Balancing equations

[zoey-rw]

Continuing discussion from opencobra/memote/issues/732

The notebook 02_balance_equations.ipynb contains examples of identifying unbalanced reactions using memote's find_charge_unbalanced_reactions(). Charges for metabolites can be investigated in MetanetX and BiGG using the R functions in 02_check_equation_stoichiometry.r Switching to R is cumbersome, but I can code much faster in it, so the R code can be translated to Python at a later time.

Ideally, each example will include a different strategy for balancing an equation (or deciding that it should be left alone)

To do:

• find a good "example model" to demonstrate fixes (having trouble getting cobrapy to read BiGG models directly)
• figure out why BiGG metabolites are not always listed in the MetanetX cross-ref, even if they're not deprecated
• determine whether deprecated IDs need to be linked in

Examples:

• example: simply adding proton to one side
• example: modifying metabolite charge or coefficient
• example: deciding not to balance an equation