callJuliaStochasticSimulation: Calls the Julia simulation function.

Description

Calls the Julia function for simulating a stochastic system. Should not be used by itself (this function is called by the wrapper functions simulateInSilicoSystem and simulateParallelInSilicoSystem).

Usage

callJuliaStochasticSimulation(
  stochmodel,
  QTLeffects,
  InitAbundance,
  genes,
  simtime,
  modelname = "MySimulation",
  ntrials,
  nepochs,
  simalgorithm,
  ev = getJuliaEvaluator()
)

Arguments

stochmodel

A Julia proxy object to retrieve the stochastic system in the Julia evaluator.

QTLeffects

The list of QTL effects coefficients of the in silico individual to be simulated (see createIndividual).

InitAbundance

The list of initial abundances of the molecules for the in silico individual to be simulated (see createIndividual).

genes

The data-frame of genes in the system.

simtime

Numeric. The amount of time to simulate the model (in seconds).

modelname

String. The name of the model. Default value "MySimulation".

ntrials

Integer. The number of times the simulation must be replicated.

nepochs

Integer. The number of times to record the state of the system during the simulation.

simalgorithm

String. The name of the simulation algorithm to use in the Julia function simulate from the module BioSimulator. Possible values are: "Direct", "EnhancedDirect", "SortingDirect", "FirstReaction", "NextReaction", "TauLeapingDG2001", "TauLeapingDGLP2003", "StepAnticipation", "HybridSAL". See https://alanderos91.github.io/BioSimulator.jl/dev/man/algorithms/ for details about the algorithms.

A Julia evaluator. If none provided select the current evaluator or create one if no evaluator exists.

Value

The result of the simulation (a data-frame).