RiSE4fun samples for Z34BioList of built-in samples for the Z34Bio in RiSE4funen-USrise4fun © 2017 Microsoft Corporationhttp://rise4fun.com//Images/Rise.gifRiSE4fun samples for Z34Bio- http://rise4fun.com/Z34Biology/Chem_NetworkChem_Network//Specification
Gate[0] = 3 and GateA[0] = 0 and GateB[0] = 0 and GateAB[0] = 0;
C[5] = 3;
//Model: Describes a DSD model of a logic AND gate
Gate + A <-> GateA
Gate + B <-> GateB
GateA + B -> GateAB + C
GateB + A -> GateAB + C
- http://rise4fun.com/Z34Biology/Boolean_NetworkBoolean_Network//Specification: Show that oscillations are possible
//1) first, proove that path depth k=6 guarantees completeness for finding cycles:
//the following should be UNSAT
simple(#path,6);
//2) Then, proove that it is possible to reach a cycle (a path that does not reach a fixed point)
//not (C[6] = C[5]);
//Settings
directive constEncoding BitVector
directive encoding BitVector
directive plot A, B
//Model: Describes a toy Boolean network used for illustration
A' = not(A)
B' = A and B
C' = A or B
- http://rise4fun.com/Z34Biology/Mixed_ModelMixed_Model//Settings:
//plotting
directive plot A,GateA,GateAB,D
//maximal number of molecules
directive maxMols 20
//chemical species are described by an integer
directive encoding Integer
//constants are encoded as integers
directive constEncoding Integer
//individual state components are separated
directive splitStates
//SPECIFICATION
cycle(#path,6);
let $mass := {A + GateA + GateAB = 5}; //conservation of mass
#path |= $mass;
#path[6] |= (D=0);
//MODEL: CRN component
Gate + A <-> GateA
Gate + B <-> GateB
GateA + B -> GateAB + C(e)
GateB + A -> GateAB + C(e)
//MODEL: BN component
D' = C(e)>5
E' = D and E
F' = D or E
- http://rise4fun.com/Z34Biology/thelperthelper// Boolean network model of the control of T-helper cell differentiation from
// "A method for the generation of standardized qualitative dynamical systems
// of regulatory networks", L. Mendoza and I. Xenarios
// J. Theor. Biol. and Medical Modelling, 2006, vol. 3, no. 13
//
// Originally studied in
// "A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks."
// E. Dubrova and M. Teslenko.IEEE/ACM Trans. on Comput. Biology and Bioinformatics, 8:1393{1399, 2011.
//
// Converted automatically from BLIF representation using Z34Bio
//Settings:
directive constantInputs
directive constEncoding BitVector
//Specification:
//To for oscillations, search for a cycle of any length.
lasso(#path,12);
//Model:
TCR' = false
NFAT' = (TCR)
IFN-bX' = false
IFN-bR' = (IFN-bX)
IL-18X' = false
IL-18R' = (IL-18X and not (STAT6))
IRAK' = (IL-18R)
SOCS1' = (STAT1) or (T-bet)
IL-12X' = false
IL-12R' = (IL-12X and not (STAT6))
STAT4' = (IL-12R and not (GATA3))
T-bet' = (STAT1 and not (GATA3)) or (T-bet and not (GATA3))
IFN-gX' = (T-bet and not (STAT3)) or (STAT4 and not (STAT3)) or (IRAK and not (STAT3)) or (NFAT and not (STAT3))
IFN-gR' = (IFN-gX)
JAK1' = (IFN-gR and not (SOCS1))
STAT1' = (JAK1) or (IFN-bR)
IL-4X' = (GATA3 and not (STAT1))
IL-4R' = (IL-4X and not (SOCS1))
STAT6' = (IL-4R)
GATA3' = (GATA3 and not (T-bet)) or (STAT6 and not (T-bet))
IL-10X' = (GATA3)
IL-10R' = (IL-10X)
STAT3' = (IL-10R)
- http://rise4fun.com/Z34Biology/arabidopsisarabidopsis// Boolean network model of the control of flower morphogenesis in Arabidobis thaliana
// "From Genes to Flower Patterns and Evolution: Dynamic Models of Gene Regulatory Networks"
// A. Chaos, M. Aldana, C. Espinosa-Soto, B. G. P. de Leon, A. G. Arroyo, E. R. Alvarez-Buylla,
// Journal of Plant Growth Regulation, vol. 25, n. 4, 2006, pp. 278-289
//
// Originally studied in
// "A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks."
// E. Dubrova and M. Teslenko.IEEE/ACM Trans. on Comput. Biology and Bioinformatics, 8:1393{1399, 2011.
//
// Converted automatically from BLIF representation using Z34Bio
//Settings:
directive constantInputs
directive constEncoding BitVector
//Specification:
//To for oscillations, search for a cycle of any length.
lasso(#path,11);
//Model:
AG' = (LFY and AG and SEP) or (not (AP2) and not (TFL1)) or (LFY and not (CLF)) or (LFY and not (LUG)) or (LFY and WUS) or (not (AP1) and LFY) or (LFY and not (AP2))
AP3' = (AG and PI and SEP and AP3) or (AP1 and PI and SEP and AP3) or (LFY and UFO)
UFO' = (UFO)
FUL' = (not (AP1) and not (TFL1))
FT' = (not (EMF1))
AP1' = (not (AG) and not (TFL1)) or (LFY and not (AG)) or (FT and not (AG))
EMF1' = (not (LFY))
LFY' = (not (TFL1)) or (not (EMF1))
AP2' = (not (TFL1))
WUS' = (WUS and not (SEP)) or (WUS and not (AG))
LUG' = true
CLF' = true
TFL1' = (not (AP1) and EMF1 and not (LFY))
PI' = (AP1 and PI and SEP and AP3) or (AG and PI and SEP and AP3) or (LFY and AG) or (LFY and AP3)
SEP' = (LFY)
- http://rise4fun.com/Z34Biology/mammalianmammalian// Boolean network model of the control of the mammalian cell cycle from
// "Dynamical Analysis of a Generic Boolean Model for the Control of the
// Mammalian Cell Cycle", A. Faure, A. Naldi, C. Chaouiya, D. Thieffry,
// Bioinformatics, 2006, vol. 22, no. 14, pp. e124-e131.
//
// Originally studied in
// "A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks."
// E. Dubrova and M. Teslenko.IEEE/ACM Trans. on Comput. Biology and Bioinformatics, 8:1393{1399, 2011.
//
// Converted automatically from BLIF representation using Z34Bio
//Settings:
directive constantInputs
directive constEncoding BitVector
//Specification:
//To for oscillations, search for a cycle of any length.
lasso(#path,12);
//Model:
CycD' = (CycD)
CycE' = (not (Rb) and E2F)
Rb' = (not (CycD) and not (CycE) and not (CycA) and not (CycB)) or (not (CycD) and p27 and not (CycB))
E2F' = (not (Rb) and p27 and not (CycB)) or (not (Rb) and not (CycA) and not (CycB))
CycA' = (not (Rb) and CycA and not (Cdc20) and not (Cdh1)) or (not (Rb) and E2F and not (Cdc20) and not (Cdh1)) or (not (Rb) and CycA and not (Cdc20) and not (UbcH10)) or (not (Rb) and E2F and not (Cdc20) and not (UbcH10))
p27' = (not (CycD) and not (CycA) and p27 and not (CycB)) or (not (CycD) and not (CycE) and p27 and not (CycB)) or (not (CycD) and not (CycE) and not (CycA) and not (CycB))
Cdc20' = (CycB)
UbcH10' = (UbcH10 and CycB) or (Cdc20 and UbcH10) or (CycA and UbcH10) or (not (Cdh1))
Cdh1' = (p27 and not (CycB)) or (not (CycA) and not (CycB)) or (Cdc20)
CycB' = (not (Cdc20) and not (Cdh1))
- http://rise4fun.com/Z34Biology/tcrtcr// Boolean network model of the T-cell receptor signalling pathway from
// "A methodology for the structural and functional analysis of signaling and
// regulatory networks", S. Klamt, J. Saez-Rodriguez, J. A. Lindquist, L. Simeoni, E. D. Gilles,
// JBMC Bioinformatics 7: 56, 2006.
//
// Originally studied in
// "A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks."
// E. Dubrova and M. Teslenko.IEEE/ACM Trans. on Comput. Biology and Bioinformatics, 8:1393{1399, 2011.
//rasX
// Converted automatically from BLIF representation using Z34Bio
//Settings:
directive constantInputs
directive constEncoding BitVector
//Specification:
//To for oscillations, search for a cycle of any length.
lasso(#path,19);
//Model:
CD45' = (CD45)
CD8' = (CD8)
TCRlig' = (TCRlig)
TCbind' = (TCRlig and not (cCbl))
PAGCsk' = (not (TCbind)) or (Fyn)
LCK' = (CD45 and CD8 and not (PAGCsk))
Fyn' = (CD45 and LCK) or (CD45 and TCbind)
Rlk' = (LCK)
TCRphos' = (TCbind and LCK) or (Fyn)
ZAP70' = (LCK and TCRphos and not (cCbl))
cCbl' = (ZAP70)
Itk' = (ZAP70 and Slp76)
LAT' = (ZAP70)
Gads' = (LAT)
Slp76' = (Gads)
PLCg_b' = (LAT)
Grb2Sos' = (LAT)
DAG' = (PLCg_a)
PLCg_a' = (ZAP70 and Itk and Slp76 and PLCg_b) or (Rlk and ZAP70 and Slp76 and PLCg_b)
RasX' = (RasGRP1) or (Grb2Sos)
RasGRP1' = (DAG and PKCth)
PKCth' = (DAG)
IP3' = (PLCg_a)
Raf' = (RasX)
MEK' = (Raf)
CaX' = (IP3)
ERK' = (MEK)
SEK' = (PKCth)
IKK' = (PKCth)
Calcin' = (CaX)
Rsk' = (ERK)
Fos' = (ERK)
JNK' = (SEK)
IkB' = (not (IKK))
CREB' = (Rsk)
Jun' = (JNK)
CRE' = (CREB)
AP1' = (Fos and Jun)
NFkB' = (not (IkB))
NFAT' = (Calcin)
- http://rise4fun.com/Z34Biology/fission_yeastfission_yeast// Boolean network model of the control of the fission yeast cell cycle regulation from
// "Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast",
// M. I. Davidich, S. Bornholdt, PLoS ONE. 2008 Feb 27, 3(2):e1672.
//
// Originally studied in
// "A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks."
// E. Dubrova and M. Teslenko.IEEE/ACM Trans. on Comput. Biology and Bioinformatics, 8:1393{1399, 2011.
//
// Converted automatically from BLIF representation using Z34Bio
//Settings:
directive constantInputs
directive constEncoding BitVector
//Specification:
//To for oscillations, search for a cycle of any length.
lasso(#path,7);
//Model:
Start' = false
SK' = (Start)
Ste9' = (not (SK) and Ste9 and not (Cdc2_Cdc13x) and not (Cdc2_Cdc13s)) or (Ste9 and not (Cdc2_Cdc13x) and PP and not (Cdc2_Cdc13s)) or (not (SK) and Ste9 and PP and not (Cdc2_Cdc13s)) or (not (SK) and Ste9 and not (Cdc2_Cdc13x) and PP) or (not (SK) and not (Cdc2_Cdc13x) and PP and not (Cdc2_Cdc13s))
Cdc2_Cdc13x' = (Cdc2_Cdc13x and not (Rum1) and not (Slp1)) or (not (Ste9) and Cdc2_Cdc13x and not (Slp1)) or (not (Ste9) and Cdc2_Cdc13x and not (Rum1)) or (not (Ste9) and not (Rum1) and not (Slp1))
Rum1' = (not (Cdc2_Cdc13x) and Rum1 and PP and Cdc2_Cdc13s) or (not (SK) and not (Cdc2_Cdc13x) and Rum1 and not (Cdc2_Cdc13s)) or (not (SK) and Rum1 and PP and not (Cdc2_Cdc13s)) or (not (SK) and not (Cdc2_Cdc13x) and PP and not (Cdc2_Cdc13s))
PP' = (Slp1)
Cdc25' = (not (PP) and Cdc25) or (Cdc2_Cdc13x and Cdc25) or (Cdc2_Cdc13x and not (PP))
Slp1' = (Cdc2_Cdc13s)
Wee1_Mik1' = (not (Cdc2_Cdc13x) and Wee1_Mik1) or (PP and Wee1_Mik1) or (not (Cdc2_Cdc13x) and PP)
Cdc2_Cdc13s' = (not (Ste9) and not (Rum1) and Cdc25 and not (Slp1) and not (Wee1_Mik1) and Cdc2_Cdc13s)
- http://rise4fun.com/Z34Biology/drosophila4drosophila4// Boolean network model of Drosophila melanogaster from
// "The topology of the regulatory interactions predicts the expression pattern of the
// segment polarity genes in Drosophila melanogaster", R. Albert and H. G. Othmer,
// Journal of Theoretical Biology, 2003, vol. 223, no. 1, pp. 1-18.
