cameo reuses and extends model data structures defined by cobrapy (COnstraints-Based Reconstruction and Analysis tool for Python). So, in addition to following this quick start guide and other cameo tutorials, we encourage you to explore cobrapy's documentation as well.
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from cameo import load_model
For example, load a genome-scale metabolic reconstruction of Escherichia coli.
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model = load_model("iJO1366")
Models, reactions, metabolites, etc., return HTML when evaluated in Jupyter notebooks and can be easily inspected.
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model
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solution = model.optimize()
A quick overview of the solution can be obtained in inspecting it.
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solution
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A data frame representation of the solution is accessible via solution.to_frame().
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solution.to_frame()
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Data frames make it very easy to process results. For example, let's take a look at reactions with flux != 0
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solution.to_frame().query('fluxes != 0')
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Objects—models, reactions, metabolites, genes—can easily be explored in the Jupyter notebook, taking advantage of tab completion. For example, place your cursor after the period in model.reactions. and press the TAB key. A dialog will appear that allows you to navigate the list of reactions encoded in the model.
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model.reactions.PGK # delete PGK, place your cursor after the period and press the TAB key.
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For example, you can access the E4PD (Erythrose 4-phosphate dehydrogenase) reaction in the model.
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model.reactions.E4PD
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Be aware that, due to variable naming restrictions in Python, dot notation access to reactions (and other objects) might not work in some cases.
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# model.reactions.12DGR120tipp # uncommenting and running this cell will produce a syntax error
In those cases you need to use the model.reactions.get_by_id.
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model.reactions.get_by_id('12DGR120tipp')
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Metabolites are accessible through model.metabolites. For example, D-glucose in the cytosol compartment.
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model.metabolites.glc__D_c
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And it is easy to find the associated reactions
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model.metabolites.glc__D_c.reactions
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A list of the genes encoded in the model can be accessed via model.genes.
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model.genes[0:10]
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Other additional attributes can be accessed to explore the model. For example, exchange reactions that allow certain metabolites to enter or leave the model can be accessed through model.exchanges.
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model.exchanges[0:10]
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Or, the current medium can be accessed through model.medium.
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model.medium
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It is also possible to get a list of essential reactions ...
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from cobra.flux_analysis import find_essential_reactions
list(find_essential_reactions(model))[0:10]
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... and essential genes.
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from cobra.flux_analysis import find_essential_genes
list(find_essential_genes(model))[0:10]
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