# Basic use¶

## Solution of ODE models¶

This is a warm-up example that illustrates model description, ODE numerical solving and plotting:

from stimator import read_model, solve

mdl = """
# Example file for S-timator
title Example 1

#reactions (with stoichiometry and rate)
vin  : -> x1     , rate = k1
v2   : x1 ->  x2 , rate = k2 * x1
vout : x2 ->     , rate = k3 * x2

#parameters and initial state
k1 = 1
k2 = 2
k3 = 1
init: (x1=0, x2=0)

#filter what you want to plot
!! x1 x2
"""

print '========= model ========================================'
print mdl
print '--------------------------------------------------------'

solve(m, tf=5.0).plot(show=True)


## Parameter estimation¶

Model parameter estimation, based on experimental time-course data (run example par_estimation_ex2.py):

from stimator import read_model, readTCs, solve
from stimator.deode import DeODEOptimizer

mdl = """
# Example file for S-timator
title Example 2

vin  : -> x1     , rate = k1
v2   : x1 ->  x2 , rate = k2 * x1
vout : x2 ->     , rate = k3 * x2

init : x1=0, x2=0
!! x2
find k1 in [0, 2]
find k2 in [0, 2]
find k3 in [0, 2]

timecourse ex2data.txt
generations = 200   # maximum generations for GA
genomesize = 60     # population size in GA
"""
print mdl

optSettings={'genomesize':60, 'generations':200}

optimizer = DeODEOptimizer(m1,optSettings, timecourses)
optimizer.run()

best = optimizer.optimum
print best.info()
best.plot()


This produces the following output:

-------------------------------------------------------
file .../examples/ex2data.txt:
11 time points, 2 variables

Solving Example 2...
0   : 3.837737
1   : 3.466418
2   : 3.466418
...  (snip)
39  : 0.426056
refining last solution ...

DONE!
Too many generations with no improvement in 40 generations.
best energy = 0.300713
best solution: [ 0.29399228  0.47824875  0.99081065]
Optimization took 8.948 s (00m 08.948s)

--- PARAMETERS           -----------------------------
k3      0.293992 +- 0.0155329
k2      0.478249 +- 0.0202763
k1      0.990811 +- 0.0384208

--- OPTIMIZATION         -----------------------------
Final Score 0.300713
generations 40
max generations     200
population size     60
Exit by     Too many generations with no improvement

--- TIME COURSES         -----------------------------
Name                Points          Score
ex2data.txt 11      0.300713