//
// Originally studied in
// "A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks."
// E. Dubrova and M. Teslenko.IEEE/ACM Trans. on Comput. Biology and Bioinformatics, 8:1393{1399, 2011.
//
// Converted automatically from BLIF representation using Z34Bio
//Settings:
directive constantInputs
directive constEncoding BitVector
//Specification:
//To for oscillations, search for a cycle of any length.
lasso(#path,35);
//Model:
SLP1' = false
SLP2' = false
SLP3' = true
SLP4' = true
wg1' = (CIA1 and SLP1 and not (CIR1)) or (wg1 and SLP1 and not (CIR1)) or (wg1 and CIA1 and not (CIR1))
wg2' = (CIA2 and SLP2 and not (CIR2)) or (wg2 and SLP2 and not (CIR2)) or (wg2 and CIA2 and not (CIR2))
wg3' = (CIA3 and SLP3 and not (CIR3)) or (wg3 and SLP3 and not (CIR3)) or (wg3 and CIA3 and not (CIR3))
wg4' = (CIA4 and SLP4 and not (CIR4)) or (wg4 and SLP4 and not (CIR4)) or (wg4 and CIA4 and not (CIR4))
WG1' = (wg1)
WG2' = (wg2)
WG3' = (wg3)
WG4' = (wg4)
en1' = (WG2 and not (SLP1))
en2' = (WG3 and not (SLP2)) or (WG1 and not (SLP2))
en3' = (WG4 and not (SLP3)) or (WG2 and not (SLP3))
en4' = (WG3 and not (SLP4))
EN1' = (en1)
EN2' = (en2)
EN3' = (en3)
EN4' = (en4)
hh1' = (EN1 and not (CIR1))
hh2' = (EN2 and not (CIR2))
hh3' = (EN3 and not (CIR3))
hh4' = (EN4 and not (CIR4))
HH1' = (hh1)
HH2' = (hh2)
HH3' = (hh3)
HH4' = (hh4)
ptc1' = (CIA1 and not (EN1) and not (CIR1))
ptc2' = (CIA2 and not (EN2) and not (CIR2))
ptc3' = (CIA3 and not (EN3) and not (CIR3))
ptc4' = (CIA4 and not (EN4) and not (CIR4))
PTC1' = (PTC1 and not (HH2)) or (ptc1)
PTC2' = (PTC2 and not (HH1) and not (HH3)) or (ptc2)
PTC3' = (PTC3 and not (HH2) and not (HH4)) or (ptc3)
PTC4' = (PTC4 and not (HH3)) or (ptc4)
ci1' = (not (EN1))
ci2' = (not (EN2))
ci3' = (not (EN3))
ci4' = (not (EN4))
CI1' = (ci1)
CI2' = (ci2)
CI3' = (ci3)
CI4' = (ci4)
CIA1' = (CI1 and hh2) or (CI1 and HH2) or (CI1 and not (PTC1))
CIA2' = (CI2 and hh3) or (CI2 and hh1) or (CI2 and HH3) or (CI2 and HH1) or (CI2 and not (PTC2))
CIA3' = (CI3 and hh4) or (CI3 and hh2) or (CI3 and HH4) or (CI3 and HH2) or (CI3 and not (PTC3))
CIA4' = (CI4 and hh3) or (CI4 and HH3) or (CI4 and not (PTC4))
CIR1' = (CI1 and PTC1 and not (HH2) and not (hh2))
CIR2' = (CI2 and PTC2 and not (HH1) and not (HH3) and not (hh1) and not (hh3))
CIR3' = (CI3 and PTC3 and not (HH2) and not (HH4) and not (hh2) and not (hh4))
CIR4' = (CI4 and PTC4 and not (HH3) and not (hh3))
- http://rise4fun.com/Z34Biology/budding_yeastbudding_yeast// Boolean network model of the control of the budding yeast cell cycle regulation from
// "The yeast cell-cycle network is robustly designed",
// Fangting Li, Tao Long, Ying Lu, Qi Ouyang, Chao Tang,
// PNAS April 6, 2004, vol. 101 no. 14 4781-4786.
//
// Originally studied in
// "A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks."
// E. Dubrova and M. Teslenko.IEEE/ACM Trans. on Comput. Biology and Bioinformatics, 8:1393{1399, 2011.
//
// Converted automatically from BLIF representation using Z34Bio
//Settings:
directive constantInputs
directive constEncoding BitVector
//Specification:
//To for oscillations, search for a cycle of any length.
lasso(#path,19);
//Model:
Cell size' = false
Cln3' = (Cell size)
SBF' = (SBF and not (Clb1_2)) or (Cln3 and SBF) or (Cln3 and not (Clb1_2))
MBF' = (MBF and not (Clb1_2)) or (Cln3 and MBF) or (Cln3 and not (Clb1_2))
Cln1_2' = (SBF)
Sic1' = (not (Cln1_2) and Sic1 and not (Cln5_6) and not (Clb1_2)) or (Sic1 and not (Cln5_6) and not (Clb1_2) and Cdc20_Cdc14) or (not (Cln1_2) and Sic1 and not (Clb1_2) and Cdc20_Cdc14) or (not (Cln1_2) and Sic1 and not (Cln5_6) and Cdc20_Cdc14) or (Sic1 and not (Cln5_6) and not (Clb1_2) and Swi5) or (not (Cln1_2) and Sic1 and not (Clb1_2) and Swi5) or (not (Cln1_2) and Sic1 and not (Cln5_6) and Swi5) or (Sic1 and not (Clb1_2) and Cdc20_Cdc14 and Swi5) or (Sic1 and not (Cln5_6) and Cdc20_Cdc14 and Swi5) or (not (Cln1_2) and Sic1 and Cdc20_Cdc14 and Swi5) or (not (Cln1_2) and not (Cln5_6) and not (Clb1_2) and Swi5) or (not (Cln5_6) and not (Clb1_2) and Cdc20_Cdc14 and Swi5) or (not (Cln1_2) and not (Clb1_2) and Cdc20_Cdc14 and Swi5) or (not (Cln1_2) and not (Cln5_6) and Cdc20_Cdc14 and Swi5) or (not (Cln1_2) and not (Cln5_6) and not (Clb1_2) and Cdc20_Cdc14)
Cln5_6' = (not (Sic1) and Cln5_6 and not (Cdc20_Cdc14)) or (MBF and Cln5_6 and not (Cdc20_Cdc14)) or (MBF and not (Sic1) and Cln5_6) or (MBF and not (Sic1) and not (Cdc20_Cdc14))
Cdh1' = (not (Cln1_2) and not (Cln5_6) and Cdh1 and not (Clb1_2)) or (not (Cln5_6) and Cdh1 and not (Clb1_2) and Cdc20_Cdc14) or (not (Cln1_2) and Cdh1 and not (Clb1_2) and Cdc20_Cdc14) or (not (Cln1_2) and not (Cln5_6) and Cdh1 and Cdc20_Cdc14) or (not (Cln1_2) and not (Cln5_6) and not (Clb1_2) and Cdc20_Cdc14)
Clb1_2' = (not (Sic1) and Cln5_6 and not (Cdh1) and Clb1_2) or (not (Sic1) and not (Cdh1) and Clb1_2 and Mcm1_SFF) or (Cln5_6 and not (Cdh1) and Clb1_2 and Mcm1_SFF) or (not (Sic1) and Cln5_6 and Clb1_2 and Mcm1_SFF) or (not (Sic1) and not (Cdh1) and Clb1_2 and not (Cdc20_Cdc14)) or (Cln5_6 and not (Cdh1) and Clb1_2 and not (Cdc20_Cdc14)) or (not (Sic1) and Cln5_6 and Clb1_2 and not (Cdc20_Cdc14)) or (not (Cdh1) and Clb1_2 and Mcm1_SFF and not (Cdc20_Cdc14)) or (not (Sic1) and Clb1_2 and Mcm1_SFF and not (Cdc20_Cdc14)) or (Cln5_6 and Clb1_2 and Mcm1_SFF and not (Cdc20_Cdc14)) or (not (Sic1) and Cln5_6 and not (Cdh1) and not (Cdc20_Cdc14)) or (not (Sic1) and not (Cdh1) and Mcm1_SFF and not (Cdc20_Cdc14)) or (Cln5_6 and not (Cdh1) and Mcm1_SFF and not (Cdc20_Cdc14)) or (not (Sic1) and Cln5_6 and Mcm1_SFF and not (Cdc20_Cdc14)) or (not (Sic1) and Cln5_6 and not (Cdh1) and Mcm1_SFF)
Mcm1_SFF' = (Clb1_2) or (Cln5_6)
Cdc20_Cdc14' = (Mcm1_SFF) or (Clb1_2)
Swi5' = (not (Clb1_2) and Cdc20_Cdc14) or (Mcm1_SFF and Cdc20_Cdc14) or (not (Clb1_2) and Mcm1_SFF)
- http://rise4fun.com/Z34Biology/DNA_transducersDNA_transducers//--------------------------------------------------------------------------
//Transducer DNA Circuits. Four transducers in series. Model generated by Visual DSD
//--------------------------------------------------------------------------
//--------------------------------------------------------------------------
//SPECIFICATIONS
//--------------------------------------------------------------------------
//FIND REACHABLE VIOLATION STATE
//at 0 $init;
//$no_rxn_enabled;
//not $no_reactive_species;
//FIND REACHABLE SAT STATE
at 0 $init;
at 50 $no_rxn_enabled;
at 50 $no_reactive_species;
//TEST INVARIANT
//#path[0]|=$invariant;
//not(#path[1]|=$invariant);
//--------------------------------------------------------------------------
//MODEL
//--------------------------------------------------------------------------
T_2 + S<->sp_1 + sp_0
sp_1 + T->sp_4 + sp_3 + sp_2
T_15 + sp_2<->sp_9 + sp_5
T_11 + sp_2<->sp_8 + sp_5
T_7 + sp_2<->sp_7 + sp_5
T_3 + sp_2<->sp_6 + sp_5
sp_9 + T_13->sp_12 + sp_11 + sp_10
sp_4 + sp_5->sp_14 + sp_13
sp_8 + T_9->sp_17 + sp_16 + sp_15
T_14 + sp_15<->sp_19 + sp_18
sp_19 + T_12->sp_20 + sp_11 + sp_2
sp_20 + sp_5->sp_21 + sp_13
sp_12 + sp_18->sp_23 + sp_22
sp_7 + T_5->sp_26 + sp_25 + sp_24
T_10 + sp_24<->sp_28 + sp_27
sp_28 + T_8->sp_29 + sp_16 + sp_2
sp_29 + sp_5->sp_30 + sp_13
sp_17 + sp_27->sp_32 + sp_31
sp_6 + T_1->sp_34 + sp_3 + sp_33
T_6 + sp_33<->sp_36 + sp_35
sp_36 + T_4->sp_37 + sp_25 + sp_2
sp_37 + sp_5->sp_38 + sp_13
sp_26 + sp_35->sp_40 + sp_39
sp_34 + sp_0->sp_42 + sp_41
//--------------------------------------------------------------------------
//PROPERTY DEFINITIONS
//--------------------------------------------------------------------------
let $init :=
