search

TASBE / CRISPRi-promoters

0 stars 0 forks source link

MATLAB generation adding lambda term for gRNA species #3

Open hgscott opened 1 month ago

hgscott commented 1 month ago

The automatically generate MATLAB equations have a stable molecule diffusion (lambda) term for all of the gRNA species, e.g.: https://github.com/TASBE/CRISPRi-promoters/blob/3cc71346ff5ea5c1b0f0799642daf394242af50f/models/Single_gRNA_repression.m#L50

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

image
hgscott commented 1 month ago

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 commented 1 month ago

The equations are manually edited on the manually-edited branch, e.g.: https://github.com/TASBE/CRISPRi-promoters/blob/40aca7ad972c4318845989b55a2872437036f542/models/Single_gRNA_repression.m#L50

hgscott commented 1 month ago

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 commented 1 month ago

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