Parameterization with NFsim

  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:

KD1__FREE__        1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]
km1__FREE__        1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]
K2RT__FREE__       1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]
km2__FREE__        1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]
kphos__FREE__      1.000000e+00 # loguniform[0.01 100] factor[0.2 0.1]
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

    NFsim produce simulations files with the following format. Please prepare data files with the same format to avoid incompatibilities.

time, RLbonds, pR
0.00000000E+00, 0.00000000E+00, 3.55300000E+02
1.00000000E+01, 1.14072000E+02, 3.56440000E+02
2.00000000E+01, 1.39183800E+02, 3.49960000E+02
3.00000000E+01, 1.49153400E+02, 3.43980000E+02
4.00000000E+01, 1.56868400E+02, 3.42600000E+02
5.00000000E+01, 1.56788000E+02, 3.35620000E+02
6.00000000E+01, 1.63666800E+02, 3.37480000E+02

  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-nfsim
#SBATCH --output=stdout.txt
#SBATCH --error=stderr.txt

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

MODEL=pysbmodel-example6-nfsim.bngl # the model should have the .bngl extension
FINAL=60
STEPS=6

PARTITION=$SLURM_JOB_PARTITION
DATA=../exp-data/nfsim/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.nfsim --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=$ERROR --equil 600 \
--slurm=$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.nfsim --help to find out the available command options.