{
sp_2 = 0 and
sp_13 = 0 and
sp_25 = 0 and
sp_16 = 0 and
sp_11 = 0 and
sp_3 = 0 and
sp_5 = 0 and
T = 1 and
T_4 = 1 and
T_8 = 1 and
T_12 = 1 and
S = 1 and
sp_33 = 0 and
sp_24 = 0 and
sp_15 = 0 and
sp_10 = 0 and
sp_0 = 0 and
sp_41 = 0 and
T_1 = 1 and
sp_35 = 0 and
sp_39 = 0 and
T_5 = 1 and
sp_27 = 0 and
sp_31 = 0 and
T_9 = 1 and
sp_18 = 0 and
sp_22 = 0 and
T_13 = 1 and
sp_14 = 0 and
sp_4 = 0 and
sp_1 = 0 and
sp_38 = 0 and
sp_37 = 0 and
sp_36 = 0 and
sp_30 = 0 and
sp_29 = 0 and
sp_28 = 0 and
sp_21 = 0 and
sp_20 = 0 and
sp_19 = 0 and
sp_42 = 0 and
T_3 = 1 and
sp_6 = 0 and
sp_34 = 0 and
sp_40 = 0 and
T_7 = 1 and
sp_7 = 0 and
sp_26 = 0 and
sp_32 = 0 and
T_11 = 1 and
sp_8 = 0 and
sp_17 = 0 and
sp_23 = 0 and
T_15 = 1 and
sp_9 = 0 and
sp_12 = 0 and
T_2 = 1 and
T_6 = 1 and
T_10 = 1 and
T_14 = 1
};
let $no_rxn_enabled :=
{
( T_2<1 or S<1) and
( sp_1<1 or sp_0<1) and
( sp_1<1 or T<1) and
( T_15<1 or sp_2<1) and
( sp_9<1 or sp_5<1) and
( T_11<1 or sp_2<1) and
( sp_8<1 or sp_5<1) and
( T_7<1 or sp_2<1) and
( sp_7<1 or sp_5<1) and
( T_3<1 or sp_2<1) and
( sp_6<1 or sp_5<1) and
( sp_9<1 or T_13<1) and
( sp_4<1 or sp_5<1) and
( sp_8<1 or T_9<1) and
( T_14<1 or sp_15<1) and
( sp_19<1 or sp_18<1) and
( sp_19<1 or T_12<1) and
( sp_20<1 or sp_5<1) and
( sp_12<1 or sp_18<1) and
( sp_7<1 or T_5<1) and
( T_10<1 or sp_24<1) and
( sp_28<1 or sp_27<1) and
( sp_28<1 or T_8<1) and
( sp_29<1 or sp_5<1) and
( sp_17<1 or sp_27<1) and
( sp_6<1 or T_1<1) and
( T_6<1 or sp_33<1) and
( sp_36<1 or sp_35<1) and
( sp_36<1 or T_4<1) and
( sp_37<1 or sp_5<1) and
( sp_26<1 or sp_35<1) and
( sp_34<1 or sp_0<1)
};
let $no_reactive_species :=
{
T_15 = 0 and
T_14 = 0 and
T_13 = 0 and
T_12 = 0 and
T_11 = 0 and
T_10 = 0 and
T_9 = 0 and
T_8 = 0 and
T_7 = 0 and
T_6 = 0 and
T_5 = 0 and
T_4 = 0 and
T_3 = 0 and
T_2 = 0 and
T_1 = 0 and
T = 0 and
S = 0
};
let $invariant :=
{
sp_38 + sp_30 + sp_21 + sp_14 + sp_5 + T_3 + T_7 + T_11 + T_15 = 4 and
sp_14 + sp_4 + T = 1 and
sp_38 + sp_37 + T_4 = 1 and
sp_30 + sp_29 + T_8 = 1 and
sp_21 + sp_20 + T_12 = 1 and
sp_14 + sp_4 + sp_1 + S = 1 and
sp_38 + sp_37 + sp_36 + sp_33 + sp_6 + T_3 = 1 and
sp_30 + sp_29 + sp_28 + sp_24 + sp_7 + T_7 = 1 and
sp_21 + sp_20 + sp_19 + sp_15 + sp_8 + T_11 = 1 and
sp_10 + sp_9 + T_15 = 1 and
sp_37 + sp_36 + sp_29 + sp_28 + sp_20 + sp_19 + sp_13 + sp_4 + sp_1 + T_2 + T_6 + T_10 + T_14 = 4 and
sp_42 + sp_40 + sp_36 + sp_34 + sp_6 + sp_32 + sp_28 + sp_26 + sp_7 + sp_23 + sp_19 + sp_17 + sp_8 + sp_12 + sp_9 + sp_2 + sp_1 + T_2 + T_6 + T_10 + T_14 = 4 and
sp_6 + sp_3 + sp_1 + T_2 + T_3 = 2 and
sp_36 + sp_25 + sp_7 + T_6 + T_7 = 2 and
sp_28 + sp_16 + sp_8 + T_10 + T_11 = 2 and
sp_19 + sp_11 + sp_9 + T_14 + T_15 = 2 and
sp_41 + sp_34 + sp_6 + T_3 = 1 and
sp_42 + sp_0 + T_2 = 1 and
sp_39 + sp_26 + sp_7 + T_7 = 1 and
sp_40 + sp_35 + T_6 = 1 and
sp_42 + sp_34 + T_1 = 1 and
sp_31 + sp_17 + sp_8 + T_11 = 1 and
sp_32 + sp_27 + T_10 = 1 and
sp_40 + sp_26 + T_5 = 1 and
sp_22 + sp_12 + sp_9 + T_15 = 1 and
sp_23 + sp_18 + T_14 = 1 and
sp_32 + sp_17 + T_9 = 1 and
sp_23 + sp_12 + T_13 = 1 and
sp_14 + sp_4 + sp_1 + T_2 = 1 and
sp_38 + sp_37 + sp_36 + T_6 = 1 and
sp_30 + sp_29 + sp_28 + T_10 = 1 and
sp_21 + sp_20 + sp_19 + T_14 = 1 and
sp_42 + sp_34 + sp_6 + T_3 = 1 and
sp_40 + sp_26 + sp_7 + T_7 = 1 and
sp_32 + sp_17 + sp_8 + T_11 = 1 and
sp_23 + sp_12 + sp_9 + T_15 = 1
};
- http://rise4fun.com/Z34Biology/DNA_square_rootDNA_square_root//--------------------------------------------------------------------------
//Qian and Winfree 4 bit square root circuit. Model generated by Visual DSD
//--------------------------------------------------------------------------
//--------------------------------------------------------------------------
//SPECIFICATION: TEST INVARIANT
//--------------------------------------------------------------------------
#path[0]|=$invariant;
not(#path[1]|=$invariant);
//--------------------------------------------------------------------------
//MODEL
//--------------------------------------------------------------------------
thresholdL_15 + signal_7->sp_1 + sp_0
thresholdL_15 + signal_7->sp_1 + sp_0
thresholdL_14 + signal_6->sp_3 + sp_2
thresholdL_14 + signal_6->sp_3 + sp_2
thresholdL_13 + signal_5->sp_5 + sp_4
thresholdL_13 + signal_5->sp_5 + sp_4
thresholdL_12 + signal_4->sp_7 + sp_6
thresholdL_12 + signal_4->sp_7 + sp_6
gateL_37 + signal_7<->sp_9 + sp_8
sp_9 + signal_23<->sp_10 + signal_7
gateL_36 + signal_7<->sp_9 + sp_11
gateL_35 + signal_7<->sp_9 + sp_12
gateL_34 + signal_6<->sp_14 + sp_13
sp_14 + signal_22<->sp_15 + signal_6
gateL_33 + signal_6<->sp_14 + sp_16
gateL_32 + signal_6<->sp_14 + sp_17
gateL_31 + signal_5<->sp_19 + sp_18
sp_19 + signal_21<->sp_20 + signal_5
gateL_30 + signal_5<->sp_19 + sp_21
gateL_29 + signal_5<->sp_19 + sp_22
gateL_28 + signal_4<->sp_24 + sp_23
sp_24 + signal_20<->sp_25 + signal_4
gateL_27 + signal_4<->sp_24 + sp_26
gateL_26 + signal_4<->sp_24 + sp_27
gateL_16 + sp_13<->sp_30 + sp_28
gateL_16 + sp_23<->sp_29 + sp_28
thresholdL_7 + sp_28->sp_34 + sp_33
thresholdL_7 + sp_28->sp_34 + sp_33
gateL_17 + sp_28<->sp_32 + sp_31
sp_32 + signal_15<->sp_35 + sp_28
gateL_22 + sp_31<->sp_37 + sp_36
thresholdL_10 + sp_36->sp_41 + sp_40
thresholdL_10 + sp_36->sp_41 + sp_40
gateL_23 + sp_36<->sp_39 + sp_38
sp_39 + signal_18<->sp_42 + sp_36
reporter_2 + sp_38->sp_44 + sp_43
gateL_14 + sp_8<->sp_47 + sp_45
gateL_14 + sp_18<->sp_46 + sp_45
thresholdL_6 + sp_45->sp_51 + sp_50
thresholdL_6 + sp_45->sp_51 + sp_50
gateL_15 + sp_45<->sp_49 + sp_48
sp_49 + signal_14<->sp_52 + sp_45
gateL_24 + sp_48<->sp_54 + sp_53
thresholdL_11 + sp_53->sp_58 + sp_57
thresholdL_11 + sp_53->sp_58 + sp_57
gateL_25 + sp_53<->sp_56 + sp_55
sp_56 + signal_19<->sp_59 + sp_53
reporter_3 + sp_55->sp_61 + sp_60
gateL_12 + sp_11<->sp_64 + sp_62
gateL_12 + sp_21<->sp_63 + sp_62
thresholdL_5 + sp_62->sp_68 + sp_67
thresholdL_5 + sp_62->sp_68 + sp_67
gateL_13 + sp_62<->sp_66 + sp_65
sp_66 + signal_13<->sp_69 + sp_62
reporter_1 + sp_65->sp_71 + sp_70
gateL_10 + sp_16<->sp_74 + sp_72
gateL_10 + sp_26<->sp_73 + sp_72
thresholdL_4 + sp_72->sp_78 + sp_77
thresholdL_4 + sp_72->sp_78 + sp_77
gateL_11 + sp_72<->sp_76 + sp_75
sp_76 + signal_12<->sp_79 + sp_72
reporter + sp_75->sp_81 + sp_80
gateL_8 + sp_17<->sp_84 + sp_82
gateL_8 + sp_22<->sp_83 + sp_82
thresholdL_3 + sp_82->sp_88 + sp_87
thresholdL_3 + sp_82->sp_88 + sp_87
gateL_9 + sp_82<->sp_86 + sp_85
sp_86 + signal_11<->sp_89 + sp_82
gateL_20 + sp_85<->sp_91 + sp_90
thresholdL_9 + sp_90->sp_95 + sp_94
thresholdL_9 + sp_90->sp_95 + sp_94
gateL_21 + sp_90<->sp_93 + sp_92
sp_93 + signal_17<->sp_96 + sp_90
gateL_22 + sp_92<->sp_97 + sp_36
gateL_6 + sp_12<->sp_100 + sp_98
gateL_6 + sp_27<->sp_99 + sp_98
thresholdL_2 + sp_98->sp_104 + sp_103
thresholdL_2 + sp_98->sp_104 + sp_103
gateL_7 + sp_98<->sp_102 + sp_101
sp_102 + signal_10<->sp_105 + sp_98
gateL_18 + sp_101<->sp_107 + sp_106
thresholdL_8 + sp_106->sp_111 + sp_110
thresholdL_8 + sp_106->sp_111 + sp_110
gateL_19 + sp_106<->sp_109 + sp_108
sp_109 + signal_16<->sp_112 + sp_106
gateL_24 + sp_108<->sp_113 + sp_53
gateL_3 + signal_2<->sp_116 + sp_114
gateL_3 + signal<->sp_115 + sp_114
thresholdL_1 + sp_114->sp_121 + sp_120
thresholdL_1 + sp_114->sp_121 + sp_120
gateL_5 + sp_114<->sp_118 + sp_119
gateL_4 + sp_114<->sp_118 + sp_117
sp_118 + signal_9<->sp_122 + sp_114
gateL_20 + sp_119<->sp_123 + sp_90
gateL_14 + sp_117<->sp_124 + sp_45
gateL + signal_3<->sp_127 + sp_125
gateL + signal_1<->sp_126 + sp_125
thresholdL + sp_125->sp_132 + sp_131
thresholdL + sp_125->sp_132 + sp_131
gateL_2 + sp_125<->sp_129 + sp_130
