Implement groups of species to enable primitive rules

[jonrkarr]

Hi Jonathan,

There is currently a few issues with reconstructing rate laws:

• RateLawEquation in wc-kb and wc-lang do not support observables. Observables here is to represent the sum of multiple ensemble proteins with the same Uniprot Ids
  • A quick alternative is to not use observables but create a new rate equation for each ensemble protein. This will create many rate laws.
• Per discussion a while ago, we are going to have a rate law for each isoenzyme. This itself will create many rate laws. If we implement this and 1a above, there will be many rate laws for each reaction. Is this a good implementation?
• The rate law has substrates/products in the expression. Ideally, we want to map the compounds in the expression to the substrates/products in the metabolic reaction. However, because the reactions in Sabio-RK is sometimes generic, we also assign rate laws if they share the same ec numbers. The issue with this now is that the compound in the expression is not mappable to our metabolic reaction.

Some possible quick alternatives:

• Make RateLawEquation support observables. Perhaps that can be brought up for discussion in the simulation meeting later, if you don’t mind me gate-crashing the meeting for a while?
• Only record kcat and all the Ks as parameters. Since FBA only cares about the bounds and we only use kcat, we do not really need rate law equation for now in the simulation.

Thanks, Yin Hoon