e-01PathwayPredictor+DifferentialFVA
41Saccharomyces cerevisiaeiMM904()(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...-0.000000-0.000000-4.357423e-112.878657e-01PathwayPredictor+DifferentialFVA
42Saccharomyces cerevisiaeiMM904(-reaction.RBFSa, -reaction.RBFSb, -reaction.R...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.0000000.000000e+000.000000e+00PathwayPredictor+DifferentialFVA
43Saccharomyces cerevisiaeiMM904(-reaction.13GS, -reaction.2OXOADPtim, -reacti...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0000000.4491233.368421e+006.060071e-09PathwayPredictor+DifferentialFVA
44Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.036297), +reaction.2DD...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...NaNNaNNaNNaNPathwayPredictor+DifferentialFVA
45Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.072594), +reaction.2OX...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...0.0167870.3498892.624170e+006.397074e-02PathwayPredictor+DifferentialFVA
46Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.108891), +reaction.2DD...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...NaNNaNNaNNaNPathwayPredictor+DifferentialFVA
47Saccharomyces cerevisiaeiMM904(-reaction.13GS, -reaction.2OXOADPtim, -reacti...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...NaN0.000000-0.000000e+000.000000e+00PathwayPredictor+DifferentialFVA
48Saccharomyces cerevisiaeiMM904(-reaction.13GS, -reaction.2OXOADPtim, -reacti...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...NaN0.000000-0.000000e+006.097441e-13PathwayPredictor+DifferentialFVA
49Saccharomyces cerevisiaeiMM904(-reaction.13GS, -reaction.2OXOADPtim, -reacti...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...NaN0.000000-0.000000e+000.000000e+00PathwayPredictor+DifferentialFVA
50Saccharomyces cerevisiaeiMM904(-reaction.13GS, -reaction.2OXOADPtim, -reacti...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...NaN0.0000000.000000e+000.000000e+00PathwayPredictor+DifferentialFVA
51Saccharomyces cerevisiaeiMM904(-reaction.13GS, -reaction.2OXOADPtim, -reacti...(+reaction.MNXR5340#metanetx:MNXR5340, +reacti...NaN0.000000-0.000000e+000.000000e+00PathwayPredictor+DifferentialFVA
52Saccharomyces cerevisiaeiMM904(-reaction.13GS, -reaction.2OXOADPtim, -reacti...(+reaction.MNXR4008#metanetx:MNXR4008, +reacti...0.0000000.7456315.592233e+005.422716e-10PathwayPredictor+DifferentialFVA
53Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.036303), +reaction.2OX...(+reaction.MNXR4008#metanetx:MNXR4008, +reacti...0.0159420.6644584.983433e+003.199016e-02PathwayPredictor+DifferentialFVA
54Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.072605), +reaction.2OX...(+reaction.MNXR4008#metanetx:MNXR4008, +reacti...0.0279890.5832844.374633e+006.398033e-02PathwayPredictor+DifferentialFVA
55Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.108908), +reaction.2OX...(+reaction.MNXR4008#metanetx:MNXR4008, +reacti...0.0361410.5021113.765834e+009.597060e-02PathwayPredictor+DifferentialFVA
56Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.14521), +reaction.2OXO...(+reaction.MNXR4008#metanetx:MNXR4008, +reacti...0.0403980.4209383.157035e+001.279605e-01PathwayPredictor+DifferentialFVA
57Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.181513), +reaction.2OX...(+reaction.MNXR4008#metanetx:MNXR4008, +reacti...0.0407590.3397642.548233e+001.599507e-01PathwayPredictor+DifferentialFVA
58Saccharomyces cerevisiaeiMM904(+reaction.13GS(value=0.217815), +reaction.2OX...(+reaction.MNXR4008#metanetx:MNXR4008, +reacti...0.0372260.2585911.939433e+001.919410e-01PathwayPredictor+DifferentialFVA
59Saccharomyces cerevisiaeiMM904()(+reaction.MNXR4008#metanetx:MNXR4008, +reacti...0.0000430.0001991.488502e-032.879114e-01PathwayPredictor+DifferentialFVA
60Saccharomyces cerevisiaeiMM904(-reaction.GLCt1, -reaction.GLNS, -reaction.GL...(+reaction.MNXR4008#metanetx:MNXR4008, +reacti...NaNNaNNaNNaNPathwayPredictor+DifferentialFVA
61Saccharomyces cerevisiaeiMM904(-reaction.13GS, -reaction.2OXOADPtim, -reacti...(+reaction.MNXR4008#metanetx:MNXR4008, +reacti...NaN0.000000-0.000000e+000.000000e+00PathwayPredictor+DifferentialFVA
\n", "

62 rows × 9 columns

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" ], "text/plain": [ " host model \\\n", "0 Saccharomyces cerevisiae iMM904 \n", "1 Saccharomyces cerevisiae iMM904 \n", "2 Saccharomyces cerevisiae iMM904 \n", "3 Saccharomyces cerevisiae iMM904 \n", "4 Saccharomyces cerevisiae iMM904 \n", "5 Saccharomyces cerevisiae iMM904 \n", "6 Saccharomyces cerevisiae iMM904 \n", "7 Escherichia coli iJO1366 \n", "8 Escherichia coli iJO1366 \n", "9 Escherichia coli iJO1366 \n", "10 Escherichia coli iJO1366 \n", "11 Escherichia coli iJO1366 \n", "12 Escherichia coli iJO1366 \n", "13 Escherichia coli iJO1366 \n", "14 Escherichia coli iJO1366 \n", "15 Escherichia coli iJO1366 \n", "16 Escherichia coli iJO1366 \n", "17 Escherichia coli iJO1366 \n", "18 Escherichia coli iJO1366 \n", "19 Escherichia coli iJO1366 \n", "20 Escherichia coli iJO1366 \n", "21 Escherichia coli iJO1366 \n", "22 Escherichia coli iJO1366 \n", "23 Escherichia coli iJO1366 \n", "24 Escherichia coli iJO1366 \n", "25 Escherichia coli iJO1366 \n", "26 Escherichia coli iJO1366 \n", "27 Escherichia coli iJO1366 \n", "28 Escherichia coli iJO1366 \n", "29 Escherichia coli iJO1366 \n", ".. ... ... \n", "32 Escherichia coli iJO1366 \n", "33 Escherichia coli iJO1366 \n", "34 Saccharomyces cerevisiae iMM904 \n", "35 Saccharomyces cerevisiae iMM904 \n", "36 Saccharomyces cerevisiae iMM904 \n", "37 Saccharomyces cerevisiae iMM904 \n", "38 Saccharomyces cerevisiae iMM904 \n", "39 Saccharomyces cerevisiae iMM904 \n", "40 Saccharomyces cerevisiae iMM904 \n", "41 Saccharomyces cerevisiae iMM904 \n", "42 Saccharomyces cerevisiae iMM904 \n", "43 Saccharomyces cerevisiae iMM904 \n", "44 Saccharomyces cerevisiae iMM904 \n", "45 Saccharomyces cerevisiae iMM904 \n", "46 Saccharomyces cerevisiae iMM904 \n", "47 Saccharomyces cerevisiae iMM904 \n", "48 Saccharomyces cerevisiae iMM904 \n", "49 Saccharomyces cerevisiae iMM904 \n", "50 Saccharomyces cerevisiae iMM904 \n", "51 Saccharomyces cerevisiae iMM904 \n", "52 Saccharomyces cerevisiae iMM904 \n", "53 Saccharomyces cerevisiae 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