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.
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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.
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.. code:: python
from cameo import api
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.. code:: python
report = api.design(product='vanillin')
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Starting searching for compound vanillin
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Found 2 compounds that match query 'vanillin'
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Id
Name
Formula
MNXM754
vanillin
C8H8O3
MNXM741
aniline
C6H7N
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Choosing best match (vanillin) ... please interrupt if this is not the desired compound.
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Predicting pathways for product vanillin in Escherichia coli (using model iJO1366).
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Predicting pathways for product vanillin in Saccharomyces cerevisiae (using model iMM904).
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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
.. code:: python
report
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[(,
+MNXR5336+MNXR5340+MNXR7229+MNXR68718),
(,
+MNXR230+MNXR640+MNXR5336+MNXR5340),
(,
+MNXR640+MNXR5336+MNXR5340+MNXR68718),
(,
+MNXR5336+MNXR5340+MNXR7734+MNXR68718),
(,
+MNXR5336+MNXR5340+MNXR68718),
(,
+MNXR5336+MNXR5340+MNXR14769),
(,
+MNXR230+MNXR5336+MNXR5340),
(,
+MNXR5336+MNXR5340+MNXR5836+MNXR7067)]
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