import tools
from DS_solver import bioDS
import numpy as np
import matplotlib.pyplot as plt
test=bioDS(path='SinIR/')
test.load()
cc=tools.scan_range(test,parameter='Spo0A_p',exp='Ptap',space=np.linspace(0,4,10),save=False,savelog=False,show=False,time=60,fname='normal_pos_2.pdf')
test.set('trr',0.15)
dd=tools.scan_range(test,parameter='Spo0A_p',exp='Ptap',space=np.linspace(0,4,10),save=False,savelog=False,show=False,time=60,fname='trans_pos_2.pdf')
test=bioDS(path='SinIR2/')
test.load()
ee=tools.scan_range(test,parameter='Spo0A_p',exp='Ptap',space=np.linspace(0,4,10),save=False,savelog=False,show=False,time=60,fname='trans_pos_2.pdf')
plt.plot(np.linspace(0,4,10),cc[0],"b--",linewidth=0.5)
plt.plot(np.linspace(0,4,10),cc[1],"b--",linewidth=0.5)
plt.plot(np.linspace(0,4,10),cc[2],label="Normal_Pos",linewidth=1.0)
plt.fill_between(np.linspace(0,4,10),cc[0],cc[1],alpha=0.1)
plt.plot(np.linspace(0,4,10),dd[0],"b--",linewidth=0.5)
plt.plot(np.linspace(0,4,10),dd[1],"b--",linewidth=0.5)
plt.plot(np.linspace(0,4,10),dd[2],label="trans_Pos",linewidth=1.0)
plt.fill_between(np.linspace(0,4,10),dd[0],dd[1],alpha=0.1)
#### #### #### #### import tools from DS_solver import bioDS import numpy as np import matplotlib.pyplot as plt kinc=bioDS(path="KinC_4_ir/") kinc.load() kina=bioDS(path="KinC_3_ir/") kina.load() cc=tools.scan_range(kinc,parameter='viKinA',exp='Spo0A_p',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30) aa=tools.scan_range(kina,parameter='viKinA',exp='Spo0A_p',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30) plt.plot(np.linspace(0,20,60),cc[0],"b--",linewidth=0.5) plt.plot(np.linspace(0,20,60),cc[1],"b--",linewidth=0.5) plt.plot(np.linspace(0,20,60),cc[2],label="0B-",linewidth=2.0) plt.fill_between(np.linspace(0,20,60),cc[0],cc[1],alpha=0.1) plt.plot(np.linspace(0,20,60),aa[0],"b--",linewidth=0.5) plt.plot(np.linspace(0,20,60),aa[1],"b--",linewidth=0.5) plt.plot(np.linspace(0,20,60),aa[2],label="KinC",linewidth=2.0)
####
####
####
####
import tools
from DS_solver import bioDS
import numpy as np
import matplotlib.pyplot as plt
kinc=bioDS(path="KinC_2/")
kinc.load()
k2=[300,200,100,50,20]
cs={}
kincc=bioDS(path="KinC_0/")
kincc.load()
cc=tools.scan_range(kincc,parameter='viKinA',exp='Spo0A_p',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30)
for i in k2:
print(i)
kinc.set("k2",i)
cs[i]=tools.scan_range(kinc,parameter='viKinA',exp='Spo0A_p',space=np.linspace(0,20,60),save=True,show=False,fname="range_k2_%d"%i,savelog=False,time=30)
for i in k2:
plt.plot(np.linspace(0,20,60),cs[i][0],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),cs[i][1],"b--",linewidth=0.5)
plt.plot(np.linspace(0,20,60),cs[i][2],label="k2=%d"%i,linewidth=1.0)
plt.fill_between(np.linspace(0,20,60),cs[i][0],cs[i][1],alpha=0.1)
import numpy as np from scipy.integrate import odeint from DS_solver import bioDS test=bioDS(path='KinC_changed/') test.load() test.simulate(tmax=40) test.display(["Spo0A_p"],save=True,v_line=[2,6,8,12,14,18,20,24,26,30,32,36,38],fname='test') #v_line=[2,6,8,12,14,18,20,24,26,30,32,36,38]
import numpy as np
from scipy.integrate import odeint
from DS_solver import bioDS
test=bioDS(path='SinIR_delay2/')
test.load()
#test.set("Spo0A_p",2)
#test.set("trr",0)
test.simulate(tmax=20)
test.update()
test.set("SlrR",1000)
test.simulate(tmin=20,tmax=50)
'''
test.update()
test.set("SinR",200)
test.simulate(tmin=20,tmax=30)
test.update()
test.set("SinR",100)
test.simulate(tmin=30,tmax=40)
test.update()
test.set("SinR",50)
test.simulate(tmin=40,tmax=50)
test.set("SinR",0)
test.simulate(tmin=50,tmax=65)
'''
test.display(test.components,save=True,fname='test')
#v_line=[2,6,8,12,14,18,20,24,26,30,32,36,38]
import numpy as np from scipy.integrate import odeint from DS_solver import bioDS test=bioDS(path='SinIRp2/') test.load() test.simulate(tmax=30) test.update() testp=bioDS(path='SinIRp/') testp.load() testp.initials=test.initials testp.simulate(tmax=30) testp.display(['SinR_t','Ptap'],save=True,v_line=[2],fname='test') #v_line=[2,6,8,12,14,18,20,24,26,30,32,36,38]
