LSA

Synopsis: Perform local sensitivity analysis using OFAT/OAT (one factor at a time) method where the last data time (end time) simulation results are recorded into results file.

Usage: python astools.py LSA [option]

where [option] can be

• modelfile: Name of model specification file in models folder. This assumes that the model file is not in models folder.
• multiple: Multiples to change each variable value. Default = 100 (which will multiple the original parameter value by 100).
• prefix: A prefixing string for the set of new model specification for identification purposes. Default = ''.
• type: Type of model specification file. Allowable types are 'ASM' (AdvanceSyn Model Specification). Default = 'ASM'.
• solver: Type of solver to use. Allowable types are 'Euler', 'Heun' (Runge-Kutta 2nd method or Trapezoidal), 'RK3' (third order Runge-Kutta), 'RK4' (fourth order Runge-Kutta), 'RK38' (fourth order Runge-Kutta method, 3/8 rule), 'CK4' (fourth order Cash-Karp), 'CK5' (fifth order Cash-Karp), 'RKF4' (fourth order Runge-Kutta-Fehlberg), 'RKF5' (fifth order Runge-Kutta-Fehlberg), 'DP4' (fourth order Dormand-Prince), and 'DP5' (fifth order Dormand-Prince). Default = 'RK4'.
• timestep: Time step interval for simulation. Default = 1.0.
• endtime: Time to end simulation - the simulation will run from 0 to end time. Default = 21600.
• lowerbound: Define lower boundary of objects. For example, "1;2" means that when the value of the object hits 1, it will be bounced back to 2. Default = 0;0; that is, when the value of the object goes to negative, it will be bounced back to zero.
• upperbound: Define upper boundary of objects. For example, "10;9" means that when the value of the object hits 1, it will be pushed down to 9. Default = 1e-3;1e-3; that is, when the value of the object above 1e-3, it will be pushed back to 1e-3.
• cleanup: Flag to determine whether to remove all generated temporary models and ODE code files. Default = True.
• outfmt: Output format. Allowable types are 'reduced' (only the final result will be saved into resultfile) and 'full' (all data, depending on sampling, will be saved into resultfile).
• sampling: Sampling frequency. If 100, means only every 100th simulation result will be written out. The first (start) and last (end) result will always be written out. Default = 100.
• resultfile: Relative or absolute file path to write out sensitivity results. Default = 'sensitivity_analysis.csv'

For example:

python genODE \
    --modelfile=models/asm/glycolysis.modelspec \
    --prefix=sen01 \
    --mtype=ASM \
    --multiple=100 \
    --solver=RK4 \
    --timestep=1 \
    --endtime=21600 \
    --cleanup=True \
    --outfmt=reduced \
    --resultfile=sensitivity_analysis.csv

Working example:

D:\Dropbox\MyProjects\astoolkit>python astools.py LSA --modelfile=models/asm/glycolysis.modelspec --prefix=sen01 --mtype=ASM --multiple=100 --solver=RK4 --timestep=1 --endtime=21600 --cleanup=True --outfmt=reduced --resultfile=sensitivity_analysis.csv
Modified hk.promoter: 1e-07 --> 9.999999999999999e-06
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.promoter.modelspec
Modified hk.rbs: 1e-05 --> 0.001
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.rbs.modelspec
Modified hk.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.kcat.modelspec
Modified hk.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.km.modelspec
Modified pgi.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgi.kcat.modelspec
Modified pgi.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgi.km.modelspec
Modified pfk.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pfk.kcat.modelspec
Modified pfk.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pfk.km.modelspec
Modified aldo.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.aldo.kcat.modelspec
Modified aldo.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.aldo.km.modelspec
Modified tpi.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.tpi.kcat.modelspec
Modified tpi.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.tpi.km.modelspec
Modified gapdh.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.gapdh.kcat.modelspec
Modified gapdh.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.gapdh.km.modelspec
Modified pkg.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pkg.kcat.modelspec
Modified pkg.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pkg.km.modelspec
Modified pgm.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgm.kcat.modelspec
Modified pgm.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgm.km.modelspec
Modified eno.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.eno.kcat.modelspec
Modified eno.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.eno.km.modelspec
Modified pk.kcat: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pk.kcat.modelspec
Modified pk.km: 1e-06 --> 9.999999999999999e-05
  New ASM model in D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pk.km.modelspec
Processing model 1 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.original.modelspec
Processing model 2 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.promoter.modelspec
Processing model 3 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.rbs.modelspec
Processing model 4 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.kcat.modelspec
Processing model 5 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.hk.km.modelspec
Processing model 6 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgi.kcat.modelspec
Processing model 7 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgi.km.modelspec
Processing model 8 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pfk.kcat.modelspec
Processing model 9 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pfk.km.modelspec
Processing model 10 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.aldo.kcat.modelspec
Processing model 11 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.aldo.km.modelspec
Processing model 12 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.tpi.kcat.modelspec
Processing model 13 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.tpi.km.modelspec
Processing model 14 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.gapdh.kcat.modelspec
Processing model 15 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.gapdh.km.modelspec
Processing model 16 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pkg.kcat.modelspec
Processing model 17 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pkg.km.modelspec
Processing model 18 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgm.kcat.modelspec
Processing model 19 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pgm.km.modelspec
Processing model 20 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.eno.kcat.modelspec
Processing model 21 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.eno.km.modelspec
Processing model 22 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pk.kcat.modelspec
Processing model 23 of 23: D:\Dropbox\MyProjects\astoolkit\models\temp\sen01.glycolysis.pk.km.modelspec