Parameterization with PISKaS

  1. Prepare the model

    Pleione finds which variables will be calibrated using the symbol # (number sign, hash or pound sign) followed by:

    • An initial distribution type: uniform, loguniform, lognormal
    • An initial search space: [min max] or [mean standard_deviation] in the case if lognormal was selected.
    • A type of parameter mutation: uniform or loguniform to use a new search space; or factor to perform a local mutation search
    • A search space for mutated parameters: [min max] or [probability fold_change] in the case if factor was selected.
    • An optional mutation rate per parameter. Without it, the global mutation rate is used.

    For instace:

%var: 'KD1__FREE__' 1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]
%var: 'km1__FREE__' 1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]
%var: 'K2RT__FREE__' 1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]
%var: 'km2__FREE__' 1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]
%var: 'kphos__FREE__' 1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]
%var: 'kdephos__FREE__' 1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]

Note

Factor mutation: This type of mutation strategy comes from BioNetFit and selects a random value from the range 0.9 * old_value, 1.1 * old_value if the declared value is 0.1 with probability 0.2.

  1. Prepare the data files

    PISKaS produce simulations files with a similar format as follows. Please prepare data files, replacing the “#” with the name of the compartments, including the initial space in each subsequent row.

example time 'RLbonds' 'pR'
 6.000000E+02 0 355.3
 6.100000E+02 114.072 356.44
 6.200000E+02 139.1838 349.96
 6.300000E+02 149.1534 343.98
 6.400000E+02 156.8684 342.6
 6.500000E+02 156.788 335.62
 6.600000E+02 163.6668 337.48

Note

An extra column name? PISKaS produces one output for each compartment declared in the model. Therefore, adding the name of the compartment as the first column allows the code to identify the corresponding experimental data with the simulated compartment and apply correctly the fitness function. Finally, the model error is the sum of each fitness per compartment.

Note

About the example model: The model has three parts: An equilibration of 600 seconds, then the model is modified to add a quantity of L(r) agents, and then perform the actual simulation for 60 seconds. Despite BNG2 and NFsim, PISKaS reports the whole simulation, so to compare effectively, we must offset the time of the experimental data by 600.

  1. Prepare a sbatch configuration file

    Use the following code as template to make a shell script and queue it with sbatch. Note that the export statement is inside the code to tell SLURM to add the path and ensure proper execution when pleione was cloned with git. Also, python3 redirects to either the system installed executable (with pandas installed either as admin or user) or redirects to the user compiled executable if an alias exists for it.

#!/bin/sh

#SBATCH --no-requeue
#SBATCH --partition=cpu

#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1

#SBATCH --job-name=pleione-piskas
#SBATCH --output=stdout.txt
#SBATCH --error=stderr.txt

export PYTHONPATH="$PYTHONPATH:$HOME/opt/pleione"

MODEL=pysbmodel-example6-piskas.kappa
FINAL=660
STEPS=66

PARTITION=$SLURM_JOB_PARTITION
DATA=../exp-data/piskas/data-*.txt

NUM_ITER=100
NUM_SIMS=10
POP_SIZE=100
POP_BEST=0

SWAP=0.5
RATE=0.5
ERROR="SDA"

python3 -m pleione.piskas --model=$MODEL --final=$FINAL --steps=$STEPS \
--iter=$NUM_ITER --pops=$POP_SIZE --sims=$NUM_SIMS --best=$POP_BEST \
--data=$DATA --rate=$RATE --swap=$SWAP --error=$ERROR \
--slurm=$PARTITION

Note

sbatch or python multiproccesing? To execute Pleione outside a SLURM queue, simple execute the shell script with sh, bash or any shell interpreter without the slurm option. Be aware that, if SLURM is running in the same machine, Pleione subprocess would impact negatively in other user’s threads, and vice versa, since SLURM could allow oversubscribe (see https://slurm.schedmd.com/sbatch.htm for more information)

Note

Need help? type python3 -m pleione.piskas --help to find out the available command options.