def test_output_with_abcsysbio_syntax(self):
""" We should be able to echo experiments with the ABC-SysBio
syntax. """
exp1 = Experiment([1, 2, 3, 4], [.1, .2, .3, .4], '')
exp2 = Experiment([1, 2, 3, 4], [.2, .4, .6, .8], '')
exps = ExperimentSet()
exps.add(exp1)
exps.add(exp2)
out = exps.get_as_abcsysbio_syntax()
expected = '<var1> 0.1 0.2 0.3 0.4 </var1>' + \
'<var2> 0.2 0.4 0.6 0.8 </var2>'
space_re = re.compile('\s|\n', re.MULTILINE)
self.assertEqual(space_re.sub('', out), space_re.sub('', expected))
odes = sbml_to_odes (sbml)
time = [30, 60, 180, 300, 900, 1800]
# Simple experiment: run final_model simulations adding a Gaussian noise
values = odes.evaluate_exp_on ('MAPK_PP + MAPK_P', time)
experiment_set = ExperimentSet ()
for i in range (3):
noised_values = list (values)
add_noise (noised_values)
experiment = Experiment (time, noised_values,
'MAPK_PP + MAPK_P')
experiment_set.add (experiment)
experiment_set.save_to_file ('gauss_noise.data')
with open ('gaus_noise_abcsysbio.data', 'w') as f:
f.write (experiment_set.get_as_abcsysbio_syntax ())
f.close ()
# More complex experiment: run final_model with perturbations on
# catalytic constants
perturbation_exp = ExperimentSet ()
# First perturbation experiments
theta = odes.get_all_parameters ()
changed_param = ''
changed_param_value = 0
for p in theta:
original_name = sbml.get_original_param_name (p)
# kcat9 is ERK dephosphorylation catalytic constant
if original_name == 'kcat9':