experiment_list1: Molecular perturbations.

In pauwels2014: Bayesian Experimental Design for Systems Biology.

Description

A list of functions that represent possible molecular perturbations to be performed on the network.

Usage

data(experiment_list1)

Details

A list of 10 functions. Each function takes as input a named numeric parameter vector theta and an initial condition named numeric vector initial_conditions. Each function outputs a list with the following slots:

• theta: A modified parameter value

• initial_conditions: A modified initial condition value

• cost: The cost of the associated molecular perturbation

The 10 functions perform the following operations on their input (parameters numbering might not be always coherent with names):

• delete_gene6

  • theta: set pro6_strength and rbs6_strength

  • initial_condtions: set p6 initial concentration to 0

  • cost: 800

• delete_gene7

  • theta: set pro7_strength and rbs8_strength

  • initial_condtions: set p7 initial concentration to 0

  • cost: 800

• delete_gene8

  • theta: set pro7_strength and rbs8_strength

  • initial_condtions: set p7 initial concentration to 0

  • cost: 800

• knockdown_gene6

  • theta: multiply mrna6_degradation_rate by 10

  • initial_condtions: Nn operation

  • cost: 350

• knockdown_gene7

  • theta: multiply mrna7_degradation_rate by 10

  • initial_condtions: no operation

  • cost: 350

• knockdown_gene8

  • theta: multiply mrna8_degradation_rate by 10

  • initial_condtions: no operation

  • cost: 350

• decrease_rbs_gene6

  • theta: divide rbs6_strength by 10

  • initial_condtions: no operation

  • cost: 350

• decrease_rbs_gene7

  • theta: divide rbs6_strength by 10

  • initial_condtions: no operation

  • cost: 350

• decrease_rbs_gene8

  • theta: divide rbs7_strength by 10

  • initial_condtions: no operation

  • cost: 350

• nothing

  • theta: no operation

  • initial_condtions: no operation

  • cost: 0

Examples

data(experiment_list1)
data(knobjs)
sapply(	
	1:length(knobjs),
	function(k){
		assign(names(knobjs)[k], knobjs[[k]], envir = .GlobalEnv)
	}
)

theta <- knobjActMult1$datas[[1]]$thetas[1,]
thetaT <- knobjActMult1$transform_params(theta)

temp <- experiment_list1$delete_gene7(thetaT, knobjActMult1$global_parameters$initial_conditions)

rbind(temp$theta, thetaT)
rbind(temp$initial_conditions, knobjActMult1$global_parameters$initial_conditions)

pauwels2014 documentation built on May 1, 2019, 6:29 p.m.