#### #### #### #### import tools from DS_solver import bioDS import numpy as np import matplotlib.pyplot as plt sc=bioDS(path="KinC_3_ir/") sc.load() sa=bioDS(path="KinA_0/") sa.load() sa.add(parameters="../s_parameter",reactions="../s_reaction") sc.add(parameters="../s_parameter",reactions="../s_reaction") atap=tools.scan_range(sa,parameter='viKinA',exp='ptapa',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30) aspo=tools.scan_range(sa,parameter='viKinA',exp='pspoIIg',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30) ctap=tools.scan_range(sc,parameter='viKinA',exp='ptapa',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30) cspo=tools.scan_range(sc,parameter='viKinA',exp='pspoIIg',space=np.linspace(0,20,60),save=False,savelog=False,show=False,time=30) plt.plot(np.linspace(0,20,60),atap[0],"b--",linewidth=0.5) plt.plot(np.linspace(0,20,60),atap[1],"b--",linewidth=0.5) plt.plot(np.linspace(0,20,60),atap[2],label="KinA_tap",linewidth=2.0)
import numpy as np
from scipy.integrate import odeint
from DS_solver import bioDS
test=bioDS(path='SinIR_simple/')
test.load()
test.set("Spo0A_p",0)
test.simulate(tmax=30)
test.update()
test.clear()
test.simulate(tmax=5)
test.set("Spo0A_p",2)
test.simulate(tmin=5,tmax=45)
test.update()
test.set("Spo0A_p",0)
test.simulate(tmin=45,tmax=65)
test.display(test.components,save=True,fname='test',v_line=[5,45])
#v_line=[2,6,8,12,14,18,20,24,26,30,32,36,38]
import numpy as np from scipy.integrate import odeint from DS_solver import bioDS test=bioDS(path='KinA_0/') test.load() test.simulate(tmax=30) test.display(test.components,save=True,v_line=[2,6,8,12,14,18,20],fname='test') #v_line=[2,6,8,12,14,18,20,24,26,30,32,36,38]
from DS_solver import bioDS
import numpy as np
import matplotlib.pyplot as plt
import tools
hill=bioDS(path="hill/")
hill.parameters["Spo0A_p"]=0
hill.parameters["kdeg"]=0.7
hill.add(parameters="../s_parameter",reactions="../s_reaction")
atap=tools.scan_range(hill,parameter='Spo0A_p',exp='ptapa',space=np.linspace(0,5,60),save=False,savelog=False,show=False,time=15,period=0.2)
aspo=tools.scan_range(hill,parameter='Spo0A_p',exp='pspoIIg',space=np.linspace(0,5,60),save=False,savelog=False,show=False,time=15,period=0.2)
plt.plot(np.linspace(0,5,60),atap[2],label="tapA")
plt.plot(np.linspace(0,5,60),aspo[2],label="spoIIg")
v_line=[0.4,0.8,2.3]
ye=list(plt.axis())[-2:]
for i in v_line:
te=np.ones(2)*i
plt.plot(te,ye,'k--')
plt.xlabel("Spo0A_p")
plt.ylabel("Reporter")
plt.legend(bbox_to_anchor=(0.95, 0.95))
plt.savefig("hill/hill.pdf")
plt.show()
import numpy as np
from scipy.integrate import odeint
from DS_solver import bioDS
test=bioDS(path='SinIR_feedback/')
test.load()
#test.set("Spo0A_p",2)
#test.set("trr",0)
test.simulate(tmax=20)
test.update()
test.set("SlrR",6000)
test.simulate(tmin=20,tmax=50)
'''
test.update()
test.set("SinR",200)
test.simulate(tmin=20,tmax=30)
test.update()
test.set("SinR",100)
test.simulate(tmin=30,tmax=40)
test.update()
test.set("SinR",50)
test.simulate(tmin=40,tmax=50)
test.set("SinR",0)
test.simulate(tmin=50,tmax=65)
'''
test.display(test.components,save=True,fname='test')
#v_line=[2,6,8,12,14,18,20,24,26,30,32,36,38]
#####
# scan the average and the range of the output of KinA_changed and KinC_changed
# save them in the directory
# 3/3/2016
####
from DS_solver import bioDS
import numpy as np
import matplotlib.pyplot as plt
kina=bioDS(path="KinA_sim/")
kinc=bioDS(path="KinC_sim/")
kina.load()
kinc.load()
a_scan=[]
c_scan=[]
#####
# for different parameters(kcat of phosphorylation)
#####
'''
c_scan={}
k2=[20,50,100,150,200,300]
ap=[2,5,8,11,14]
for i in ap:
c_scan[i]=[]
for i in np.linspace(1,10,30):
kina.set("viKinA",i)
T,Pa=kina.simulate(tmax=20)
kina.display(["Spo0A_p"],save=True,show=False,fname="vkina=%f"%i)
