Easy strain design using a high-level interface =============================================== .. container:: alert alert-warning If you’re running this notebook on `try.cameo.bio `__, things might run very slow due to our inability to provide access to the `CPLEX `__ solver on a public webserver. Furthermore, Jupyter kernels might crash and restart due to memory limitations on the server. To avoid that, we encourage the users to shutdown previously opened notebooks. You can do from the `Home` page that by selecting the notebooks highlighted in green and pressing the `Shutdown` button on the top of the menu. Users primarily interested in using cameo as a tool for enumerating metabolic engineering strategies have access to cameo’s advanced programming interface via `cameo.api` that provides access to potential products (`cameo.api.products`), host organisms (`cameo.api.hosts`) and a configurable design function (`cameo.api.design`). Running `cameo.api.design` requires only minimal input and will run the following workflow. Import the advanced interface. .. code:: ipython3 from cameo import api Searching for products ---------------------- Search by trivial name. .. code:: ipython3 api.products.search('caffeine') .. raw:: html
InChI SMILES charge formula mass name source search_rank
MNXM680 InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)... CN1C=NC2=C1C(=O)N(C)C(=O)N2C 0 C8H10N4O2 194.1906 caffeine chebi:27732 0
Search by ChEBI ID. .. code:: ipython3 api.products.search('chebi:27732') .. raw:: html
InChI SMILES charge formula mass name source search_rank
MNXM680 InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)... CN1C=NC2=C1C(=O)N(C)C(=O)N2C 0 C8H10N4O2 194.1906 caffeine chebi:27732 0
Host organisms -------------- 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). .. code:: ipython3 for host in api.hosts: for model in host.models: print(host.name, model.id) .. parsed-literal:: Escherichia coli iJO1366 Saccharomyces cerevisiae iMM904 Computing strain engineering strategies --------------------------------------- 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). .. code:: ipython3 from cameo.parallel import MultiprocessingView mp_view = MultiprocessingView() Limit the number of predicted heterlogous pathways to 4. .. code:: ipython3 api.design.options.max_pathway_predictions = 4 Set a time limit of 30 minutes on individual heuristic optimizations. .. code:: ipython3 api.design.options.heuristic_optimization_timeout = 30 .. code:: ipython3 report = api.design(product='vanillin', view=mp_view) .. raw:: html Starting searching for compound vanillin .. raw:: html Found 1 compounds that match query 'vanillin' .. raw:: html
Id Name Formula
MNXM754vanillinC8H8O3
.. raw:: html Choosing best match (vanillin) ... please interrupt if this is not the desired compound. .. raw:: html

.. raw:: html .. raw:: html Predicting pathways for product vanillin in Escherichia coli (using model iJO1366). .. raw:: html Pathway 1 .. raw:: html
equation lower_bound upper_bound
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR2795 S-adenosyl-L-methionine + glycine <=> H(+) + S... -1000 1000
MNXR68718 H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... -1000 1000
.. parsed-literal:: Max flux: 4.29196 .. raw:: html Pathway 2 .. raw:: html
equation lower_bound upper_bound
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR84169 (6R)-5,10-methylenetetrahydrofolate + glycine ... -1000 1000
MNXR68718 H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... -1000 1000
.. parsed-literal:: Max flux: 7.28363 .. raw:: html Pathway 3 .. raw:: html
equation lower_bound upper_bound
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR68718 H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... -1000 1000
MNXR651 2.0 H(+) + NADH + formate <=> H2O + formaldehy... -1000 1000
.. parsed-literal:: Max flux: 7.58479 .. raw:: html Pathway 4 .. raw:: html
equation lower_bound upper_bound
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR230 H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ... -1000 1000
MNXR640 methanol + NAD(+) <=> H(+) + NADH + formaldehyde -1000 1000
.. parsed-literal:: .. parsed-literal:: This is the format of your plot grid: [ (1,1) x1,y1 ] [ (1,2) x2,y2 ] [ (2,1) x3,y3 ] [ (2,2) x4,y4 ] .. raw:: html .. raw:: html
.. raw:: html .. raw:: html Predicting pathways for product vanillin in Saccharomyces cerevisiae (using model iMM904). .. raw:: html Pathway 1 .. raw:: html
equation lower_bound upper_bound
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR68718 H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... -1000 1000
.. parsed-literal:: Max flux: 3.36842 .. raw:: html Pathway 2 .. raw:: html
equation lower_bound upper_bound
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR230 H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ... -1000 1000
.. parsed-literal:: Max flux: 1.90533 .. raw:: html Pathway 3 .. raw:: html
equation lower_bound upper_bound
MNXR4008 H(+) + 3-oxoadipate <=> H2O + 5-oxo-4,5-dihydr... -1000 1000
MNXR184 3-oxoadipyl-CoA + succinate <=> 3-oxoadipate +... -1000 1000
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR228 CO2 + 5-oxo-4,5-dihydro-2-furylacetate <=> H(+... -1000 1000
MNXR4119 2.0 H(+) + 3-carboxy-cis,cis-muconate <=> 3,4-... -1000 1000
MNXR209 CoA + 3-oxoadipyl-CoA <=> acetyl-CoA + succiny... -1000 1000
MNXR3655 2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate ... -1000 1000
.. parsed-literal:: Max flux: 5.59223 .. parsed-literal:: .. parsed-literal:: This is the format of your plot grid: [ (1,1) x1,y1 ] [ (1,2) x2,y2 ] [ (2,1) x3,y3 ] [ (2,2) x4,y4 ] .. raw:: html
.. parsed-literal:: Optimizing 6 pathways Starting optimization at Tue, 06 Feb 2018 14:06:57 Starting optimization at Tue, 06 Feb 2018 14:07:50 Starting optimization at Tue, 06 Feb 2018 14:07:57 Starting optimization at Tue, 06 Feb 2018 14:07:58 .. raw:: html

