High-level interface for users

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.

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. Drawing

Import the advanced interface.

In [1]:
from cameo import api

Searching for products

Search by trivial name.

In [2]:
api.products.search('caffeine')
Out[2]:
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.

In [3]:
api.products.search('chebi:27732')
Out[3]:
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).

In [4]:
for host in api.hosts:
    for model in host.models:
        print(host.name, model.id)
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).

In [5]:
from cameo.parallel import MultiprocessingView
mp_view = MultiprocessingView()

Limit the number of predicted heterlogous pathways to 4.

In [6]:
api.design.options.max_pathway_predictions = 4

Set a time limit of 30 minutes on individual heuristic optimizations.

In [7]:
api.design.options.heuristic_optimization_timeout = 30
In [8]:
report = api.design(product='vanillin', view=mp_view)
Starting searching for compound vanillin
Found 1 compounds that match query 'vanillin'
Id Name Formula
MNXM754vanillinC8H8O3
Choosing best match (vanillin) ... please interrupt if this is not the desired compound.

CH 3 O HO O - OBDepict

Predicting pathways for product vanillin in Escherichia coli (using model iJO1366).
Pathway 1
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
Max flux: 7.58479
Pathway 2
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
Max flux: 4.29196
Pathway 3
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
MNXR7147 3-methyl-2-oxobutanoate + formaldehyde <=> 2-d... -1000 1000
Max flux: 7.33229
Pathway 4
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
Predicting pathways for product vanillin in Saccharomyces cerevisiae (using model iMM904).
Pathway 1
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
Max flux: 1.90533
Pathway 2
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
Max flux: 3.36842
Pathway 3
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
Max flux: 5.59223
Optimizing 6 pathways
Starting optimization at Wed, 07 Jun 2017 08:50:22
Starting optimization at Wed, 07 Jun 2017 08:51:06
Starting optimization at Wed, 07 Jun 2017 08:51:07
Starting optimization at Wed, 07 Jun 2017 08:51:10
Finished after 00:30:13
Finished after 00:30:05
Starting optimization at Wed, 07 Jun 2017 09:21:19
Starting optimization at Wed, 07 Jun 2017 09:22:00
Finished after 00:31:49
Finished after 00:32:06
Finished after 00:18:19
Finished after 00:30:43
/Users/niso/Dev/cameo/cameo/strain_design/heuristic/evolutionary/objective_functions.py:289: RuntimeWarning:

