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Heat Shock Response

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Artur Meski
2016-03-03 09:22:33 +01:00
parent 063e8063cc
commit 975c01edea
9 changed files with 59 additions and 1 deletions
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57
rs_examples.py
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@@ -446,3 +446,60 @@ def blood_glucose_regulation(print_system=True):
smt_rsc.check_reachability(prop,max_level=10) smt_rsc.check_reachability(prop,max_level=10)
# smt_rsc.show_encoding(prop,print_time=True,max_level=maxConc*chainLen+10) # smt_rsc.show_encoding(prop,print_time=True,max_level=maxConc*chainLen+10)
def heat_shock_response(print_system=True):
r = ReactionSystemWithConcentrations()
r.add_bg_set_entity(("hsp",1))
r.add_bg_set_entity(("hsf",1))
r.add_bg_set_entity(("hsf2",1))
r.add_bg_set_entity(("hsf3",1))
r.add_bg_set_entity(("hse",1))
r.add_bg_set_entity(("mfp",1))
r.add_bg_set_entity(("prot",1))
r.add_bg_set_entity(("hsf3:hse",1))
r.add_bg_set_entity(("hsp:mfp",1))
r.add_bg_set_entity(("hsp:hsf",1))
r.add_bg_set_entity(("temp",50))
stress_temp = 42
r.add_reaction([("hsf",1)],[("hsp",1)],[("hsf3",1)])
r.add_reaction([("hsf",1),("hsp",1),("mfp",1)],[],[("hsf3",1)])
r.add_reaction([("hsf3",1)],[("hsp",1),("hse",1)],[("hsf",1)])
r.add_reaction([("hsp",1),("hsf3",1),("mfp",1)],[("hse",1)],[("hsf",1)])
r.add_reaction([("hsf3",1),("hse",1)],[("hsp",1)],[("hsf3:hse",1)])
r.add_reaction([("hsp",1),("hsf3",1),("mfp",1),("hse",1)],[],[("hsf3:hse",1)])
r.add_reaction([("hse",1)],[("hsf3",1)],[("hse",1)])
r.add_reaction([("hsp",1),("hsf3",1),("hse",1)],[("mfp",1)],[("hse",1)])
r.add_reaction([("hsf3:hse",1)],[("hsp",1)],[("hsp",1),("hsf3:hse",1)])
r.add_reaction([("hsp",1),("mfp",1),("hsf3:hse",1)],[],[("hsp",1),("hsf3:hse",1)])
r.add_reaction([("hsf",1),("hsp",1)],[("mfp",1)],[("hsp:hsf",1)])
r.add_reaction([("hsp:hsf",1),("temp",stress_temp)],[],[("hsf",1),("hsp",1)])
r.add_reaction([("hsp:hsf",1)],[("temp",stress_temp)],[("hsp:hsf",1)])
r.add_reaction([("hsp",1),("hsf3:hse",1)],[("mfp",1)],[("hse",1),("hsp:hsf",1)])
r.add_reaction([("temp",stress_temp),("prot",1)],[],[("mfp",1),("prot",1)])
r.add_reaction([("prot",1)],[("temp",stress_temp)],[("mfp",1),("prot",1)])
r.add_reaction([("hsp",1),("mfp",1)],[],[("hsp:mfp",1)])
r.add_reaction([("mfp",1)],[("hsp",1)],[("mfp",1)])
r.add_reaction([("hsp:mfp",1)],[],[("hsp",1),("prot",1)])
c = ContextAutomatonWithConcentrations(r)
c.add_init_state("0")
c.add_state("1")
c.add_transition("0", [("hsf",1),("prot",1),("hse",1),("temp",36)], "1")
c.add_transition("0", [("hse",1),("prot",1),("hsp:hsf",1),("temp",stress_temp)], "1")
c.add_transition("0", [("hsp",1),("prot",1),("hsf3:hse",1),("mfp",1),("hsp:mfp",1),("temp",36)], "1")
c.add_transition("1", [("temp",36)], "1")
c.add_transition("1", [("temp",43)], "1")
# c.add_transition("1", [("sugar",1)], "1")
rc = ReactionSystemWithAutomaton(r,c)
if print_system:
rc.show()
smt_rsc = SmtCheckerRSC(rc)
prop = [("hsp",1)]
smt_rsc.check_reachability(prop,max_level=10)

3
rssmt.py
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@@ -30,7 +30,8 @@ def process():
# rs_examples.run_counter_exp() # rs_examples.run_counter_exp()
# rs_examples.chain_reaction(print_system=True) # rs_examples.chain_reaction(print_system=True)
rs_examples.blood_glucose_regulation() # rs_examples.blood_glucose_regulation()
rs_examples.heat_shock_response()
################################################################## ##################################################################