gateL_1 + sp_125<->sp_129 + sp_128
sp_129 + signal_8<->sp_133 + sp_125
gateL_18 + sp_130<->sp_134 + sp_106
gateL_16 + sp_128<->sp_135 + sp_28
//--------------------------------------------------------------------------
//Property definitions
//--------------------------------------------------------------------------
let $invariant :=
{
sp_60 + reporter_3 = 75 and
sp_127 + signal_3 = 5 and
sp_24 + sp_7 + signal_4 = 5 and
sp_6 + thresholdL_12 = 10 and
sp_99 + sp_27 + gateL_26 = 50 and
sp_73 + sp_26 + gateL_27 = 50 and
sp_29 + sp_23 + gateL_28 = 50 and
sp_25 + signal_20 = 300 and
sp_19 + sp_5 + signal_5 = 45 and
sp_4 + thresholdL_13 = 10 and
sp_83 + sp_22 + gateL_29 = 50 and
sp_63 + sp_21 + gateL_30 = 50 and
sp_46 + sp_18 + gateL_31 = 50 and
sp_20 + signal_21 = 300 and
sp_14 + sp_3 + signal_6 = 45 and
sp_2 + thresholdL_14 = 10 and
sp_84 + sp_17 + gateL_32 = 50 and
sp_74 + sp_16 + gateL_33 = 50 and
sp_30 + sp_13 + gateL_34 = 50 and
sp_15 + signal_22 = 300 and
sp_9 + sp_1 + signal_7 = 5 and
sp_0 + thresholdL_15 = 10 and
sp_100 + sp_12 + gateL_35 = 50 and
sp_64 + sp_11 + gateL_36 = 50 and
sp_47 + sp_8 + gateL_37 = 50 and
sp_10 + signal_23 = 300 and
sp_129 + sp_132 + sp_125 + gateL = 100 and
sp_131 + thresholdL = 30 and
sp_135 + sp_128 + gateL_1 = 50 and
sp_134 + sp_130 + gateL_2 = 50 and
sp_133 + signal_8 = 200 and
sp_118 + sp_121 + sp_114 + gateL_3 = 100 and
sp_120 + thresholdL_1 = 60 and
sp_124 + sp_117 + gateL_4 = 50 and
sp_123 + sp_119 + gateL_5 = 50 and
sp_122 + signal_9 = 200 and
sp_102 + sp_104 + sp_98 + gateL_6 = 100 and
sp_103 + thresholdL_2 = 30 and
sp_107 + sp_101 + gateL_7 = 50 and
sp_105 + signal_10 = 100 and
sp_86 + sp_88 + sp_82 + gateL_8 = 100 and
sp_87 + thresholdL_3 = 60 and
sp_91 + sp_85 + gateL_9 = 50 and
sp_89 + signal_11 = 100 and
sp_76 + sp_78 + sp_72 + gateL_10 = 100 and
sp_77 + thresholdL_4 = 60 and
sp_81 + sp_75 + gateL_11 = 50 and
sp_79 + signal_12 = 100 and
sp_66 + sp_68 + sp_62 + gateL_12 = 100 and
sp_67 + thresholdL_5 = 30 and
sp_71 + sp_65 + gateL_13 = 50 and
sp_69 + signal_13 = 100 and
sp_49 + sp_51 + sp_45 + gateL_14 = 150 and
sp_50 + thresholdL_6 = 110 and
sp_54 + sp_48 + gateL_15 = 50 and
sp_52 + signal_14 = 100 and
sp_32 + sp_34 + sp_28 + gateL_16 = 150 and
sp_33 + thresholdL_7 = 30 and
sp_37 + sp_31 + gateL_17 = 50 and
sp_35 + signal_15 = 100 and
sp_109 + sp_111 + sp_106 + gateL_18 = 100 and
sp_110 + thresholdL_8 = 60 and
sp_113 + sp_108 + gateL_19 = 50 and
sp_112 + signal_16 = 100 and
sp_93 + sp_95 + sp_90 + gateL_20 = 100 and
sp_94 + thresholdL_9 = 30 and
sp_97 + sp_92 + gateL_21 = 50 and
sp_96 + signal_17 = 100 and
sp_39 + sp_41 + sp_36 + gateL_22 = 100 and
sp_40 + thresholdL_10 = 60 and
sp_44 + sp_38 + gateL_23 = 50 and
sp_42 + signal_18 = 100 and
sp_56 + sp_58 + sp_53 + gateL_24 = 100 and
sp_57 + thresholdL_11 = 30 and
sp_61 + sp_55 + gateL_25 = 50 and
sp_59 + signal_19 = 100 and
sp_80 + reporter = 75 and
sp_70 + reporter_1 = 75 and
sp_43 + reporter_2 = 75 and
sp_115 + signal = 45 and
sp_126 + signal_1 = 5 and
sp_116 + signal_2 = 45 and
sp_7 + thresholdL_12 = 10 and
sp_5 + thresholdL_13 = 10 and
sp_3 + thresholdL_14 = 10 and
sp_1 + thresholdL_15 = 10 and
sp_132 + thresholdL = 30 and
sp_121 + thresholdL_1 = 60 and
sp_104 + thresholdL_2 = 30 and
sp_88 + thresholdL_3 = 60 and
sp_78 + thresholdL_4 = 60 and
sp_68 + thresholdL_5 = 30 and
sp_51 + thresholdL_6 = 110 and
sp_34 + thresholdL_7 = 30 and
sp_111 + thresholdL_8 = 60 and
sp_95 + thresholdL_9 = 30 and
sp_41 + thresholdL_10 = 60 and
sp_58 + thresholdL_11 = 30 and
sp_61 + reporter_3 = 75 and
gateL_26 + gateL_27 + sp_25 + sp_24 + gateL_28 = 150 and
gateL_29 + gateL_30 + sp_20 + sp_19 + gateL_31 = 150 and
gateL_32 + gateL_33 + sp_15 + sp_14 + gateL_34 = 150 and
gateL_35 + gateL_36 + sp_10 + sp_9 + gateL_37 = 150 and
sp_126 + sp_127 + gateL = 100 and
sp_133 + sp_129 + gateL_1 + gateL_2 = 100 and
sp_115 + sp_116 + gateL_3 = 100 and
sp_122 + sp_118 + gateL_4 + gateL_5 = 100 and
sp_99 + sp_100 + gateL_6 = 100 and
sp_105 + sp_102 + gateL_7 = 50 and
sp_83 + sp_84 + gateL_8 = 100 and
sp_89 + sp_86 + gateL_9 = 50 and
sp_73 + sp_74 + gateL_10 = 100 and
sp_79 + sp_76 + gateL_11 = 50 and
sp_63 + sp_64 + gateL_12 = 100 and
sp_69 + sp_66 + gateL_13 = 50 and
sp_124 + sp_46 + sp_47 + gateL_14 = 150 and
sp_52 + sp_49 + gateL_15 = 50 and
sp_135 + sp_29 + sp_30 + gateL_16 = 150 and
sp_35 + sp_32 + gateL_17 = 50 and
sp_134 + sp_107 + gateL_18 = 100 and
sp_112 + sp_109 + gateL_19 = 50 and
sp_123 + sp_91 + gateL_20 = 100 and
sp_96 + sp_93 + gateL_21 = 50 and
sp_97 + sp_37 + gateL_22 = 100 and
sp_42 + sp_39 + gateL_23 = 50 and
sp_113 + sp_54 + gateL_24 = 100 and
sp_59 + sp_56 + gateL_25 = 50 and
sp_81 + reporter = 75 and
sp_71 + reporter_1 = 75 and
sp_44 + reporter_2 = 75
};
let $init :=
{
signal_3 = 5 and
sp_127 = 0 and
signal_4 = 5 and
sp_24 = 0 and
sp_7 = 0 and
sp_27 = 0 and
sp_26 = 0 and
sp_23 = 0 and
signal_20 = 300 and
sp_6 = 0 and
sp_99 = 0 and
sp_73 = 0 and
sp_29 = 0 and
signal_5 = 45 and
sp_19 = 0 and
sp_5 = 0 and
sp_22 = 0 and
sp_21 = 0 and
sp_18 = 0 and
signal_21 = 300 and
sp_4 = 0 and
sp_83 = 0 and
sp_63 = 0 and
sp_46 = 0 and
signal_6 = 45 and
sp_14 = 0 and
sp_3 = 0 and
sp_17 = 0 and
sp_16 = 0 and
sp_13 = 0 and
signal_22 = 300 and
sp_2 = 0 and
sp_84 = 0 and
sp_74 = 0 and
sp_30 = 0 and
signal_7 = 5 and
sp_9 = 0 and
sp_1 = 0 and
sp_12 = 0 and
sp_11 = 0 and
sp_8 = 0 and
signal_23 = 300 and
sp_0 = 0 and
sp_100 = 0 and
sp_64 = 0 and
sp_47 = 0 and
sp_125 = 0 and
sp_129 = 0 and
sp_132 = 0 and
sp_128 = 0 and
sp_130 = 0 and
signal_8 = 200 and
sp_131 = 0 and
sp_135 = 0 and
sp_134 = 0 and
sp_114 = 0 and
sp_118 = 0 and
sp_121 = 0 and
sp_117 = 0 and
sp_119 = 0 and
signal_9 = 200 and
sp_120 = 0 and
sp_124 = 0 and
sp_123 = 0 and
sp_98 = 0 and
sp_102 = 0 and
sp_104 = 0 and
sp_101 = 0 and
signal_10 = 100 and
sp_103 = 0 and
sp_107 = 0 and
sp_82 = 0 and
sp_86 = 0 and
sp_88 = 0 and
sp_85 = 0 and
signal_11 = 100 and
sp_87 = 0 and
sp_91 = 0 and
sp_72 = 0 and
sp_76 = 0 and
sp_78 = 0 and
sp_75 = 0 and
signal_12 = 100 and
sp_77 = 0 and
sp_81 = 0 and
sp_62 = 0 and
sp_66 = 0 and
sp_68 = 0 and
sp_65 = 0 and
signal_13 = 100 and
sp_67 = 0 and
sp_71 = 0 and
sp_45 = 0 and
sp_49 = 0 and
sp_51 = 0 and
sp_48 = 0 and
signal_14 = 100 and
sp_50 = 0 and
sp_54 = 0 and
sp_28 = 0 and
sp_32 = 0 and
sp_34 = 0 and
sp_31 = 0 and
signal_15 = 100 and
sp_33 = 0 and
sp_37 = 0 and
sp_106 = 0 and
sp_109 = 0 and
sp_111 = 0 and
sp_108 = 0 and
signal_16 = 100 and
sp_110 = 0 and
sp_113 = 0 and
sp_90 = 0 and
sp_93 = 0 and
sp_95 = 0 and
sp_92 = 0 and
signal_17 = 100 and
sp_94 = 0 and
sp_97 = 0 and
sp_36 = 0 and
sp_39 = 0 and
sp_41 = 0 and
sp_38 = 0 and
signal_18 = 100 and
sp_40 = 0 and
sp_44 = 0 and
sp_53 = 0 and
sp_56 = 0 and
sp_58 = 0 and
sp_55 = 0 and
signal_19 = 100 and
sp_57 = 0 and
sp_61 = 0 and
sp_80 = 0 and
sp_70 = 0 and
sp_43 = 0 and
sp_60 = 0 and
signal = 45 and
sp_115 = 0 and
signal_1 = 5 and
sp_126 = 0 and
signal_2 = 45 and
sp_116 = 0 and
thresholdL_12 = 10 and
thresholdL_13 = 10 and
thresholdL_14 = 10 and
thresholdL_15 = 10 and
thresholdL = 30 and
thresholdL_1 = 60 and
thresholdL_2 = 30 and
thresholdL_3 = 60 and
thresholdL_4 = 60 and
thresholdL_5 = 30 and
thresholdL_6 = 110 and
thresholdL_7 = 30 and
thresholdL_8 = 60 and
thresholdL_9 = 30 and
thresholdL_10 = 60 and
thresholdL_11 = 30 and
gateL_26 = 50 and
gateL_27 = 50 and
gateL_28 = 50 and
sp_25 = 0 and
gateL_29 = 50 and
gateL_30 = 50 and
gateL_31 = 50 and
sp_20 = 0 and
gateL_32 = 50 and
gateL_33 = 50 and
gateL_34 = 50 and
sp_15 = 0 and
gateL_35 = 50 and
gateL_36 = 50 and
gateL_37 = 50 and
sp_10 = 0 and
gateL = 100 and
gateL_1 = 50 and
