ptransmodelODE {magi} | R Documentation |
Protein transduction model
Description
The protein transduction equations model a biochemical reaction involving a signaling protein that degrades over time. The system components X = (S, S_d, R, S_R, R_{pp})
represent the levels of signaling protein, its degraded form, inactive state of R
, S-R
complex, and activated state of R
.
S
, S_d
, R
, S_R
and R_{pp}
are governed by the following differential equations:
\frac{dS}{dt} = -k_1 \cdot S -k_2 \cdot S \cdot R + k_3 \cdot S_R
\frac{dS_d}{dt} = k_1 \cdot S
\frac{dR}{dt} = -k_2 \cdot S \cdot R + k_3 \cdot S_R + \frac{V \cdot R_{pp}}{K_m + R_{pp}}
\frac{dS_R}{dt} = k_2 \cdot S \cdot R - k_3 \cdot S_R - k_4 \cdot S_R
\frac{dR_{pp}}{dt} = k_4 \cdot S_R - \frac{V \cdot R_{pp}}{K_m + R_{pp}}
where \theta = (k_1, k_2, k_3,k_4, V, K_m)
are system parameters.
Usage
ptransmodelODE(theta, x, tvec)
ptransmodelDx(theta, x, tvec)
ptransmodelDtheta(theta, x, tvec)
Arguments
theta |
vector of parameters. |
x |
matrix of system states (one per column) at the time points in |
tvec |
vector of time points |
Value
ptransmodelODE
returns an array with the values of the derivatives \dot{X}
.
ptransmodelDx
returns a 3-D array with the values of the gradients with respect to X
.
ptransmodelDtheta
returns a 3-D array with the values of the gradients with respect to \theta
.
References
Vyshemirsky, V., & Girolami, M. A. (2008). Bayesian Ranking of Biochemical System Models. Bioinformatics, 24(6), 833-839.
Examples
theta <- c(0.07, 0.6, 0.05, 0.3, 0.017, 0.3)
x <- matrix(1:25, nrow = 5, ncol = 5)
tvec <- 1:5
ptransmodelODE(theta, x, tvec)