invalid value encountered in double_scalars

In [9]:
report
Out[9]:
host model manipulations heterologous_pathway fitness yield product biomass method
0 Saccharomyces cerevisiae iMM904 (-YOR347C, -YAL038W, -YJL121C, -YPL061W) (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.007529 0.212878 1.282230e-01 4.715766e-02 PathwayPredictor+OptGene
1 Saccharomyces cerevisiae iMM904 (-YOR347C, -YAL038W, -YJL121C, -YDL022W) (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.007315 0.206474 1.233825e-01 4.724036e-02 PathwayPredictor+OptGene
2 Saccharomyces cerevisiae iMM904 (-YOR347C, -YAL038W, -YJL121C, -YNL111C) (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.007307 0.206212 1.231918e-01 4.724920e-02 PathwayPredictor+OptGene
3 Saccharomyces cerevisiae iMM904 (-YOR347C, -YAL038W, -YGR010W, -YJL026W, -YFR0... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.007305 0.206115 1.231222e-01 4.725242e-02 PathwayPredictor+OptGene
4 Saccharomyces cerevisiae iMM904 (-YDL021W, -YOR347C, -YAL038W, -YNR001C, -YFR0... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.007305 0.206115 1.231222e-01 4.725242e-02 PathwayPredictor+OptGene
5 Saccharomyces cerevisiae iMM904 (-YOR347C, -YAL038W, -YJL121C) (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.007305 0.206115 1.231222e-01 4.725242e-02 PathwayPredictor+OptGene
6 Saccharomyces cerevisiae iMM904 (-YOR347C, -YAL038W, -YJL121C, -YIR032C) (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.007305 0.206115 1.231222e-01 4.725242e-02 PathwayPredictor+OptGene
7 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 1.011305 7.584790e+00 0.000000e+00 PathwayPredictor+DifferentialFVA
8 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.008511), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.073736 0.900710 6.755327e+00 1.091526e-01 PathwayPredictor+DifferentialFVA
9 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.01699), +reaction.3... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.129365 0.790116 5.925867e+00 2.183049e-01 PathwayPredictor+DifferentialFVA
10 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.025485), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.166864 0.679434 5.095758e+00 3.274573e-01 PathwayPredictor+DifferentialFVA
11 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.033979), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.185506 0.566505 4.248787e+00 4.366097e-01 PathwayPredictor+DifferentialFVA
12 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.042474), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.185581 0.453387 3.400405e+00 5.457622e-01 PathwayPredictor+DifferentialFVA
13 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.050969), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.167136 0.340270 2.552028e+00 6.549146e-01 PathwayPredictor+DifferentialFVA
14 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... -0.000000 0.000000 0.000000e+00 9.823718e-01 PathwayPredictor+DifferentialFVA
15 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.000000 0.000000e+00 9.823718e-01 PathwayPredictor+DifferentialFVA
16 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.572262 4.291964e+00 0.000000e+00 PathwayPredictor+DifferentialFVA
17 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.008512), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.041647 0.508734 3.815508e+00 1.091527e-01 PathwayPredictor+DifferentialFVA
18 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.017023), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.072893 0.445207 3.339052e+00 2.183054e-01 PathwayPredictor+DifferentialFVA
19 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.025534), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.093738 0.381680 2.862597e+00 3.274579e-01 PathwayPredictor+DifferentialFVA
20 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.034045), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.104182 0.318152 2.386141e+00 4.366107e-01 PathwayPredictor+DifferentialFVA
21 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.042474), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.104223 0.254625 1.909685e+00 5.457622e-01 PathwayPredictor+DifferentialFVA
22 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.050969), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.093864 0.191097 1.433230e+00 6.549146e-01 PathwayPredictor+DifferentialFVA
23 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.000000 0.000000e+00 9.823718e-01 PathwayPredictor+DifferentialFVA
24 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.000000 0.000000e+00 9.823718e-01 PathwayPredictor+DifferentialFVA
25 Escherichia coli iJO1366 (-reaction.3OAR140, -reaction.3OAS140, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.977639 7.332293e+00 1.052398e-07 PathwayPredictor+DifferentialFVA
26 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.008495), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.877917 6.584378e+00 0.000000e+00 PathwayPredictor+DifferentialFVA
27 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.01699), +reaction.3... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.125362 0.765667 5.742501e+00 2.183052e-01 PathwayPredictor+DifferentialFVA
28 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.025485), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.161517 0.657664 4.932479e+00 3.274573e-01 PathwayPredictor+DifferentialFVA