gateL_2 = 50 and
sp_133 = 0 and
gateL_3 = 100 and
gateL_4 = 50 and
gateL_5 = 50 and
sp_122 = 0 and
gateL_6 = 100 and
gateL_7 = 50 and
sp_105 = 0 and
gateL_8 = 100 and
gateL_9 = 50 and
sp_89 = 0 and
gateL_10 = 100 and
gateL_11 = 50 and
sp_79 = 0 and
gateL_12 = 100 and
gateL_13 = 50 and
sp_69 = 0 and
gateL_14 = 150 and
gateL_15 = 50 and
sp_52 = 0 and
gateL_16 = 150 and
gateL_17 = 50 and
sp_35 = 0 and
gateL_18 = 100 and
gateL_19 = 50 and
sp_112 = 0 and
gateL_20 = 100 and
gateL_21 = 50 and
sp_96 = 0 and
gateL_22 = 100 and
gateL_23 = 50 and
sp_42 = 0 and
gateL_24 = 100 and
gateL_25 = 50 and
sp_59 = 0 and
reporter = 75 and
reporter_1 = 75 and
reporter_2 = 75 and
reporter_3 = 75
};
let $no_rxn_enabled :=
{
( thresholdL_15<1 or signal_7<1) and
( thresholdL_15<1 or signal_7<1) and
( thresholdL_14<1 or signal_6<1) and
( thresholdL_14<1 or signal_6<1) and
( thresholdL_13<1 or signal_5<1) and
( thresholdL_13<1 or signal_5<1) and
( thresholdL_12<1 or signal_4<1) and
( thresholdL_12<1 or signal_4<1) and
( gateL_37<1 or signal_7<1) and
( sp_9<1 or sp_8<1) and
( sp_9<1 or signal_23<1) and
( sp_10<1 or signal_7<1) and
( gateL_36<1 or signal_7<1) and
( sp_9<1 or sp_11<1) and
( gateL_35<1 or signal_7<1) and
( sp_9<1 or sp_12<1) and
( gateL_34<1 or signal_6<1) and
( sp_14<1 or sp_13<1) and
( sp_14<1 or signal_22<1) and
( sp_15<1 or signal_6<1) and
( gateL_33<1 or signal_6<1) and
( sp_14<1 or sp_16<1) and
( gateL_32<1 or signal_6<1) and
( sp_14<1 or sp_17<1) and
( gateL_31<1 or signal_5<1) and
( sp_19<1 or sp_18<1) and
( sp_19<1 or signal_21<1) and
( sp_20<1 or signal_5<1) and
( gateL_30<1 or signal_5<1) and
( sp_19<1 or sp_21<1) and
( gateL_29<1 or signal_5<1) and
( sp_19<1 or sp_22<1) and
( gateL_28<1 or signal_4<1) and
( sp_24<1 or sp_23<1) and
( sp_24<1 or signal_20<1) and
( sp_25<1 or signal_4<1) and
( gateL_27<1 or signal_4<1) and
( sp_24<1 or sp_26<1) and
( gateL_26<1 or signal_4<1) and
( sp_24<1 or sp_27<1) and
( gateL_16<1 or sp_13<1) and
( sp_30<1 or sp_28<1) and
( gateL_16<1 or sp_23<1) and
( sp_29<1 or sp_28<1) and
( thresholdL_7<1 or sp_28<1) and
( thresholdL_7<1 or sp_28<1) and
( gateL_17<1 or sp_28<1) and
( sp_32<1 or sp_31<1) and
( sp_32<1 or signal_15<1) and
( sp_35<1 or sp_28<1) and
( gateL_22<1 or sp_31<1) and
( sp_37<1 or sp_36<1) and
( thresholdL_10<1 or sp_36<1) and
( thresholdL_10<1 or sp_36<1) and
( gateL_23<1 or sp_36<1) and
( sp_39<1 or sp_38<1) and
( sp_39<1 or signal_18<1) and
( sp_42<1 or sp_36<1) and
( reporter_2<1 or sp_38<1) and
( gateL_14<1 or sp_8<1) and
( sp_47<1 or sp_45<1) and
( gateL_14<1 or sp_18<1) and
( sp_46<1 or sp_45<1) and
( thresholdL_6<1 or sp_45<1) and
( thresholdL_6<1 or sp_45<1) and
( gateL_15<1 or sp_45<1) and
( sp_49<1 or sp_48<1) and
( sp_49<1 or signal_14<1) and
( sp_52<1 or sp_45<1) and
( gateL_24<1 or sp_48<1) and
( sp_54<1 or sp_53<1) and
( thresholdL_11<1 or sp_53<1) and
( thresholdL_11<1 or sp_53<1) and
( gateL_25<1 or sp_53<1) and
( sp_56<1 or sp_55<1) and
( sp_56<1 or signal_19<1) and
( sp_59<1 or sp_53<1) and
( reporter_3<1 or sp_55<1) and
( gateL_12<1 or sp_11<1) and
( sp_64<1 or sp_62<1) and
( gateL_12<1 or sp_21<1) and
( sp_63<1 or sp_62<1) and
( thresholdL_5<1 or sp_62<1) and
( thresholdL_5<1 or sp_62<1) and
( gateL_13<1 or sp_62<1) and
( sp_66<1 or sp_65<1) and
( sp_66<1 or signal_13<1) and
( sp_69<1 or sp_62<1) and
( reporter_1<1 or sp_65<1) and
( gateL_10<1 or sp_16<1) and
( sp_74<1 or sp_72<1) and
( gateL_10<1 or sp_26<1) and
( sp_73<1 or sp_72<1) and
( thresholdL_4<1 or sp_72<1) and
( thresholdL_4<1 or sp_72<1) and
( gateL_11<1 or sp_72<1) and
( sp_76<1 or sp_75<1) and
( sp_76<1 or signal_12<1) and
( sp_79<1 or sp_72<1) and
( reporter<1 or sp_75<1) and
( gateL_8<1 or sp_17<1) and
( sp_84<1 or sp_82<1) and
( gateL_8<1 or sp_22<1) and
( sp_83<1 or sp_82<1) and
( thresholdL_3<1 or sp_82<1) and
( thresholdL_3<1 or sp_82<1) and
( gateL_9<1 or sp_82<1) and
( sp_86<1 or sp_85<1) and
( sp_86<1 or signal_11<1) and
( sp_89<1 or sp_82<1) and
( gateL_20<1 or sp_85<1) and
( sp_91<1 or sp_90<1) and
( thresholdL_9<1 or sp_90<1) and
( thresholdL_9<1 or sp_90<1) and
( gateL_21<1 or sp_90<1) and
( sp_93<1 or sp_92<1) and
( sp_93<1 or signal_17<1) and
( sp_96<1 or sp_90<1) and
( gateL_22<1 or sp_92<1) and
( sp_97<1 or sp_36<1) and
( gateL_6<1 or sp_12<1) and
( sp_100<1 or sp_98<1) and
( gateL_6<1 or sp_27<1) and
( sp_99<1 or sp_98<1) and
( thresholdL_2<1 or sp_98<1) and
( thresholdL_2<1 or sp_98<1) and
( gateL_7<1 or sp_98<1) and
( sp_102<1 or sp_101<1) and
( sp_102<1 or signal_10<1) and
( sp_105<1 or sp_98<1) and
( gateL_18<1 or sp_101<1) and
( sp_107<1 or sp_106<1) and
( thresholdL_8<1 or sp_106<1) and
( thresholdL_8<1 or sp_106<1) and
( gateL_19<1 or sp_106<1) and
( sp_109<1 or sp_108<1) and
( sp_109<1 or signal_16<1) and
( sp_112<1 or sp_106<1) and
( gateL_24<1 or sp_108<1) and
( sp_113<1 or sp_53<1) and
( gateL_3<1 or signal_2<1) and
( sp_116<1 or sp_114<1) and
( gateL_3<1 or signal<1) and
( sp_115<1 or sp_114<1) and
( thresholdL_1<1 or sp_114<1) and
( thresholdL_1<1 or sp_114<1) and
( gateL_5<1 or sp_114<1) and
( sp_118<1 or sp_119<1) and
( gateL_4<1 or sp_114<1) and
( sp_118<1 or sp_117<1) and
( sp_118<1 or signal_9<1) and
( sp_122<1 or sp_114<1) and
( gateL_20<1 or sp_119<1) and
( sp_123<1 or sp_90<1) and
( gateL_14<1 or sp_117<1) and
( sp_124<1 or sp_45<1) and
( gateL<1 or signal_3<1) and
( sp_127<1 or sp_125<1) and
( gateL<1 or signal_1<1) and
( sp_126<1 or sp_125<1) and
( thresholdL<1 or sp_125<1) and
( thresholdL<1 or sp_125<1) and
( gateL_2<1 or sp_125<1) and
( sp_129<1 or sp_130<1) and
( gateL_1<1 or sp_125<1) and
( sp_129<1 or sp_128<1) and
( sp_129<1 or signal_8<1) and
( sp_133<1 or sp_125<1) and
( gateL_18<1 or sp_130<1) and
( sp_134<1 or sp_106<1) and
( gateL_16<1 or sp_128<1) and
( sp_135<1 or sp_28<1)
};
let $no_reactive_species :=
{
thresholdL_15 = 0 and
thresholdL_14 = 0 and
thresholdL_13 = 0 and
thresholdL_12 = 0 and
thresholdL_11 = 0 and
thresholdL_10 = 0 and
thresholdL_9 = 0 and
thresholdL_8 = 0 and
thresholdL_7 = 0 and
thresholdL_6 = 0 and
thresholdL_5 = 0 and
thresholdL_4 = 0 and
thresholdL_3 = 0 and
thresholdL_2 = 0 and
thresholdL_1 = 0 and
thresholdL = 0 and
signal_23 = 0 and
signal_22 = 0 and
signal_21 = 0 and
signal_20 = 0 and
signal_19 = 0 and
signal_18 = 0 and
signal_17 = 0 and
signal_16 = 0 and
signal_15 = 0 and
signal_14 = 0 and
signal_13 = 0 and
signal_12 = 0 and
signal_11 = 0 and
signal_10 = 0 and
signal_9 = 0 and
signal_8 = 0 and
signal_7 = 0 and
signal_6 = 0 and
signal_5 = 0 and
signal_4 = 0 and
signal_3 = 0 and
signal_2 = 0 and
signal_1 = 0 and
signal = 0 and
reporter_3 = 0 and
reporter_2 = 0 and
reporter_1 = 0 and
reporter = 0 and
gateL_37 = 0 and
gateL_36 = 0 and
gateL_35 = 0 and
gateL_34 = 0 and
gateL_33 = 0 and
gateL_32 = 0 and
gateL_31 = 0 and
gateL_30 = 0 and
gateL_29 = 0 and
gateL_28 = 0 and
gateL_27 = 0 and
gateL_26 = 0 and
gateL_25 = 0 and
gateL_24 = 0 and
gateL_23 = 0 and
gateL_22 = 0 and
gateL_21 = 0 and
gateL_20 = 0 and
gateL_19 = 0 and
gateL_18 = 0 and
gateL_17 = 0 and
gateL_16 = 0 and
gateL_15 = 0 and
gateL_14 = 0 and
gateL_13 = 0 and
gateL_12 = 0 and
gateL_11 = 0 and
gateL_10 = 0 and
gateL_9 = 0 and
gateL_8 = 0 and
gateL_7 = 0 and
gateL_6 = 0 and
gateL_5 = 0 and
gateL_4 = 0 and
gateL_3 = 0 and
gateL_2 = 0 and
gateL_1 = 0 and
gateL = 0
};
- http://rise4fun.com/Z34Biology/met_regulationmet_regulation//Regulatory network of E. coli metabolism model
//
// Originally studied in
//"The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and exibility of response."
//A. Samal and S. Jain.
//BMC Systems Biology, 2(1):21, 2008.
