Simulation

In this section, we describe how to simulate given BCSL model. Simulation tool provides a stochastic simulation of the model using an adapted variant of the standard Gillespie algorithm. Despite the natural probabilistic semantics, the deterministic simulation of the model is also possible. There are available step by step Galaxy tours showing how to use stochastic and deterministic variants of the tool.

Input specification

• Model file: Selected model in BCSL language (see Model syntax for details).

• Choose simulation method:

  • For the stochastic simulation of the system, the Number of runs can be specified (default 1) to average individual runs (due to the stochastic nature of the method).

  • For the deterministic simulation of the system, a set of constructed ODEs is simulated. In this case, the Volume argument has to be filled in to deal with molecular counts in the initial state and Time step argument defining distance between two time points.

• Maximum simulation time: specification of simulation time.

Output specification

Simulation tool generates time series with respect to each agent. The result is stored in a .csv file, where the first column represents time, and the rest of the columns store values of for individual agents. The simulation time series can be visualised in an interactive chart called Simulation Plot.

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Command line arguments

usage: Simulation.py [-h] --model MODEL --output OUTPUT --deterministic
                     DETERMINISTIC --runs RUNS --max_time MAX_TIME --volume
                     VOLUME --step STEP

Simulation

required arguments:
  --model MODEL
  --output OUTPUT
  --deterministic DETERMINISTIC
  --runs RUNS
  --max_time MAX_TIME
  --volume VOLUME
  --step STEP