- OBDepict

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. .. raw:: html

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. .. raw:: html

.. code:: python from cameo import api .. raw:: html .. code:: python report = api.design(product='vanillin') .. raw:: html Starting searching for compound vanillin .. raw:: html Found 2 compounds that match query 'vanillin' .. raw:: html

Id	Name	Formula
MNXM754	vanillin	C8H8O3
MNXM741	aniline	C6H7N

.. raw:: html Choosing best match (vanillin) ... please interrupt if this is not the desired compound. .. raw:: html

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.. raw:: html Predicting pathways for product vanillin in Escherichia coli (using model iJO1366). .. parsed-literal:: .. raw:: html

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.. raw:: html Predicting pathways for product vanillin in Saccharomyces cerevisiae (using model iMM904). .. parsed-literal:: .. raw:: html

.. parsed-literal:: 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 .. parsed-literal:: [(, +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)] IPython notebook ~~~~~~~~~~~~~~~~ Click `here `__ to download this page as an IPython notebook.