def build_rules():
""" Actin network rules.
Changes from initial model:
* direct activation link RhoA -> Rac1
* ROCK inhibition delay: RhoA -> ROCK -> ROCK_ -| Rac1
* weaker RhoA inhibition rule: not Rac1 or not PAK
Changes from v1:
* strong inhibitors for Arp2_3 (reworked voting rule)
* reworked rule for Cortactin
"""
Actin_BR = "Actin_BR"
Actin_ST = "Actin_ST"
Arp2_3 = "Arp2_3"
CP = "CP"
Cdc42 = "Cdc42"
Cofilin = "Cofilin"
Coronin = "Coronin"
Cortactin = "Cortactin"
Dia1 = "Dia1"
Dia2 = "Dia2"
Ena_Vasp = "Ena_Vasp"
IRSp53 = "IRSp53"
LIMK = "LIMK"
PAK = "PAK"
PIP2 = "PIP2"
PKD = "PKD"
Profilin = "Profilin"
ROCK = "ROCK"
ROCK_ = "ROCK_"
Rac1 = "Rac1"
RhoA = "RhoA"
SSH = "SSH"
Thymosin = "Thymosin"
WASP = "WASP"
WAVE = "WAVE"
G = nx.DiGraph()
rules = ""
G.add_weighted_edges_from(
get_edges(WASP, [Rac1, Cdc42, PIP2, Cortactin, IRSp53], [Thymosin]))
rules += "1: WASP* = not Thymosin and (Rac1 or Cdc42 or PIP2 or Cortactin or IRSp53) \n"
G.add_weighted_edges_from(get_edges(WAVE, [Rac1], []))
rules += "1: WAVE* = Rac1 \n" # or IRSp53
G.add_weighted_edges_from(
get_edges(Arp2_3, [PAK, WASP, WAVE, Cortactin],
[Profilin, Thymosin, Coronin]))
rules += "1: Arp2_3* = PAK and (" + voting_rule(
[WASP, WAVE, Cortactin], [Profilin, Thymosin, Coronin],
strongInhibition=False) + ")\n"
G.add_weighted_edges_from(get_edges(Rac1, [Arp2_3, Dia1, RhoA], [ROCK_]))
rules += "1: Rac1* = not ROCK_ and (Arp2_3 or Dia1 or RhoA) \n" # intermediate ROCK_ node + activation from RhoA
G.add_weighted_edges_from(get_edges(RhoA, [], [Rac1, PAK]))
rules += "1: RhoA* = not Rac1 or not PAK \n"
G.add_weighted_edges_from(get_edges(Thymosin, [], [WASP, Cofilin]))
rules += "1: Thymosin* = not WASP and not Cofilin \n"
G.add_weighted_edges_from(get_edges(Cortactin, [Rac1, PAK],
[Coronin, PKD]))
rules += "1: Cortactin* = (Rac1 and PAK) or (Rac1 and not (Coronin and PKD) ) \n"
# rules += "1: Cortactin* = (Rac1 and not (Coronin and PKD) \n"
G.add_weighted_edges_from(get_edges(IRSp53, [Cdc42, Rac1], []))
rules += "1: IRSp53* = Cdc42 or Rac1 \n"
G.add_weighted_edges_from(get_edges(PAK, [Rac1, Cdc42, PKD], []))
rules += "1: PAK* = Rac1 or Cdc42 or PKD \n"
G.add_weighted_edges_from(get_edges(Dia1, [RhoA], [CP]))
rules += "1: Dia1* = RhoA and not CP \n"
G.add_weighted_edges_from(get_edges(Dia2, [Rac1, RhoA], []))
rules += "1: Dia2* = Rac1 or RhoA \n"
G.add_weighted_edges_from(get_edges(Ena_Vasp, [IRSp53, WASP, PKD], []))
rules += "1: Ena_Vasp* = IRSp53 or WASP or PKD \n"
G.add_weighted_edges_from(
get_edges(Profilin, [WASP, Dia1, WAVE], [Thymosin, PIP2]))
