High-level interface for users

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.

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.
In [1]:
from cameo import api
In [2]:
report = api.design(product='vanillin')
Starting searching for compound vanillin
Found 2 compounds that match query 'vanillin'
Id Name Formula
MNXM754vanillinC8H8O3
MNXM741anilineC6H7N
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).
Predicting pathways for product vanillin in Saccharomyces cerevisiae (using model iMM904).
Optimizing 8 pathways
Starting optimization at Tue, 24 May 2016 12:00:41
Finished after 00:02:56
Starting optimization at Tue, 24 May 2016 12:04:07
Finished after 00:03:40
Starting optimization at Tue, 24 May 2016 12:08:26
Finished after 00:04:09
Starting optimization at Tue, 24 May 2016 12:12:53
Finished after 00:01:57
Starting optimization at Tue, 24 May 2016 12:15:11
Finished after 00:01:27
Starting optimization at Tue, 24 May 2016 12:16:49
Finished after 00:01:22
Starting optimization at Tue, 24 May 2016 12:18:22
Finished after 00:01:09
Starting optimization at Tue, 24 May 2016 12:19:40
Finished after 00:02:31
In [3]:
report
Out[3]:
[(<cameo.strain_design.heuristic.evolutionary_based.OptGeneResult at 0x122f12400>,
  +MNXR5336+MNXR5340+MNXR7229+MNXR68718),
 (<cameo.strain_design.heuristic.evolutionary_based.OptGeneResult at 0x122e54c50>,
  +MNXR230+MNXR640+MNXR5336+MNXR5340),
 (<cameo.strain_design.heuristic.evolutionary_based.OptGeneResult at 0x122f79358>,
  +MNXR640+MNXR5336+MNXR5340+MNXR68718),
 (<cameo.strain_design.heuristic.evolutionary_based.OptGeneResult at 0x122ee6278>,
  +MNXR5336+MNXR5340+MNXR7734+MNXR68718),
 (<cameo.strain_design.heuristic.evolutionary_based.OptGeneResult at 0x123025da0>,
  +MNXR5336+MNXR5340+MNXR68718),
 (<cameo.strain_design.heuristic.evolutionary_based.OptGeneResult at 0x122fe90b8>,
  +MNXR5336+MNXR5340+MNXR14769),
 (<cameo.strain_design.heuristic.evolutionary_based.OptGeneResult at 0x122de4cf8>,
  +MNXR230+MNXR5336+MNXR5340),
 (<cameo.strain_design.heuristic.evolutionary_based.OptGeneResult at 0x122cb6518>,
  +MNXR5336+MNXR5340+MNXR5836+MNXR7067)]

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