Exercise 10.1: Making a stand-alone app for exploring parameters


Recall that in our lesson on dashboarding, we built a dashboard investigating how fold change in gene expression varies with repressor copy number \(R\) and inducer concentration \(c\). The theoretical curve is

\begin{align} \text{fold change} = \left[1 + \frac{\frac{R}{K}\left(1 + c/K_\mathrm{d}^\mathrm{A}\right)^2}{\left(1 + c/K_\mathrm{d}^\mathrm{A}\right)^2 + K_\mathrm{switch}\left(1 + c/K_\mathrm{d}^\mathrm{I}\right)^2}\right]^{-1}, \end{align}

with parameters given in the table below.

Parameter

Description

\(K_\mathrm{d}^\mathrm{A}\)

dissoc. const. for active repressor binding IPTG

\(K_\mathrm{d}^\mathrm{I}\)

dissoc. const. for inactive repressor binding IPTG

\(K_\mathrm{switch}\)

equil. const. for switching active/inactive

\(K\)

dissoc. const. for active repressor binding operator

\(R\)

number of repressors in cell

Rebuild that dashboard, but use JavaScript callbacks so you can have full interactivity with a stand-alone HTML file.