rules += "1: Profilin* = " + voting_rule(["WASP", "Dia1", "WAVE"],
["Thymosin", "PIP2"]) + " \n"
G.add_weighted_edges_from(get_edges(CP, [Arp2_3], [Ena_Vasp, PIP2]))
rules += "1: CP* = (Arp2_3 and not Ena_Vasp) or not PIP2 \n"
G.add_weighted_edges_from(get_edges(Coronin, [SSH], []))
rules += "1: Coronin* = SSH \n"
G.add_weighted_edges_from(get_edges(ROCK, [RhoA], [SSH, Coronin]))
rules += "1: ROCK* = RhoA and not (SSH and Coronin) \n"
G.add_weighted_edges_from(get_edges(ROCK_, [ROCK], []))
rules += "1: ROCK_* = ROCK \n"
G.add_weighted_edges_from(get_edges(PKD, [ROCK], []))
rules += "1: PKD* = ROCK \n"
G.add_weighted_edges_from(get_edges(LIMK, [ROCK, PAK], [SSH]))
rules += "1: LIMK* = (ROCK or PAK) and not SSH \n"
G.add_weighted_edges_from(
get_edges(Cofilin, [SSH, Arp2_3], [PIP2, Thymosin, LIMK, Cortactin]))
rules += "1: Cofilin* = " + voting_rule(
["SSH", "Arp2_3"], ["PIP2", "Thymosin", "LIMK", "Cortactin"]) + "\n"
G.add_weighted_edges_from(get_edges(SSH, [Coronin, Rac1], [PKD]))
rules += "1: SSH* = (Coronin or Rac1) and not PKD \n"
G.add_weighted_edges_from(get_edges(Actin_BR, [Arp2_3], []))
rules += "1: Actin_BR* = (Arp2_3) \n" # or Cofilin) and not Thymosin
G.add_weighted_edges_from(
get_edges(Actin_ST, [Profilin, Dia1, Dia2, Ena_Vasp], [CP, Cofilin]))
rules += "1: Actin_ST* = Profilin and (" + voting_rule(
["Dia1", "Dia2", "Ena_Vasp"], ["CP", "Cofilin"]) + ")\n"
return {"rules": rules, "graph": G}
def build_rules():
""" Actin network rules.
Changes from initial model:
* direct activation link RhoA -> Rac1
* ROCK inhibition delay: RhoA -> ROCK -> ROCK_ -| Rac1
* weaker RhoA inhibition rule: not Rac1 or not PAK
Changes from v1:
* strong inhibitors for Arp2_3 (reworked voting rule)
* reworked rule for Cortactin
Changes from v2:
* deleted PKD activates PAK
* added link PKD activates LIMK
* Option A: deleted PAK -> Cortactin link
* deleted IRSp53 -> WAVE link
* deleted Rac1 -> IRSp53 link
Changes from v3:
* separate IRSp53 variants Cdc42 and Rac1 activations
"""
UPSTREAM = "UPSTREAM"
G = nx.DiGraph()
rules = ""
rules += "1: UPSTREAM* = not UPSTREAM \n"
G.add_weighted_edges_from(
get_edges(WASP, [Rac1, Cdc42, PIP2, Cortactin, IRSp53_Cdc42],
[Thymosin]))
rules += "1: WASP* = not Thymosin and (Rac1 or Cdc42 or PIP2 or Cortactin or IRSp53_Cdc42) \n"
G.add_weighted_edges_from(get_edges(WAVE, [Rac1, IRSp53_Rac1], []))
rules += "1: WAVE* = Rac1 or IRSp53_Rac1 \n"
G.add_weighted_edges_from(
get_edges(Arp2_3, [PAK, WASP, WAVE, Cortactin],
[Profilin, Thymosin, Coronin]))
rules += "1: Arp2_3* = PAK and (" + voting_rule(
[WASP, WAVE, Cortactin], [Profilin, Thymosin, Coronin]) + ")\n"
