A general rule for biological diagrams

All regulatory interactions (inhibition, activation, etc.) should be indicated as an effect of a species on a reaction. The resulting diagram is called a process diagram and it unambiguously translates to a system of differential equations.

You will recall that an SBML species is a molecule or molecular complex in a place or compartment and a SBML reaction is a process (biochemical, transport, or binding)

I blogged about this a few years ago and the blog post is here:

http://symbolsandarrows.blogspot.com/2008/08/general-rule-for-cell-biological-map.html

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