RMA Kinetics

Source code for "Modeling kinetics of synthetic serum markers for monitoring deep tissue gene expression".

Getting Started

Basic Usage

There are three main model classes for constitutive or drug induced RMA expression.

1. ConstitutiveRMA.
2. TetRMA (Tet-Off based marker expression).
3. ChemogeneticRMA (CNO induced marker expression with Tet-Off gating).

Models can be initialized from these classes and ran using the simulate method.

For example, to run the constitutive RMA expression model for 72 hours,

from rma_kinetics.models import ConstitutiveRMA
import matplotlib.pyplot as plt

# initialize constitutive RMA model
model = ConstitutiveRMA(
    rma_prod_rate=7e-3,
    rma_rt_rate=1,
    rma_deg_rate=7e-3
)

# simulate model and plot plasma RMA
solution = model.simulate(t0=0, t1=72, y0=(0,0))
solution.plot_plasma_rma()
plt.gcf()

Web App

To run locally, install marimo (available in the development dependencies) in your virtual environment and run marimo run app/main.py or use the provided Just command just app-serve to start the server. Alternatively, if using uvx, uvx marimo run app/main.py.

Notebooks

Notebooks can be found in the notebooks directory and require installing development dependencies.

Note that the diffopt package requires OpenMPI. Please install openMPI or use the provided Nix shell (i.e., with nix shell from the project root).