MATLAB generation adding lambda term for gRNA species

[hgscott]

The automatically generate MATLAB equations have a stable molecule diffusion (lambda) term for all of the gRNA species, e.g.:

CRISPRi-promoters/models/Single_gRNA_repression.m

Line 50 in 3cc7134

d_gRNA1 = alpha_r_gRNA1*sp.V1 - Cas_gRNA_binding*sp.gRNA1*sp.dCas9 - delta_g*sp.gRNA1 - lambda*sp.gRNA1;

But I only want degradation, no diffusion, per SI equation 1:

[hgscott]

I need to edit the MATLAB generation script, but since ontobee is down (as discovered in #1), I will manually edit the equations for now.

[hgscott]

The equations are manually edited on the manually-edited branch, e.g.:

CRISPRi-promoters/models/Single_gRNA_repression.m

Line 50 in 40aca7a

d_gRNA1 = alpha_r_gRNA1*sp.V1 - Cas_gRNA_binding*sp.gRNA1*sp.dCas9 - delta_g*sp.gRNA1;

[hgscott]

Removing the lambda doesn't look like it affected the results much. Fold repression for my single target site model went from 4.068 to 4.075 and everything qualitatively looks the same.

[hgscott]

Ontobee is now back up, which allows us to fix this in the MATLAB generation script.