//Settings:
directive constantInputs
directive constEncoding BitVector
//Specification:
//To check for oscillations, search for a cycle of any length.
lasso(#path,8);
//Model:
nhaA' = ((NhaR) or (RpoS))
thrA' = (not (thr-L(e) > 0 or ile-L(e) > 0))
thrB' = (not (thr-L(e) > 0 or ile-L(e) > 0))
thrC' = (not (thr-L(e) > 0 or ile-L(e) > 0))
yaaJ' =
talB' =
nhaR' = (na1(e) > 0)
ribF' =
lytB' =
dapB' = (not lys-L(e) > 0)
carA' = (not ArgR)
carB' = (not ArgR)
caiF' = (Fnr and Crp and not NarL)
caiD' = (Crp and CaiF)
caiB' = (Crp and CaiF)
caiT' = (Crp and CaiF)
folA' =
apaH' =
pdxA' = (RpoE)
araD' = (AraC or (AraC and Crp))
araA' = (AraC or (AraC and Crp))
araB' = (AraC or (AraC and Crp))
araC' = (arab-L(e) > 0)
sfuC' =
sfuB' =
sfuA' =
leuD' = (not(leu-L(e) > 0) or Lrp)
leuC' = (not(leu-L(e) > 0) or Lrp)
leuB' = (not(leu-L(e) > 0) or Lrp)
leuA' = (not(leu-L(e) > 0) or Lrp)
ilvI' = (Lrp and not (leu-L(e) > 0))
ilvH' = (Lrp and not (leu-L(e) > 0))
fruR' = true
murE' =
murF' =
mraY' =
murD' =
murG' =
murC' =
ddlB' =
lpxC' =
mutT' =
guaC' = (not ((gln-L(e) > 0) or (gua(e) > 0)))
nadC' =
aroP' = (not (TyrR and ((phe-L(e)>0) or (tyr-L(e)>0) or (trp-L(e)>0))))
pdhR' = true
aceE' = ((not(PdhR)) or (Fis))
aceF' = ((not(PdhR)) or (Fis))
lpdA' = (true)
acnB' = (true)
speD' =
speE' =
gcd' = (not Crp)
hpt' = (Crp)
yadF' =
pand' =
panC' =
panB' =
folK' =
hemL' =
yadT' =
mtn' =
dgt' =
sdaR' = ((glcr(e)>0) or (galct-D(e)>0))
dapD' =
glnD' = (Lrp)
pyrH' =
dxr' =
uppS' =
cdsA' =
lpxD' =
fabZ' = true
lpxA' =
lpxB' =
accA' =
ldcC' =
yaeC' = (not MetJ)
yaeE' = (not MetJ)
abc' = (not MetJ)
yaeD' =
yafB' =
gloB' =
fadF' = (not (FaDR2) or not (ArcA))
gmhA' =
gpt' =
proB' =
proA' =
argF' = (not ArgR)
betB' = (not (ArcA or BetI))
betI' = (chol(e) > 0)
betT' = (not (BetI))
yahI' =
prpB' = (ppa(e)>0)
prpC' = (ppa(e)>0)
prpD' = (ppa(e)>0)
prpE' = (ppa(e)>0)
codB' = (not (PurR) or (NRI_hi))
codA' = (not (PurR) or NRI_hi)
cynR' = (cynt(e)>0)
cynT' =
cynS' = (CynR)
cynX' = (cynt(e)>0)
lacY' = ((not((glcn(e) > 0) or (glc-D(e) > 0))) and not(LacI))
lacZ' = ((not((glcn(e) > 0) or (glc-D(e) > 0))) and not(LacI))
lacI' = ( not ( lcts(e)>0 ) )
mhpR' = (3hPppn(e)>0)
mhpA' = (MhpR)
mhpB' = (MhpR)
mhpC' = (MhpR)
mhpD' = (MhpR)
mhpF' = (MhpR)
mhpE' = (MhpR)
mhpT' =
adhC' =
tauA' = (Cbl and CysB)
tauB' = (Cbl and CysB)
tauC' = (Cbl and CysB)
tauD' = (Cbl and CysB)
hemB' =
ddlA' =
proC' =
aroL' = (not( (TyrR and (tyr-L(e)>0)) or (TyrR and (tyr-L(e)>0) and TrpR) ))
phoB' = (Phor)
phor' = (not (pi(e) > 0))
brnQ' =
malZ' = (MalT)
ribD' =
ribH' =
thiL' =
pgpA' =
dxs' =
ispA' =
thiI' =
panE' =
cyoE' = (not (ArcA or Fnr))
cyoD' = (not (ArcA or Fnr))
cyoC' = (not (ArcA or Fnr))
cyoB' = (not (ArcA or Fnr))
cyoA' = (not (ArcA or Fnr))
amtB' =
apt' =
adk' =
hemH' =
gsk' =
ushA' =
ybaS' =
ybbS' = (not(ox2(e)>0) and not AllR and not (nh4(e)>0))
allA' = (not AllR)
allR' = (false)
gcl' = (not AllR)
hyi' =
glxR' = (not AllR)
allP' =
allB' = (not AllR)
glxK' = (not AllR)
allC' = (AllS)
arcC' =
purK' = (not (PurR))
purE' = (not (PurR))
folD' =
appY' = (not CitB)
pheP' =
entD' = (not (Fur))
entF' =
entC' = (not (Fur))
entE' = (not (Fur))
entB' = (not (Fur))
entA' = (not (Fur))
citT' = (CitB and (not (ox2(e) > 0)))
citF' = (CitB)
citE' = (CitB)
citD' = (CitB)
dpiB' = (cit(e)>0)
dpiA' = (CitA)
dcuC' = (Fnr or ArcA)
phpB' =
nadD' =
gltL' = (not (glc-D(e) > 0))
gltK' = (not (glc-D(e) > 0))
gltJ' = (not (glc-D(e) > 0))
gltI' = (not (glc-D(e) > 0))
ubiF' =
asnB' =
nagC' = (not((acGam(e) > 0) or AGDC(e)>0))
nagA' = (not (NagC))
nagB' = (not (NagC) or (gam(e)>0))
nagE' = (not (NagC))
fur' = ((fe2(e) > 0) and (OxyR or SoxS))
pgm' =
potE' =
speF' =
kdpE' = (KdpD)
kdpD' = (not (k(e) > 0))
kdpC' = (KdpE)
kdpB' = (KdpE)
kdpA' = (KdpE)
gltA' =
sdhC' = (not((ArcA) or (Fnr)) or (Crp) or (Fis))
sdhD' = (not((ArcA) or (Fnr)) or (Crp) or (Fis))
sdhA' = (not((ArcA) or (Fnr)) or (Crp) or (Fis))
sdhB' = (not((ArcA) or (Fnr)) or (Crp) or (Fis))
sucA' =
sucB' =
sucC' =
sucD' =
cydA' = ((not Fnr) or (ArcA))
cydB' = ((not Fnr) or (ArcA))
nadA' =
pnuC' =
aroG' = ( not(( (phe-L(e)>0) or (trp-L(e)>0) ) and TyrR ))
gpmA' =
galK' = (not(glc-D(e) > 0) and (not(GalR or GalS)) or not (Rob))
galT' = (not(glc-D(e) > 0) and (not(GalR or GalS)) or not (Rob))
galE' = (not(glc-D(e) > 0) and (not(GalR or GalS)) or not (Rob))
bioA' = (not (BirA))
bioB' = (not (BirA))
bioF' = (not (BirA))
bioD' = (not (BirA))
glnQ' =
glnP' =
glnH' =
fsa' =
ybiK' =
deor' = (not PPM2(e))
potF' =
potG' =
potH' =
potI' =
artJ' =
artM' =
artQ' =
artP' =
ltaA' =
poxB' = ((not (Growth(e) > 0)) and (RpoS))
trxB' =
lrp' = (not leu-L(e) >0)
dmsA' = (Fnr and not NarL)
dmsB' = (Fnr and not NarL)
dmsC' = (Fnr and not NarL)
pflA' = (ArcA or Fnr and (Crp or not(NarL)))
pflB' = (ArcA or Fnr and (Crp or not(NarL)))
focA' = (ArcA or Fnr and (Crp or not (NarL)))
serC' = (Lrp or (not (Crp)))
aroA' =
cmk' =
lpxK' =
kdsB' =
aspC' =
pncB' = (not (NadR))
pyrD' = ((not (csn(e) > 0)) or (gua(e) > 0) or not PurR)
fabA' = true
mgsA' =
hyaA' = ((ArcA or Fnr) and (AppY))
hyaB' = ((ArcA or Fnr) and (AppY))
hyaC' = ((ArcA or Fnr) and (AppY))
torS' = (tmao(e)>0)
torR' = (TorS)
torC' = (TorR or not (NarL))
torA' = (TorR or not (NarL))
agp' =
ycdG' =
putA' = ( (pro-L(e) > 0) or Crp or Nac)
putP' = ( (pro-L(e) > 0) or Crp or Nac)
ycdW' =
lpxL' =
pyrC' = ((not (csn(e) > 0)) or (gua(e) > 0) or not PurR)
fabH' = true
fabD' = true
fabG' = true
fabF' = true
pabC' =
tmk' =
ptsG' = (not(Mlc) or not(Cra))
ndh' = (not (Fnr))
potD' =
potC' =
potB' =
potA' =
purB' = (not (PurR))
icdA' =
nhaB' =
fadR' = ( glc-D(e) > 0 or not (ac(e) > 0 ) )
dadA' = (ala-L(e) > 0 and not Crp)
dadX' = (((ala-L(e) > 0) or (ala-D(e) > 0)) and Crp)
treA' = (RpoS)
dhaH' =
dhaK2' =
dhaK1' =
prsA' = (not PurR)
ispE' =
hemA' =
kdsA' =
chaA' =
narL' = ((NO3(e)>0) or (NO2(e)>0))
narK' = (Fnr or NarL)
narG' = (Fnr and NarL)
narH' = (Fnr and NarL)
narJ' = (Fnr and NarL)
narI' = (Fnr and NarL)
purU' =
galU' =
tdk' =
adhE' = (not (ox2(e) > 0) or (not ((ox2(e) > 0) and (Cra))) or (Fis) or not (NarL) or (RpoS))
cls' =
trpA' = (not TrpR)
trpB' = (not TrpR)
trpC' = (not TrpR)
trpD' = (not TrpR)
trpE' = (not TrpR)
btuR' =
cysB' = (not (cys-L(e) > 0))
acnA' = (SoxS)
ribA' =
pgpB' =
pyrF' =
fabI' = true
ycjK' =
aldH' =
goaG' =
tyrR' = ( (trp-L(e)>0) or (tyr-L(e)>0) or (phe-L(e)>0) )
fnr' = ( not ( ox2(e)>0 ) )
trkG' =
ldhA' =
feaR' = (Crp)
feaB' = (FeaR)
tynA' = (FeaB)
paaK' =
aldA' =
gapC_2' =
gapC_1' =
ydcS' =
ydcT' =
ydcU' =
ydcV' =
narU' =
fdnG' = (Fnr or NarL)
fdnH' = (Fnr or NarL)
fdnI' = (Fnr or NarL)
sfcA' =
xasA' =
gadB' = ((not (Growth(e) > 0)))
tam' = (not (Growth(e)>0))
uxaB' = (not ExuR)
yneH' = ((not (glc-D(e) > 0) or ((nh4(e) > 0) and not Crp)))
marA' = false
speG' =
mlc' = ( not ( glc-D(e)>0 ) )
pntB' =
pntA' =
arcD' =
fumC' = (MarA or Rob or SoxS and (not(ArcA)))
fumA' = (not(ArcA or Fnr))
manA' =
malI' = (not (malt(e) > 0))
malX' = ((MalT and Crp) or MalT)
malY' = (not (MalI))
add' = ((ade(e) > 0) or (hxan(e) > 0))
pdxY' =
pdxH' =
sodC' = (not(Growth(e)>0) and not Fnr)
gloA' =
sodB' =
purR' = ((hxan(e) > 0) or (gua(e) > 0))
ribE' =
pykF' = (not(Cra))
ydiB' =
aroD' =
pps' = (Cra)
aroH' = (not TrpR)
btuD' =
btuC' =
pfkB' =
katE' = (not(Growth(e)>0))
nadE' =
astE' = ((not(Growth(e)>0) and RpoS) or (NRI_hi and RpoN))
astB' = ((not(Growth(e)>0) and RpoS) or (NRI_hi and RpoN))
astD' = ((not(Growth(e)>0) and RpoS) or (NRI_hi and RpoN))
astA' = ((not(Growth(e)>0) and RpoS) or (NRI_hi and RpoN))
astC' = ((not(Growth(e)>0) and RpoS) or (NRI_hi and RpoN))
gdhA' = (not ((Nac) or (glu-L(e) > 0)) )
selD' =
ansA' =
pncA' =
b1773' =
gapA' =
yeaV' =
fadD' = (not (FaDR2) or not (ArcA))
pabB' =
sdaA' = ((gly(e) > 0 or leu-L(e) > 0 or not (ox2(e) > 0)) and ((not Lrp) or (Lrp and leu-L(e) > 0)))
