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EGFR_pybionetfit.conf
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EGFR_pybionetfit.conf
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# Fitting the EGF model
# Model specification
# Base Models
model = EGFR_no_Shp.xml : EGFR_no_Shp_.exp
model = EGFR.xml : EGFR_.exp
mutant = EGFR_no_Shp 1 Lig=0.00495 : EGFR_no_Shp_1.exp
mutant = EGFR_no_Shp 2 Lig=0.0165 : EGFR_no_Shp_2.exp
mutant = EGFR_no_Shp 3 Lig=0.0495 : EGFR_no_Shp_3.exp
mutant = EGFR_no_Shp 4 Lig=0.165 : EGFR_no_Shp_4.exp
mutant = EGFR_no_Shp 5 Lig=0.495 : EGFR_no_Shp_5.exp
mutant = EGFR_no_Shp 6 Lig=1.65 : EGFR_no_Shp_6.exp
mutant = EGFR_no_Shp 7 Lig=4.95 : EGFR_no_Shp_7.exp
mutant = EGFR_no_Shp 8 Lig=16.5 : EGFR_no_Shp_8.exp
mutant = EGFR 1 Lig=0.00495 : EGFR_1.exp
mutant = EGFR 2 Lig=0.0165 : EGFR_2.exp
mutant = EGFR 3 Lig=0.0495 : EGFR_3.exp
mutant = EGFR 4 Lig=0.165 : EGFR_4.exp
mutant = EGFR 5 Lig=0.495 : EGFR_5.exp
mutant = EGFR 6 Lig=1.65 : EGFR_6.exp
mutant = EGFR 7 Lig=4.95 : EGFR_7.exp
mutant = EGFR 8 Lig=16.5 : EGFR_8.exp
output_dir=/home/michael/PycharmProjects/EGFR_reference_models/src/
# Algorithm and objective function choice
fit_type = de
# fit_type = sim
# objfunc = sos
objfunc = sod
# objfunc = norm_sos
# objfunc = ave_norm_sos
population_size = 200
max_iterations = 500
stop_tolerance = 0.000001
# Parameters
##### - Starting parameter values for fitted species - #####
# kp1 0.004
# kp5 0.0538
# k2 1.7
# kp2 0.0125
# k3 0.28
# k5 0.5
# kp3 0.0072
# k_3 0.0058
# k6 0.23
# kp4 0.06
# k_11 0.011
# kr1a 0.015
# kr2a 0.015
# k_12 0.011
# kr1b 0.015
# kr2b 0.015
# k_13 0.043
# kr1c 0.015
# kr2c 0.015
# k14 0.18
# k15 0.0164
loguniform_var = kp1 0.002 0.008
loguniform_var = kp5 0.0269 0.1076
loguniform_var = k2 0.85 3.4
loguniform_var = kp2 0.00625 0.025
loguniform_var = k3 0.14 0.56
loguniform_var = k5 0.25 1
loguniform_var = kp3 0.0036 0.0144
loguniform_var = k6 0.115 0.46
loguniform_var = kp4 0.03 0.12
loguniform_var = k11 0.045 0.18
loguniform_var = k_11 0.0055 0.022
loguniform_var = kr1a 0.0075 0.03
loguniform_var = kr2a 0.0075 0.03
loguniform_var = k12 0.0525 0.21
loguniform_var = k_12 0.0055 0.022
loguniform_var = kr1b 0.0075 0.03
loguniform_var = kr2b 0.0075 0.03
loguniform_var = k_13 0.0215 0.086
loguniform_var = kr1c 0.0075 0.03
loguniform_var = kr2c 0.0075 0.03
loguniform_var = k14 0.09 0.36
loguniform_var = k15 0.0082 0.0328
verbosity=2
# Actions
time_course = model:EGFR_no_Shp, time:720, suffix:EGFR_no_Shp_
time_course = model:EGFR, time:720, suffix:EGFR_