Removing extraneous reactions

[vipulsinghal02]

Remove a couple of unnecessary reactions that are present, or make them optional. For example, sigma 70 binding to RNAP does nothing for us modeling wise, unless we need to design a circuit with different sigma factors. Right now the forward rate is just a billion times that of the reverse rate, effectively removing sigma 70 as a species separate from RNAP.

One way to do this might be to make some of these unnecessary reactions optional. For example, the sigma 70 reactions only show up when other sigma factors are present.

[murrayrm]

Another approach to handle this might be to link it to the idea of enabling core mechanisms as individual functions, which is being discussed in issue #25 (python version of toolbox). In MATLAB syntax, we could say something like

txtl_enable(['sigma factors'])

if we want to turn on support for processing of sigma factors (which could be left off by default). This would set some flags inside of the toolbox so that when reactions are created in the drivers, we turn on the reactions related to sigma factors.

[vipulsinghal02]

few other features to add as optional: 1) Cross talk between inducers and activators. 2) Between activators and promoters. 2) Leaky promoter expression

These can be added as part specific arguments.

[vipulsinghal02]

The commit 6d8338b4e84cdf548129fc2ddbfdc8ee812b5e1c removed sigma factors as a mechanism. To be re-added as an optional module as mentioned above.