manX' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0) or (glyc(e) > 0) or (sbt-D(e) > 0) or (lac-D(e) > 0))) or (not (Mlc)))
manY' = (((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0) or (glyc(e) > 0) or (sbt-D(e) > 0) or (lac-D(e) > 0)))) or (not (Mlc)))
manZ' = (((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0) or (glyc(e) > 0) or (sbt-D(e) > 0) or (lac-D(e) > 0)))) or (not (Mlc)))
kdgR' = (not(2ddGxcn(e)>0) and not(MNNH(e)>0) and not(ALTRH(e)>0))
purT' = (not (PurR))
eda' = ((true) or (not (GntR)))
edd' = (not (GntR))
zwf' =
pykA' =
msbB' =
ntpA' =
torZ' =
torY' =
otsA' = (RpoS)
otsB' = (RpoS)
araH_2' = (AraC or (AraC and Crp))
araH_1' = (AraC or (AraC and Crp))
araG' = (AraC or (AraC and Crp))
araF' = (AraC or (AraC and Crp))
tyrP' = (not(TyrR and (tyr-L(e)>0)))
pgsA' =
amn' =
cbl' = (not ((so4(e) > 0) or (cys-L(e) > 0 )) and CysB )
nac' = (NRI_low and RpoN)
cobT' = (cbi(e)>0)
cobS' = (cbi(e)>0)
cobU' = (cbi(e)>0)
hisG' =
hisD' =
hisC' =
hisB' =
hisH' =
hisA' =
hisF' =
hisI' =
ugd' =
gnd' =
glf' =
rfbC' =
rfbA' =
rfbD' =
rfbB' =
galF' =
wcaK' =
cpsG' =
manC' =
fcl' =
gmd' =
dcd' =
udk' = (not ((thym(e) > 0) or (csn(e) > 0) or (ura(e) > 0)))
gatR_1' = (not (galt(e) > 0))
gatR_2' = (not (galt(e) > 0))
gatD' = (not (GaTR))
gatC' = (not (GaTR))
gatB' = (not (GaTR))
gatA' = (not (GaTR))
gatZ' = (not (GaTR))
gatY' = (not (GaTR))
fbaB' = ((pyr(e)>0) or (lac-D(e)>0) and not(glc-D(e)>0))
thiD' =
thiM' =
yehW' =
yehX' =
yehY' =
yehZ' =
bglX' =
dld' =
cdd' = (Crp and not (CytR))
mglC' = (Crp and not (GalS))
mglA' = (Crp and not (GalS))
mglB' = (Crp and not (GalS))
galS' = ( not ( lcts(e)>0 ) or not (gal(e)>0) )
folE' =
lysP' =
fruA' = (not (Cra))
fruK' = (not (Cra))
fruB' = (not (Cra))
mqo' = (not ArcA)
atoS' = (acAXc(e) > 0)
atoC' = (AtoS)
atoD' = (AtoC)
atoA' = (AtoC)
atoE' = (AtoC)
atoB' = (AtoC)
ubiG' = ((ox2(e) > 0) and Crp)
nrdA' = (not (ArcA))
nrdB' = (not (ArcA))
glpQ' = ((not GlpR or Fnr) and Crp)
glpT' = (not (GlpR) and Crp)
glpA' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0))) and (Fnr or ArcA) and (not(GlpR)))
glpB' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0))) and (Fnr or ArcA) and (not(GlpR)))
glpC' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0))) and (Fnr or ArcA) and (not(GlpR)))
menE' =
menC' =
menB' =
menD' =
menF' =
nutrue' = (not (ArcA or Fnr) or NarL)
nuoM' = (not (ArcA or Fnr) or NarL)
nuoL' = (not (ArcA or Fnr) or NarL)
nuoK' = (not (ArcA or Fnr) or NarL)
nuoJ' = (not (ArcA or Fnr) or NarL)
nuoI' = (not (ArcA or Fnr) or NarL)
nuoH' = (not (ArcA or Fnr) or NarL)
nuoG' = (not (ArcA or Fnr) or NarL)
nuoF' = (not (ArcA or Fnr) or NarL)
nuoE' = (not (ArcA or Fnr) or NarL)
nuoC' = (not (ArcA or Fnr) or NarL)
nuoB' = (not (ArcA or Fnr) or NarL)
nuoA' = (not (ArcA or Fnr) or NarL)
ackA' =
pta' =
hisP' = (not (lys-L(e) > 0))
hisM' = (not (lys-L(e) > 0))
hisQ' = (not (lys-L(e) > 0))
hisJ' = (not (lys-L(e) > 0))
argT' = (not (lys-L(e) > 0))
ubiX' = (not (PurR))
purF' = (not (PurR))
folC' =
accD' =
pdxB' =
fabB' = true
aroC' =
fadL' = ((not (Crp or FadR or OmpR)))
dsdC' = (ser-D(e) > 0)
dsdA' = ((Crp and DsdC) or DsdC)
lpxP' =
glk' =
nupC' = (Crp or not (CytR))
gltX' =
xapR' = (xtsn(e) > 0)
xapB' = (XapR)
xapA' = (XapR)
lig' =
cysZ' = (CysB)
cysK' = (CysB)
ptsH' = (true)
ptsI' = (true)
crr' = (true)
pdxK' =
cysM' = (CysB)
cysA' = (CysB)
cysW' = (CysB)
cysU' = (CysB)
cysP' = (CysB)
yfeV' =
hemF' =
eutC' =
eutB' =
eutD' =
maeB' =
talA' =
tktB' =
dapE' =
purC' = (not (PurR))
dapA' =
gcvR' = (not (gly(e) > 0))
focB' = (ArcA or Fnr and (Crp or not (NarL)))
uraA' =
upp' =
purM' = (not (PurR))
purN' = (not (PurR))
guaA' = (not (PurR and Crp))
guaB' = (not (PurR and Crp))
gcpE' =
ndk' =
iscS' =
suhB' =
hcaT' =
hcaR' = (pppn(e)>0)
hcaE' = (HcaR)
hcaF' = (HcaR)
hcaC' = (HcaR)
hcaB' = (HcaR)
hcaD' = (HcaR)
glyA' = (not (gly(e) > 0) or MetR or not (PurR))
glnB' = (Lrp)
purL' = (not (PurR))
acpS' =
pdxJ' = (RpoE)
rpoE' = false
nadB' = (not (NadR))
pssA' =
kgtP' =
pheA' = (not (phe-L(e)>0) )
tyrA' = ( not(( (phe-L(e)>0) or (tyr-L(e)>0) ) and TyrR ))
aroF' = ( not(( (phe-L(e)>0) or (tyr-L(e)>0) ) and TyrR ))
yfjB' =
gabD' =
gabT' =
gabP' =
nrdE' =
nrdF' =
proV' =
proW' =
proX' =
luxS' =
gshA' =
yqaB' =
srlA' = ((not GutR) and (not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0) or (glyc(e) > 0))))
srlE' = ((not GutR) and (not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0) or (glyc(e) > 0))))
srlB' = ((not GutR) and (not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0) or (glyc(e) > 0))))
srlD' = (GutM and (not GutR) and (not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0) or (glyc(e) > 0))))
gutM' = (true)
srlR' = (not (sbt-D(e) > 0))
hycG' = (FhlA and RpoN and (not (ox2(e) > 0)))
hycF' = (FhlA and RpoN and (not (ox2(e) > 0)))
hycE' = (FhlA and RpoN and (not (ox2(e) > 0)))
hycD' = (FhlA and RpoN and (not (ox2(e) > 0)))
hycC' = (FhlA and RpoN and (not (ox2(e) > 0)))
hycB' = (FhlA and RpoN and (not (ox2(e) > 0)))
fhlA' = ((not (ox2(e) > 0)) and (not (NO3(e) > 0)) and (not (NO2(e) > 0)) and (not (tmao(e) > 0)) and (not (dmso(e) > 0)) and (for(e)>0))
ygbL' =
rpoS' = (not (Growth(e) > 0))
ispF' =
ispD' =
cysC' = (CysB)
cysN' = (CysB)
cysD' = (CysB)
cysH' = (CysB)
cysI' = (CysB)
cysJ' = (CysB)
eno' =
pyrG' =
mazG' =
gudD' = (SdaR)
ygcY' =
gudP' =
sdaC' = (Crp or (not (Lrp) and (leu-L(e) > 0) and Crp))
sdaB' = (true)
fucO' = (((((FucR) or (rmn(e) > 0)) and (not (ox2(e) > 0))) and Crp) or (((FucR) or (rmn(e) > 0)) and (not (ox2(e) > 0))))
fucA' = ((FucR and Crp) or FucR)
fucP' = ((FucR and Crp) or FucR)
fucI' = ((FucR and Crp) or FucR)
fucK' = ((FucR and Crp) or FucR)
fucR' = (fuc-L(e) > 0)
gcvA' = (not GcvR)
argA' = (not ArgR)
thyA' =
aas' =
galR' = ( not ( lcts(e)>0 ) or not (gal(e)>0) )
lysA' = (LysR and not lys-L(e) > 0)
lysR' = (not (lys-L(e) > 0))
araE' = (Crp)
yqeA' =
ygfP' =
idi' =
bglA' =
gcvP' = ((Fis and not PdhR) and ((not(GcvR) and GcvA) or Lrp or not PurR))
gcvH' = ((Fis and not PdhR) and ((not(GcvR) and GcvA) or Lrp or not PurR))
gcvT' = ((Fis and not PdhR) and ((not(GcvR) and GcvA) or Lrp or not PurR))
ubiH' =
serA' =
rpiA' =
sbm' =
ygfG' =
ygfH' =
fbaA' =
pgk' = (true)
epd' = (Crp)
tktA' =
speB' =
speA' = (not (PurR))
metK' =
galP' = ((not (GalR)) or (GalS) and (Crp or not (Crp)))
gshB' =
ansB' = (Fnr and Crp)
nupG' = (Crp or not (CytR) or not (Deor))
speC' = (not (Crp))
glcA' = (not ArcA and GlcC)
glcB' = (not (ArcA) and (GlcC))
glcF' =
glcD' =
glcC' = ((ac(e)>0) or (glyclt(e)>0))
pitB' = (not (PhoB))
gsp' =
hybC' = (FhlA and RpoN and (not (ox2(e) > 0)))
hybO' = (FhlA and RpoN and (not (ox2(e) > 0)))
metC' = (not MetJ)
yqhE' =
plsC' =
ribB' =
rfaE' =
folB' =
ttdA' = (not(ox2(e)>0) and (tartr-L(e)>0))
ttdB' = (not(ox2(e)>0) and (tartr-L(e)>0))
ygjE' =
ygjG' =
sstT' =
uxaA' = (not ExuR)
uxaC' = (not ExuR)
exuT' = (not ExuR)
exuR' = (not(GUI1(e)>0) and not(GUI2(e)>0) and not(MANAO(e)>0) and not(TAGURr(e)>0))
tdcGa' = (Crp or not(ox2(e)>0))
tdcGb' = (Crp or not(ox2(e)>0))
tdcE' = (Crp or Fnr or LysR or TdcA or not TdcR)
tdcD' = (Crp or Fnr or LysR or TdcA or not TdcR)
tdcC' = (Crp or Fnr or LysR or TdcA or not TdcR)
tdcB' = (Crp or Fnr or LysR or TdcA or not TdcR)
tdcA' = ((thr-L(e) > 0) and (ser-L(e) > 0) and (val-L(e) > 0) and (ile-L(e) > 0) and not (ox2(e) > 0))
tdcR' = ((thr-L(e) > 0) and (ser-L(e) > 0) and (val-L(e) > 0) and (ile-L(e) > 0) and not (ox2(e) > 0))
garK' = (SdaR)
garR' = (SdaR)
garL' = (SdaR)
garP' =
garD' = (SdaR)
agaZ' =
agaY' =
mtr' = (not TrpR or (TyrR and ((phe-L(e)>0) or (tyr-L(e)>0))))
argG' =
mrsA' =
folP' =
ispB' =
murA' =
rpoN' = (true)
gltB' = ( (Lrp and not (leu-L(e) > 0)) or not(NRI_hi and ((glu-L(e) > 0) or (arg-L(e) > 0) or (asp-L(e) > 0) or (his-L(e) > 0) or (pro-L(e) > 0) )))