G.add_weighted_edges_from(get_edges(Rac1, [UPSTREAM], []))
rules += "1: Rac1* = UPSTREAM \n"
G.add_weighted_edges_from(get_edges(RhoA, [], [UPSTREAM]))
rules += "1: RhoA* = not UPSTREAM \n"
G.add_weighted_edges_from(get_edges(Thymosin, [], [WASP, Cofilin]))
rules += "1: Thymosin* = (not WASP and not Cofilin) \n"
G.add_weighted_edges_from(get_edges(Cortactin, [Rac1], [Coronin, PKD]))
rules += "1: Cortactin* = " + voting_rule([Rac1], [Coronin, PKD]) + " \n"
G.add_weighted_edges_from(get_edges(IRSp53_Cdc42, [Cdc42], []))
rules += "1: IRSp53_Cdc42* = Cdc42 \n"
G.add_weighted_edges_from(get_edges(IRSp53_Rac1, [Rac1], []))
rules += "1: IRSp53_Rac1* = Rac1 \n"
G.add_weighted_edges_from(get_edges(PAK, [Rac1, Cdc42], []))
rules += "1: PAK* = Rac1 or Cdc42 \n"
G.add_weighted_edges_from(get_edges(Dia1, [RhoA], [CP]))
rules += "1: Dia1* = RhoA and not CP \n"
G.add_weighted_edges_from(get_edges(Dia2, [Rac1, RhoA], []))
rules += "1: Dia2* = Rac1 or RhoA \n"
G.add_weighted_edges_from(
get_edges(Ena_Vasp, [IRSp53_Cdc42, WASP, PKD], []))
rules += "1: Ena_Vasp* = IRSp53_Cdc42 or WASP or PKD \n"
G.add_weighted_edges_from(
get_edges(Profilin, [WASP, Dia1, WAVE], [Thymosin, PIP2]))
rules += "1: Profilin* = " + voting_rule(["WASP", "Dia1", "WAVE"],
["Thymosin", "PIP2"]) + " \n"
G.add_weighted_edges_from(get_edges(CP, [Arp2_3], [Ena_Vasp, PIP2]))
rules += "1: CP* = (Arp2_3 and not Ena_Vasp) or not PIP2 \n"
G.add_weighted_edges_from(get_edges(Coronin, [SSH], []))
rules += "1: Coronin* = SSH \n"
G.add_weighted_edges_from(get_edges(ROCK, [RhoA], [SSH, Coronin]))
rules += "1: ROCK* = RhoA and not (SSH and Coronin) \n"
G.add_weighted_edges_from(get_edges(PKD, [ROCK], []))
rules += "1: PKD* = ROCK \n"
G.add_weighted_edges_from(get_edges(LIMK, [ROCK, PAK, PKD], [SSH]))
rules += "1: LIMK* = (ROCK or PAK or PKD) and not SSH \n"
G.add_weighted_edges_from(
get_edges(Cofilin, [SSH, Arp2_3], [PIP2, Thymosin, LIMK, Cortactin]))
rules += "1: Cofilin* = " + voting_rule(
["SSH", "Arp2_3"], ["PIP2", "Thymosin", "LIMK", "Cortactin"]) + "\n"
G.add_weighted_edges_from(get_edges(SSH, [Coronin, Rac1], [PKD]))
rules += "1: SSH* = (Coronin or Rac1) and not PKD \n"
G.add_weighted_edges_from(get_edges(Actin_BR, [Arp2_3], []))
rules += "1: Actin_BR* = Arp2_3 \n"
G.add_weighted_edges_from(
get_edges(Actin_ST, [Profilin, Dia1, Dia2, Ena_Vasp], [CP, Cofilin]))
rules += "1: Actin_ST* = Profilin and (" + voting_rule(
["Dia1", "Dia2", "Ena_Vasp"], ["CP", "Cofilin"]) + ")\n"
return {"rules": rules, "graph": G}
def build_rules():
""" Original Actin network rules.
