1.3 Running OptMet
======================

.. code:: ipython3

    from bokeh.io import output_notebook
    output_notebook()



.. raw:: html

    
        <div class="bk-root">
            <a href="http://bokeh.pydata.org" target="_blank" class="bk-logo bk-logo-small bk-logo-notebook"></a>
            <span id="1e432909-f940-4472-b3ec-bdc118c7a702">Loading BokehJS ...</span>
        </div>




.. code:: ipython3

    from cameo import models
    from marsi.cobra.strain_design import OptMet

.. code:: ipython3

    model = models.bigg.iJO1366

.. code:: ipython3

    optimization = OptMet(model=model)

.. code:: ipython3

    target = model.metabolites.succ_c
    biomass = model.reactions.BIOMASS_Ec_iJO1366_core_53p95M
    substrate = model.reactions.EX_glc__D_e
    
    # Succinate production needs to be anaerobic to yield growth coupled designs.
    model.reactions.EX_o2_e.lower_bound = 0

.. code:: ipython3

    result = optimization.run(target=target, biomass=biomass, substrate=substrate, max_evaluations=3000)

.. code:: ipython3

    result