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.. parsed-literal:: Finished after 00:32:09 Starting optimization at Tue, 06 Feb 2018 14:39:37 .. raw:: html

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.. parsed-literal:: Finished after 00:33:43 Starting optimization at Tue, 06 Feb 2018 14:41:56 .. raw:: html

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.. raw:: html

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.. parsed-literal:: Finished after 00:30:09 Finished after 00:30:02 .. parsed-literal:: /Users/joaca/Documents/repositories/cameo/cameo/strain_design/heuristic/evolutionary/objective_functions.py:287: RuntimeWarning: invalid value encountered in double_scalars /Users/joaca/Documents/repositories/cameo/cameo/strain_design/heuristic/evolutionary/objective_functions.py:354: RuntimeWarning: invalid value encountered in double_scalars .. code:: ipython3 report .. raw:: html
host model manipulations heterologous_pathway fitness yield product biomass method
0 Saccharomyces cerevisiae iMM904 (-YPL110C) (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.000043 0.000199 0.001489 2.879114e-01 PathwayPredictor+OptGene
1 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.572262 4.291964 8.136452e-08 PathwayPredictor+DifferentialFVA
2 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.000000 0.000000 0.000000e+00 PathwayPredictor+DifferentialFVA
3 Escherichia coli iJO1366 (reaction.3OAR140(value=0.01699), reaction.3OA... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.508185 3.351657 0.000000e+00 PathwayPredictor+DifferentialFVA
4 Escherichia coli iJO1366 (reaction.3OAR140(value=0.025534), reaction.3O... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.093738 0.381679 2.862596 3.274580e-01 PathwayPredictor+DifferentialFVA
5 Escherichia coli iJO1366 (reaction.3OAR140(value=0.034045), reaction.3O... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.475180 3.563847 0.000000e+00 PathwayPredictor+DifferentialFVA
6 Escherichia coli iJO1366 (reaction.3OAR140(value=0.042474), reaction.3O... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.104223 0.254625 1.909686 5.457622e-01 PathwayPredictor+DifferentialFVA
7 Escherichia coli iJO1366 (reaction.3OAR140(value=0.050969), reaction.3O... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.093864 0.191097 1.433230 6.549146e-01 PathwayPredictor+DifferentialFVA
8 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.000000 0.000000 9.823718e-01 PathwayPredictor+DifferentialFVA
9 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... -0.000000 0.000000 0.000000 9.823718e-01 PathwayPredictor+DifferentialFVA
10 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.971150 7.283628 0.000000e+00 PathwayPredictor+DifferentialFVA
11 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN 0.000000 0.000000e+00 PathwayPredictor+DifferentialFVA
12 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN 0.000000 0.000000e+00 PathwayPredictor+DifferentialFVA
13 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN -0.000000 0.000000e+00 PathwayPredictor+DifferentialFVA
14 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN 0.000000 0.000000e+00 PathwayPredictor+DifferentialFVA
15 Escherichia coli iJO1366 (reaction.3OAR140(value=0.042474), reaction.3O... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.178214 0.435389 3.265417 5.457622e-01 PathwayPredictor+DifferentialFVA
16 Escherichia coli iJO1366 (reaction.3OAR140(value=0.050969), reaction.3O... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.160501 0.326762 2.450714 6.549146e-01 PathwayPredictor+DifferentialFVA
17 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.000000 0.000000 9.823718e-01 PathwayPredictor+DifferentialFVA
18 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... -0.000000 0.000000 0.000000 9.823718e-01 PathwayPredictor+DifferentialFVA
19 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 1.011305 7.584790 0.000000e+00 PathwayPredictor+DifferentialFVA
20 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN -0.000000 0.000000e+00 PathwayPredictor+DifferentialFVA
21 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN 0.000000 0.000000e+00 PathwayPredictor+DifferentialFVA
22 Escherichia coli iJO1366 (reaction.3OAR140(value=0.025485), reaction.3O... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
23 Escherichia coli iJO1366 (reaction.3OAR140(value=0.034045), reaction.3O... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.668001 4.390359 0.000000e+00 PathwayPredictor+DifferentialFVA
24 Escherichia coli iJO1366 (reaction.3OAR140(value=0.042474), reaction.3O... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.185581 0.453387 3.400405 5.457622e-01 PathwayPredictor+DifferentialFVA
25 Escherichia coli iJO1366 (reaction.3OAR140(value=0.050969), reaction.3O... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.167136 0.340270 2.552028 6.549146e-01 PathwayPredictor+DifferentialFVA
26 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... -0.000000 0.000000 0.000000 9.823718e-01 PathwayPredictor+DifferentialFVA