"""
Actin_BR = "Actin_BR"
Actin_ST = "Actin_ST"
Arp2_3 = "Arp2_3"
CP = "CP"
Cdc42 = "Cdc42"
Cofilin = "Cofilin"
Coronin = "Coronin"
Cortactin = "Cortactin"
Dia1 = "Dia1"
Dia2 = "Dia2"
Ena_Vasp = "Ena_Vasp"
IRSp53 = "IRSp53"
LIMK = "LIMK"
PAK = "PAK"
PIP2 = "PIP2"
PKD = "PKD"
Profilin = "Profilin"
ROCK = "ROCK"
Rac1 = "Rac1"
RhoA = "RhoA"
SSH = "SSH"
Thymosin = "Thymosin"
WASP = "WASP"
WAVE = "WAVE"
G = nx.DiGraph()
rules = ""
G.add_weighted_edges_from(get_edges(WASP, [Rac1, Cdc42, PIP2, Cortactin, IRSp53], [Thymosin]))
rules += "1: WASP* = not Thymosin and (Rac1 or Cdc42 or PIP2 or Cortactin or IRSp53) \n"
G.add_weighted_edges_from(get_edges(WAVE, [Rac1], []))
rules += "1: WAVE* = Rac1 \n" # or IRSp53
G.add_weighted_edges_from(get_edges(Arp2_3, [PAK, WASP, WAVE, Cortactin], [Profilin, Thymosin, Coronin]))
rules += "1: Arp2_3* = PAK and (" + voting_rule([WASP, WAVE, Cortactin],
[Profilin, Thymosin, Coronin]) + ")\n"
G.add_weighted_edges_from(get_edges(Rac1, [Arp2_3, Dia1, RhoA], [ROCK]))
rules += "1: Rac1* = not ROCK and (Arp2_3 or Dia1) \n"
G.add_weighted_edges_from(get_edges(RhoA, [], [Rac1, PAK]))
rules += "1: RhoA* = not Rac1 and not PAK \n"
G.add_weighted_edges_from(get_edges(Thymosin, [], [WASP, Cofilin]))
rules += "1: Thymosin* = not WASP and not Cofilin \n"
G.add_weighted_edges_from(get_edges(Cortactin, [Rac1, PAK], [Coronin, PKD]))
rules += "1: Cortactin* = (Rac1 and PAK) or ((Rac1 or PAK) and not (Coronin and PKD)) \n" # voting
G.add_weighted_edges_from(get_edges(IRSp53, [Cdc42, Rac1], []))
rules += "1: IRSp53* = Cdc42 or Rac1 \n"
G.add_weighted_edges_from(get_edges(PAK, [Rac1, Cdc42, PKD], []))
rules += "1: PAK* = Rac1 or Cdc42 or PKD \n"
G.add_weighted_edges_from(get_edges(Dia1, [RhoA], [CP]))
rules += "1: Dia1* = RhoA and not CP \n"
G.add_weighted_edges_from(get_edges(Dia2, [Rac1, RhoA], []))
rules += "1: Dia2* = Rac1 or RhoA \n"
G.add_weighted_edges_from(get_edges(Ena_Vasp, [IRSp53, WASP, PKD], []))
rules += "1: Ena_Vasp* = IRSp53 or WASP or PKD \n"
G.add_weighted_edges_from(get_edges(Profilin, [WASP, Dia1, WAVE], [Thymosin, PIP2]))
rules += "1: Profilin* = " + voting_rule(["WASP", "Dia1", "WAVE"], ["Thymosin", "PIP2"]) + " \n"
G.add_weighted_edges_from(get_edges(CP, [Arp2_3], [Ena_Vasp, PIP2]))
rules += "1: CP* = (Arp2_3 and not Ena_Vasp) or not PIP2 \n"
G.add_weighted_edges_from(get_edges(Coronin, [SSH], []))
rules += "1: Coronin* = SSH \n"
G.add_weighted_edges_from(get_edges(ROCK, [RhoA], [SSH, Coronin]))
rules += "1: ROCK* = RhoA and not (SSH and Coronin) \n"
G.add_weighted_edges_from(get_edges(PKD, [ROCK], []))
rules += "1: PKD* = ROCK \n"
G.add_weighted_edges_from(get_edges(LIMK, [ROCK, PAK], [SSH]))
rules += "1: LIMK* = (ROCK or PAK) and not SSH \n"
G.add_weighted_edges_from(get_edges(Cofilin, [SSH, Arp2_3], [PIP2, Thymosin, LIMK, Cortactin]))
rules += "1: Cofilin* = " + voting_rule(["SSH", "Arp2_3"],
["PIP2", "Thymosin", "LIMK", "Cortactin"]) + "\n"
G.add_weighted_edges_from(get_edges(SSH, [Coronin, Rac1], [PKD]))
rules += "1: SSH* = (Coronin or Rac1) and not PKD \n"
G.add_weighted_edges_from(get_edges(Actin_BR, [Arp2_3], []))
rules += "1: Actin_BR* = (Arp2_3) \n" # or Cofilin) and not Thymosin
G.add_weighted_edges_from(get_edges(Actin_ST, [Profilin, Dia1, Dia2, Ena_Vasp], [CP, Cofilin]))
rules += "1: Actin_ST* = Profilin and (" + voting_rule(["Dia1", "Dia2", "Ena_Vasp"],
["CP", "Cofilin"]) + ")\n"
return {"rules":rules, "graph":G}