Why does the CDS part of a DNA Assembly have a dimerize parameter? A maturation time parameters?

[WilliamIX]

This seems oddly specific and strikes me as the kind of reaction that should be incorporated into a mechanism (involving a specific protein type, and possibly higher orders of complex being formed) rather than a Component.

Similarly, maturation_time should be part of the different translation mechanisms.

[murrayrm]

I think the idea was to try to make it easy for the user to create a dimerized protein without having to specify everything in detail. So you could say, for example,

cds_myProtein = CDS('myProtein', dimerize=True, maturation_rate=1)
my_dna = assemble_dna(prom=prom_ptet, utr5 = utr5_bcd2, cds=cds_myProtein)

and you would now have a set of components (and hence species and reactions) that created all of the species and reactions required to form proteins that mature at a given rate and form a dimer (which could then act on some other component).

I agree that maturation time could be moved to a mechanism (if not listed, then all proteins are automatically assumed to mature in zero time).

Dimerization is a property of a protein that you may not want to move to a mechanism, since if a protein has to former a dimer to act then this may matter as a fundamental property of the CRN (eg, you get Hill functions with different Hill coefficients). The mechanism could be that dimerization happens instantaneously (I guess), but I would be careful.

What would the corresponding code look like if you didn't include that argument?

[WilliamIX]

Currently dimerization is not even used as far as I can tell. I will be putting all of this stuff into mechanisms.

[murrayrm]

Agree it is not used in the proof-of-concept implementation, but I would encourage you to think through what the user code will look like for creating a dimerized protein before getting rid of the current interface. If one line gets replaced by 6, you should think about whether that is the right approach.