29 Escherichia coli iJO1366 (+reaction.3OAR140(value=0.033979), +reaction.... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.179513 0.548201 4.111511e+00 4.366097e-01 PathwayPredictor+DifferentialFVA
... ... ... ... ... ... ... ... ... ...
32 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.000000 0.000000e+00 9.823718e-01 PathwayPredictor+DifferentialFVA
33 Escherichia coli iJO1366 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.000000 0.000000e+00 9.823718e-01 PathwayPredictor+DifferentialFVA
34 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.254043 1.905325e+00 5.018186e-08 PathwayPredictor+DifferentialFVA
35 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.036297), +reaction.2OX... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.005438 0.226674 1.700055e+00 3.198510e-02 PathwayPredictor+DifferentialFVA
36 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.072594), +reaction.2OX... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.009562 0.199305 1.494785e+00 6.397018e-02 PathwayPredictor+DifferentialFVA
37 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.10889), +reaction.2OXO... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.012374 0.171935 1.289514e+00 9.595523e-02 PathwayPredictor+DifferentialFVA
38 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.145187), +reaction.2OX... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.013872 0.144566 1.084244e+00 1.279404e-01 PathwayPredictor+DifferentialFVA
39 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.181484), +reaction.2OX... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.014057 0.117197 8.789740e-01 1.599255e-01 PathwayPredictor+DifferentialFVA
40 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.217781), +reaction.2OX... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.012757 0.088634 6.647550e-01 1.919105e-01 PathwayPredictor+DifferentialFVA
41 Saccharomyces cerevisiae iMM904 () (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... -0.000000 -0.000000 -4.357423e-11 2.878657e-01 PathwayPredictor+DifferentialFVA
42 Saccharomyces cerevisiae iMM904 (-reaction.RBFSa, -reaction.RBFSb, -reaction.R... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.000000 0.000000e+00 0.000000e+00 PathwayPredictor+DifferentialFVA
43 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.000000 0.449123 3.368421e+00 6.060071e-09 PathwayPredictor+DifferentialFVA
44 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.036297), +reaction.2DD... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
45 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.072594), +reaction.2OX... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... 0.016787 0.349889 2.624170e+00 6.397074e-02 PathwayPredictor+DifferentialFVA
46 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.108891), +reaction.2DD... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
47 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN 0.000000 -0.000000e+00 0.000000e+00 PathwayPredictor+DifferentialFVA
48 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN 0.000000 -0.000000e+00 6.097441e-13 PathwayPredictor+DifferentialFVA
49 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN 0.000000 -0.000000e+00 0.000000e+00 PathwayPredictor+DifferentialFVA
50 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN 0.000000 0.000000e+00 0.000000e+00 PathwayPredictor+DifferentialFVA
51 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR5340#metanetx:MNXR5340, +reacti... NaN 0.000000 -0.000000e+00 0.000000e+00 PathwayPredictor+DifferentialFVA
52 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.000000 0.745631 5.592233e+00 5.422716e-10 PathwayPredictor+DifferentialFVA
53 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.036303), +reaction.2OX... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.015942 0.664458 4.983433e+00 3.199016e-02 PathwayPredictor+DifferentialFVA
54 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.072605), +reaction.2OX... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.027989 0.583284 4.374633e+00 6.398033e-02 PathwayPredictor+DifferentialFVA
55 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.108908), +reaction.2OX... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.036141 0.502111 3.765834e+00 9.597060e-02 PathwayPredictor+DifferentialFVA
56 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.14521), +reaction.2OXO... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.040398 0.420938 3.157035e+00 1.279605e-01 PathwayPredictor+DifferentialFVA
57 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.181513), +reaction.2OX... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.040759 0.339764 2.548233e+00 1.599507e-01 PathwayPredictor+DifferentialFVA
58 Saccharomyces cerevisiae iMM904 (+reaction.13GS(value=0.217815), +reaction.2OX... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.037226 0.258591 1.939433e+00 1.919410e-01 PathwayPredictor+DifferentialFVA
59 Saccharomyces cerevisiae iMM904 () (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... 0.000043 0.000199 1.488502e-03 2.879114e-01 PathwayPredictor+DifferentialFVA
60 Saccharomyces cerevisiae iMM904 (-reaction.GLCt1, -reaction.GLNS, -reaction.GL... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... NaN NaN NaN NaN PathwayPredictor+DifferentialFVA
61 Saccharomyces cerevisiae iMM904 (-reaction.13GS, -reaction.2OXOADPtim, -reacti... (+reaction.MNXR4008#metanetx:MNXR4008, +reacti... NaN 0.000000 -0.000000e+00 0.000000e+00 PathwayPredictor+DifferentialFVA

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