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RACIPE Script

Overview

The racipe script provides a default implementation of the RACIPE pipeline. This script is fairly limited in customizablity. If you prefer to customize refer to the tutorial and the RACIPE API.

Usage

racipe [-h] [--topodir TOPODIR] [--outdir OUTDIR] [--num_paras NUM_PARAS] [--num_inits NUM_INITS] [--num_reps NUM_REPS] [--num_cores NUM_CORES] [--sampling SAMPLING] [topo]
- Run simulations for 100 initial conditions across 1000 parameter sets for all the topo files in the folder TOPOS. 
racipe --topodir TOPOS --outdir SimulResults --num_inits 100 --num_paras 1000
- Run simulation for 1000 initial conditions across 10000 parameters for the TS.topo file. 
racipe --outdir SimulResults --num_inits 1000 --num_paras 10000 TS.topo

Options

  • -h, --help Shows the help message with all available options.
  • --topodir TOPODIR Directory containing the topology files. Useful if your topology files are stored in a specific directory. Default: TOPOS.
  • --outdir OUTDIR Output directory for simulation results. Default: SimulResults.
  • --num_paras NUM_PARAS Number of parameter sets to generate. This determines the size of the ensemble you want to simulate. Default: 10000.
  • --num_inits NUM_INITS Number of initial conditions to use for each simulation. This allows for exploring different starting points in your model. Default: 1000.
  • --num_reps NUM_REPS Number of replicates per topofile. Default: 3.
  • --num_cores NUM_CORES Number of cores to use for parallel parameter generation. Default: All available cores.
  • --sampling SAMPLING Sampling method to generate parameter sets. Choices include: 'Sobol', 'LHS', 'Uniform', 'LogUniform', 'Normal', 'LogNormal'. Default: Sobol.