gltD' = ( (Lrp and not (leu-L(e) > 0)) or not(NRI_hi and ((glu-L(e) > 0) or (arg-L(e) > 0) or (asp-L(e) > 0) or (his-L(e) > 0) or (pro-L(e) > 0) )))
nanK' =
nanE' =
nanT' =
nanA' =
mdh' = (not(ArcA))
argR' = (arg-L(e) > 0)
accB' =
accC' =
panF' =
fis' = (Growth(e) > 0)
acrE' =
acrF' =
aroE' =
crp' = (not((glcn(e) > 0) or (glc-D(e) > 0)))
argD' = (not ArgR)
pabA' =
nirB' = (Fnr and NarL)
nirD' = (Fnr and NarL)
nirC' = (Fnr and NarL)
cysG' = (Fnr or NarL)
yhfW' =
gph' =
rpe' =
aroB' =
aroK' =
pckA' =
ompR' = false
feoB' =
gntT' = (not (GntR) and (glcn(e) > 0))
malQ' = (MalT)
malP' = (MalT)
malT' = ((malt(e) > 0) or (malttr(e) > 0) or (maltttr(e) > 0) or (malthx(e) > 0) or (maltpt(e) >0))
glpR' = ( not ( glyc(e)>0 ) )
glpE' = (Crp)
glpD' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0))) and (not(ArcA or GlpR)))
glgP' = (Crp)
glgA' =
glgC' =
asd' =
gntK' = (not (GntR) and (glcn(e) > 0))
gntR' = (not (glcn(e) > 0))
ugpC' = (Crp or PhoB)
ugpE' = (Crp or PhoB)
ugpA' = (Crp or PhoB)
ugpB' = (Crp or PhoB)
livF' = (not(leu-L(e) > 0) or Lrp)
livG' = (not(leu-L(e) > 0) or Lrp)
livM' = (not(leu-L(e) > 0) or Lrp)
livH' = (not(leu-L(e) > 0) or Lrp)
livK' = (not(leu-L(e) > 0) or Lrp)
livJ' = (not(leu-L(e) > 0) or Lrp)
pitA' =
gor' = (OxyR or RpoS)
gadA' = ((not (Growth(e) > 0 ) and not Crp) )
treF' = (RpoS)
kdgK' = (not KdgR)
dctA' = ((((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0) or (glyc(e) > 0) or (sbt-D(e) > 0) or (lac-D(e) > 0) or (man(e) > 0)))) and not(ArcA) and (DcuR)) and RpoN)
bisC' =
yiaE' =
xylB' = ((XylR and Crp) or XylR)
xylA' = ((XylR and Crp) or XylR)
xylF' = ((XylR and Crp) or XylR)
xylG' = ((XylR and Crp) or XylR)
xylH' = ((XylR and Crp) or XylR)
xylR' = (xyl-D(e) > 0)
avtA' = (not (ala-L(e) > 0 or leu-L(e) > 0 ))
yiaJ' = (not (fuc-L(e)>0))
yiaK' = ((not YiaJ) and Crp)
yiaO' = (Crp or YiaJ)
sgbH' = (not YiaJ)
sgbE' = (not YiaJ)
aldB' = (RpoS and (Crp))
mtlA' = (not (MtlR))
mtlD' = (not MtlR)
mtlR' = (not (mnl(e) > 0))
lldP' = (not (ArcA))
lldD' = (lac-L(e) > 0 and ox2(e) > 0)
cysE' = (CysB)
gpsA' =
yibO' =
tdh' = (not (Lrp) and (leu-L(e) > 0))
kbl' = (not (Lrp) and (leu-L(e) > 0))
rfaD' =
rfaF' =
rfaC' =
rfaL' =
rfaJ' =
rfaI' =
rfaG' =
kdtA' =
coaD' =
dut' =
pyrE' = (not (ura(e) > 0 or gua(e) > 0))
gmk' =
gltS' = (asp-L(e) > 0)
yicE' =
yicP' =
uhpT' = (Crp or UhpA)
uhpB' = (g6p(e) > 0)
uhpA' = (UhpB)
ilvN' = (not(leu-L(e) > 0 or val-L(e) > 0) and Crp)
ilvB' = (not(leu-L(e) > 0 or val-L(e) > 0) and Crp)
dgoT' = (galctn-D(e)>0)
dgoA' = (galctn-D(e)>0)
dgoK' = (galctn-D(e)>0)
tnaA' = (Crp and (trp-L(e)>0 or cys-L(e) > 0) )
tnaB' = (Crp and (trp-L(e)>0) )
pstB' = (PhoB)
pstA' = (PhoB)
pstC' = (PhoB)
pstS' = (PhoB)
glmS' =
glmU' = (NagC)
atpC' =
atpD' =
atpG' =
atpA' =
atpH' =
atpF' =
atpE' =
atpB' =
atpI' =
asnC' = ( not ( asn-L(e) > 0 ) and NRI_hi )
asnA' = (not (asn-L(e) > 0) and AsnC)
rbsD' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0))) and not(RbsR))
rbsA' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0))) and not(RbsR))
rbsC' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0))) and not(RbsR))
rbsB' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0))) and not(RbsR))
rbsK' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0))) and not(RbsR))
rbsR' = ( not ( rib-D(e)>0 ) )
ilvG_1' = (not(leu-L(e) > 0 or ile-L(e) > 0 or val-L(e) > 0) and Lrp)
ilvG_2' = (not(leu-L(e) > 0 or ile-L(e) > 0 or val-L(e) > 0) and Lrp)
ilvM' = (not(leu-L(e) > 0 or ile-L(e) > 0 or val-L(e) > 0) and Lrp)
ilvE' =
ilvD' =
ilvA' =
ilvY' = (not val-L(e) > 0 )
ilvC' = (IlvY)
wecA' =
wecB' =
wecC' =
rffG' =
rffH' =
wecD' =
wecE' =
wecF' =
wecG' =
hemX' =
hemD' =
hemC' =
cyaA' = (not Crp)
dapF' =
pldA' =
pldB' =
metR' = (not (met-L(e) > 0))
metE' = ((not MetJ) and MetR)
udp' = (not (CytR) or Crp)
ubiE' =
ubiB' =
yigC' =
fadA' = (not (FaDR2) or not (ArcA))
fadB' = (not (FaDR2) or not (ArcA))
trkH' =
hemG' =
glnG' = (not (nh4(e) > 0))
glnL' = (true)
glnA' = (Crp and RpoN)
fdoI' = ((ox2(e) > 0) or ((not (ox2(e) > 0) and (NO3(e) > 0))))
fdoH' = ((ox2(e) > 0) or ((not (ox2(e) > 0) and (NO3(e) > 0))))
fdoG' = ((ox2(e) > 0) or ((not (ox2(e) > 0) and (NO3(e) > 0))))
rhaD' = (RhaS or (RhaS and Crp))
rhaA' = (RhaS or (RhaS and Crp))
rhaB' = (RhaS or (RhaS and Crp))
rhaS' = (RhaR)
rhaR' = (rmn(e) > 0)
rhaT' = (RhaS or (RhaS and Crp))
sodA' = (not (ArcA or Fur) or (MarA or Rob or SoxS))
kdgT' = (not KdgR)
cpxR' = false
pfkA' =
sbp' = (CysB)
cdh' =
tpiA' =
glpK' = ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0))) and (not(GlpR)))
glpF' =
menG' =
menA' =
cytR' = (cytd(e) > 0)
metJ' = (met-L(e) > 0)
metB' = (not MetJ)
metL' = (not MetJ)
metF' =
katG' = ((Growth(e)>0) and OxyR and RpoS)
gldA' =
talC' =
pflD' = (ArcA or Fnr)
pflC' = (ArcA or Fnr)
ppc' =
argE' = (not ArgR)
argC' = (not ArgR)
argB' = (not ArgR)
argH' = (not ArgR)
oxyR' = (h2O2(e) > 0)
sthA' =
btuB' =
murI' =
murB' =
birA' = (btn(e) > 0)
coaA' =
thiH' =
thiG' =
thiF' =
thiE' =
thiC' =
hemE' =
purD' = (not (PurR))
purH' =
metA' = (not (MetJ) or MetR)
aceB' = (not (IclR) and (not (ArcA) or not (Cra)))
aceA' = (not (IclR) and (not (ArcA) or not (Cra)))
iclR' = ( FadR )
metH' = (MetR)
lysC' = (not lys-L(e) > 0)
pgi' =
xylE' = (XylR)
malG' = ((MalT and Crp) or MalT)
malF' = ((MalT and Crp) or MalT)
malE' = ((MalT and Crp) or MalT)
malK' = ((MalT and Crp) or MalT)
lamB' = ((MalT and Crp) or MalT)
ubiC' = ((not Fnr) and Crp)
ubiA' = ((not Fnr) and Crp)
plsB' =
dgkA' =
alr' =
tyrB' = (not(( (phe-L(e)>0) or (tyr-L(e)>0) ) and TyrR ))
soxS' = (SoxR)
soxR' = (h2O2(e) > 0)
acs' = (RpoS or Fnr or ((not IclR) and ((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0) or (glyc(e) > 0) or (sbt-D(e) > 0) or (lac-D(e) > 0) or (man(e) > 0) or (succ(e) > 0))))))
gltP' =
fdhF' = (FhlA and RpoN and (not (ox2(e) > 0)))
rpiR' = ( not ( rib-D(e)>0 ) )
rpiB' = (not(RpiR))
proP' = (not (Crp) and Fis and RpoS)
adiY' = (not (ox2(e) > 0))
adiA' = (AdiY)
melR' = ((melib(e) > 0) or (melib(e) > 0 and Crp))
melA' = ((MelR) or (MelR and Crp))
melB' = ((MelR) or (MelR and Crp))
fumB' = ((Fnr) or not (Crp) or (DcuR) or not (NarL))
dcuB' = ((((not((glcn(e) > 0) or (glc-D(e) > 0) or (arab-L(e) > 0) or (xyl-D(e) > 0) or (rib-D(e) > 0) or (mal-L(e) > 0) or (glyc(e) > 0) or (sbt-D(e) > 0) or (lac-D(e) > 0) or (man(e) > 0)))) and (Fnr) and (DcuR)) and not (NarL))
dcuR' = ( DcuS )
dcuS' = ( (succ(e) > 0) or (asp-L(e) > 0) or (fum(e) > 0) or (mal-L(e) > 0) )
cadA' = (ArcA or CadC)
cadB' = (ArcA or CadC)
cadC' = (lys-L(e) > 0)
dcuA' =
aspA' = ((Crp and not (Fnr)) or Fnr)
frdD' = (Fnr or DcuR or not (NarL))
frdC' = (Fnr or DcuR or not (NarL))
frdB' = (Fnr or DcuR or not (NarL))
frdA' = (Fnr or DcuR or not (NarL))
psd' =
purA' = (not (PurR) or RpoE)
sgaH' =
sgaU' =
sgaE' =
cycA' =
ytfQ' =
ytfR' =
ytfS' =
ytfT' =
yjfF' =
fbp' =
nrdD' = (Fnr)
treC' = (((not TreR) and Crp) or (not TreR))
treB' = (((not TreR) and Crp) or (not TreR))
treR' = (not (tre(e) > 0))
pyrI' = (not (ura(e) > 0 or gua(e) > 0))
pyrB' = (not (ura(e) > 0 or gua(e) > 0))
argI' = (not ArgR)
idnR' = ((idon-L(e)>0) or (5dGlXcn(e)>0))
idnT' = (IdnR)
idnO' = (IdnR)
idnD' = (IdnR)
idnK' =
sgcE' =
gntP' = (Crp and not (glcn(e)>0))
uxuA' = (not ExuR and not UxuR)
uxuB' = (not ExuR and not UxuR)
uxuR' = (not(MANAO(e)>0) and not(GUI1(e)>0))
deoC' = ((not Deor) or ((not Deor) and (Crp) and (not CytR)))
deoA' = (not (Deor or CytR) and Crp)
deoB' = ((not Deor) or ((not Deor) and (Crp) and (not CytR)) or ((ins(e) > 0) or (gua(e) > 0)))
deoD' = ((not Deor) or ((not Deor) and (not CytR)) or (ins(e) > 0) or (gua(e) > 0))
serB' =
nadR' = false
trpR' = (trp-L(e)>0)
gpmB' =
rob' = false
arcA' = ( not ( ox2(e) > 0 ) )
thiS' =
NRI_hi' = (NRI_low and RpoN)
NRI_low' = (GlnG and GlnB and GlnD)
allS' = (AllS)
citB' = (CitB)
citA' = (CitA)
cra' = (Cra)
gaTR' = (GaTR)
gutR' = (GutR)
faDR2' = (FaDR2)