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#103 No way to describe autocatalysis
Since PD notation describes pools of nodes, there is no way to describe the fact that a modulation must be perfromed by the same instance as is participating in the reaction. The obvious example of this is autophosphorylation, where a protein catalyses its own phosphorylation.
Discussion
We will think about this for L 1.1 or L2.
Needs discussion
I agree. This is a subproblem of the instance and generics issue. To be discussed conjointly with ER maybe.
I think this should be added in the postponed issues section. Appendix C. Perhaps we should rename this as Unresoved issues.
Index.. Huh, really? :)
I think this is a non-issue. The mistake was to preclude several arcs coming from the same EPNs. If I was to develop a model involving autophosphorylation, I would use the concentration of the enzyme as the substrate and the enzyme. In SBML, I would use the species as reactant and modifier.
Trans versus cis is an ER problem. Or a problem for an advanced version of the solution to the genericity problem. But this is not the issue here. The autocatalysis is solved by removing a restricting and unecessary rule of SBGN PD. We should not restrict the number of arcs going from one EPN to a PN. (and what if there are two consumption arcs going from one EPN to a PN? How is it a problem, except cluttering the map?)