Structural Modelling

Methods acting on the model

All structural modelling analyses can be implemented by actions on the model's stoichiometry matrices. A number of common analyses are provided as methods of the model itself:

Orphan Metabolites

An orphan metabolite is one that cannot be balanced at steady-state because it is involved with only one reaction, and can therefore be only consumed or produced. These are identified by the OrphanMets() method.

   1 >>> orphans = m.OrphanMets()
   2 >>> len(orphans)
   3 7
   4 >>> print orphans
   5 ['x_CO2', 'x_NADPH_ch', 'x_Proton_ch', 'x_NADP_ch', 'x_PGA_cyt', 'x_GAP_cyt', 'x_DHAP_cyt']
   6 >>> 

Here the model has 7 orphan metabolites, but, as denoted by the x_ prefix, they are all external metabolites, and so this does not indicate a problem with model. In general, when practical , it is desirable to associate external metabolites with exactly one transport reaction, as it can considerably simplify subsequent analys of results obtained from the model.

Dead Reactions

A dead reaction is one which can carry no flux at steady-state. This is usually, but not always, caused by the presence of internal orphan metabolites. The inability to carry flux applies to any further analysis of the model - for example, a dead reaction will nver be present as part of an LP solution, will never show up in an elementary mode and will always carry zero flux (within machine prescision) in any kinetic steady-state determination. They are identified by the DeadReactions() method:

   1 >>> dead = m.DeadReactions()
   2 >>> len(dead)
   3 1
   4 >>> print dead
   5 ['GlcTx']

Here we see that a glucose 6 phosphate transporter is dead, despite the fact that in this case the internal substrate, G6P, is not an orphan metabolite.

   1 GlcTx:
   2          x_G6P <>  G6P
   3         ~

The reason that the reaction is dead is that phosphate (in this model) is a conserved moiety, and the transporter cannot carry steady-state flux unless an external phosphate is exchanged for the internal G6P.

Conserved Moieties

Enzyme (reaction) subsets

The Matrix Class

Fully described in utility section - enough here to understand SMs, datasets and monitors.