27 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... -0.000000 0.000000 0.000000 9.823718e-01 PathwayPredictor+DifferentialFVA
28 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.449123 3.368421 5.205722e-09 PathwayPredictor+DifferentialFVA
29 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN 0.000000 4.984455e-12 PathwayPredictor+DifferentialFVA
30 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.072594), reaction.2DDA7... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
31 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.108891), reaction.2DDA7... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
32 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.145187), reaction.2DDA7... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
33 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.181484), reaction.2DDA7... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
34 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.217781), reaction.2DDA7... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
35 Saccharomyces cerevisiae iMM904 (-reaction.SULR, -reaction.THRS, -reaction.TMD... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 -0.000000 -0.000000 0.000000e+00 PathwayPredictor+DifferentialFVA
36 Saccharomyces cerevisiae iMM904 (-reaction.ENO, -reaction.ERGSTter, -reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
37 Saccharomyces cerevisiae iMM904 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... -0.000000 0.000000 0.000000 2.878657e-01 PathwayPredictor+DifferentialFVA
38 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.254043 1.905325 4.603305e-08 PathwayPredictor+DifferentialFVA
39 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.036297), reaction.2OXOA... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.005438 0.226674 1.700055 3.198537e-02 PathwayPredictor+DifferentialFVA
40 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.072594), reaction.2OXOA... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.009562 0.199305 1.494785 6.397013e-02 PathwayPredictor+DifferentialFVA
41 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.108891), reaction.2OXOA... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.012374 0.171935 1.289514 9.595523e-02 PathwayPredictor+DifferentialFVA
42 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.145187), reaction.2OXOA... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.013872 0.144566 1.084244 1.279406e-01 PathwayPredictor+DifferentialFVA
43 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.181484), reaction.2OXOA... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.014057 0.117197 0.878974 1.599255e-01 PathwayPredictor+DifferentialFVA
44 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.21778), reaction.2OXOAD... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.012757 0.088634 0.664755 1.919105e-01 PathwayPredictor+DifferentialFVA
45 Saccharomyces cerevisiae iMM904 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... -0.000000 -0.000000 -0.000000 2.878657e-01 PathwayPredictor+DifferentialFVA
46 Saccharomyces cerevisiae iMM904 (-reaction.ACOTAim, -reaction.ACS, -reaction.A... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN -0.000000 -1.316513e-12 PathwayPredictor+DifferentialFVA
47 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... -0.000000 0.745631 5.592233 -7.750803e-11 PathwayPredictor+DifferentialFVA
48 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.036303), reaction.2OXOA... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.015942 0.664458 4.983433 3.199022e-02 PathwayPredictor+DifferentialFVA
49 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.072605), reaction.2OXOA... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.027989 0.583284 4.374633 6.398044e-02 PathwayPredictor+DifferentialFVA
50 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.108908), reaction.2OXOA... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.036141 0.502111 3.765833 9.597049e-02 PathwayPredictor+DifferentialFVA
51 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.14521), reaction.2OXOAD... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.040398 0.420938 3.157035 1.279606e-01 PathwayPredictor+DifferentialFVA
52 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.181513), reaction.2OXOA... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.040759 0.339765 2.548235 1.599507e-01 PathwayPredictor+DifferentialFVA
53 Saccharomyces cerevisiae iMM904 (reaction.13GS(value=0.217815), reaction.2OXOA... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.037226 0.258591 1.939434 1.919409e-01 PathwayPredictor+DifferentialFVA
54 Saccharomyces cerevisiae iMM904 () (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.000043 0.000199 0.001489 2.879114e-01 PathwayPredictor+DifferentialFVA
55 Saccharomyces cerevisiae iMM904 (-reaction.GLCt1, -reaction.GLNS, -reaction.GL... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
56 Saccharomyces cerevisiae iMM904 () (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.000043 0.000199 0.001489 2.879114e-01 PathwayPredictor+DifferentialFVA
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