++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/2-cascade.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Number of possible topologies: 3
COST = 0.95
10
0	INPUT 	aTc	Ligand	aTc	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
1	OUTPUT 	yfp	Protein	yfp	Module yfp(output)
2	mRNA	pCONST	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
3	Protein	tetR	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
4	mRNA	pTET	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
5	Protein	lacI	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
6	mRNA	pLAC	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
7	Protein	cI	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
8	mRNA	pLAMBDA	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
9	Protein	yfp	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
0 3  REP 
2 3  ACT 
3 4  REP 
4 5  ACT 
5 6  REP 
6 7  ACT 
7 8  REP 
8 9  ACT 
9 1  UNKNOWN 
Running time: 0.31
--------------------------------
4
0	NOTGate 		
1	NOTGate 		
2	INPUT 			
3	OUTPUT 			
0 1  UNKNOWN 
1 3  UNKNOWN 
2 0  UNKNOWN 
Expanded topology size: 15
COST = 1.95
10
0	INPUT 	aTc	Ligand	aTc	pCRT2: pCONST>+tetR+pTET>+lacI
1	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
2	mRNA	pCONST	pCRT2: pCONST>+tetR+pTET>+lacI
3	Protein	tetR	pCRT2: pCONST>+tetR+pTET>+lacI
4	mRNA	pTET	pCRT2: pCONST>+tetR+pTET>+lacI
5	SELECTOR 	lacI	Protein	lacI	pCRT2: pCONST>+tetR+pTET>+lacI
6	mRNA	pLAC	pTAK106-107: gfp+pLAMBDA<+pLAC>+cI
7	SELECTOR 	cI	Protein	cI	pTAK106-107: gfp+pLAMBDA<+pLAC>+cI
8	mRNA	pLAMBDA	pTAK106-107: gfp+pLAMBDA<+pLAC>+cI
9	Protein	gfp	pTAK106-107: gfp+pLAMBDA<+pLAC>+cI
0 3  REP 
2 3  ACT 
3 4  REP 
4 5  ACT 
5 6  REP 
6 7  ACT 
7 8  REP 
8 9  ACT 
9 1  UNKNOWN 
Running time: 0.08
--------------------------------
4
0	NOTGate 		
1	NOTGate 		
2	INPUT 			
3	OUTPUT 			
0 1  UNKNOWN 
1 3  UNKNOWN 
2 0  UNKNOWN 
Expanded topology size: 15
COST = 0.95
10
0	INPUT 	aTc	Ligand	aTc	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
1	OUTPUT 	yfp	Protein	yfp	Module yfp(output)
2	mRNA	pCONST	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
3	Protein	tetR	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
4	mRNA	pTET	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
5	SELECTOR 	lacI	Protein	lacI	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
6	mRNA	pLAC	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
7	SELECTOR 	cI	Protein	cI	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
8	mRNA	pLAMBDA	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
9	Protein	yfp	pCRT3: pCONST>+tetR+pTET>+lacI+pLAC>+cI+pLAMBDA>+yfp
0 3  REP 
2 3  ACT 
3 4  REP 
4 5  ACT 
5 6  REP 
6 7  ACT 
7 8  REP 
8 9  ACT 
9 1  UNKNOWN 
Running time: 0.18
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/3-cascade.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Number of possible topologies: 3
COST = 2
13
0	INPUT 	Sal	Ligand	Sal	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
1	OUTPUT 	yfp	Protein	yfp	Module yfp(output)
2	Protein	lacI	pCRT3: lacI+pLAC>+cI+pLAMBDA>+yfp
3	mRNA	pLAC	pCRT3: lacI+pLAC>+cI+pLAMBDA>+yfp
4	mRNA	pCONST	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
5	Protein	nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
6	LigandProteinComplex	Sal-nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
7	mRNA	pSAL	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
8	Protein	mcbR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
9	mRNA	pMCBR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
10	Protein	cI	pCRT3: lacI+pLAC>+cI+pLAMBDA>+yfp
11	mRNA	pLAMBDA	pCRT3: lacI+pLAC>+cI+pLAMBDA>+yfp
12	Protein	yfp	pCRT3: lacI+pLAC>+cI+pLAMBDA>+yfp
0 6  ACT 
2 3  REP 
3 10  ACT 
4 5  ACT 
5 6  ACT 
6 7  ACT 
7 8  ACT 
8 9  REP 
9 2  UNKNOWN 
10 11  REP 
11 12  ACT 
12 1  UNKNOWN 
Running time: 0.42
--------------------------------
5
0	NOTGate 		
1	NOTGate 		
2	NOTGate 		
3	INPUT 			
4	OUTPUT 			
0 1  UNKNOWN 
1 2  UNKNOWN 
2 4  UNKNOWN 
3 0  UNKNOWN 
Expanded topology size: 17
COST = 2.95
8
0	INPUT 	Mg2+	Ligand	Mg2+	Module pmgrB
1	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
2	mRNA	pmgrB	Module pmgrB
3	SELECTOR 	cI	Protein	cI	Module cI
4	mRNA	pLAMBDA	pTAK102-103a: lacI+pLAMBDA<+pLAC>+gfp
5	Protein	lacI	pTAK102-103a: lacI+pLAMBDA<+pLAC>+gfp
6	mRNA	pLAC	pTAK102-103a: lacI+pLAMBDA<+pLAC>+gfp
7	Protein	gfp	pTAK102-103a: lacI+pLAMBDA<+pLAC>+gfp
0 2  REP 
2 3  ACT 
3 4  REP 
4 5  ACT 
5 6  REP 
6 7  ACT 
7 1  UNKNOWN 
Running time: 0.1
--------------------------------
5
0	NOTGate 		
1	NOTGate 		
2	NOTGate 		
3	INPUT 			
4	OUTPUT 			
0 1  UNKNOWN 
1 2  UNKNOWN 
2 4  UNKNOWN 
3 0  UNKNOWN 
Expanded topology size: 17
COST = 2
8
0	INPUT 	Mg2+	Ligand	Mg2+	Module pmgrB
1	OUTPUT 	yfp	Protein	yfp	Module yfp(output)
2	mRNA	pmgrB	Module pmgrB
3	SELECTOR 	lacI	Protein	lacI	pCRT3: lacI+pLAC>+cI+pLAMBDA>+yfp
4	mRNA	pLAC	pCRT3: lacI+pLAC>+cI+pLAMBDA>+yfp
5	Protein	cI	pCRT3: lacI+pLAC>+cI+pLAMBDA>+yfp
6	mRNA	pLAMBDA	pCRT3: lacI+pLAC>+cI+pLAMBDA>+yfp
7	Protein	yfp	pCRT3: lacI+pLAC>+cI+pLAMBDA>+yfp
0 2  REP 
2 3  ACT 
3 4  REP 
4 5  ACT 
5 6  REP 
6 7  ACT 
7 1  UNKNOWN 
Running time: 0.21
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/4-cascade.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Number of possible topologies: 3
COST = 2.95
15
0	INPUT 	Sal	Ligand	Sal	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
1	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
2	Protein	cI	pLD: cI+pLAMBDA>+lacI
3	mRNA	pLAMBDA	pLD: cI+pLAMBDA>+lacI
4	Protein	lacI	pLD: cI+pLAMBDA>+lacI
5	mRNA	pLAC	pIKE108-110: gfp+pTET<+pLAC>+tetR
6	mRNA	pCONST	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
7	Protein	nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
8	LigandProteinComplex	Sal-nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
9	mRNA	pSAL	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
10	Protein	mcbR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
11	mRNA	pMCBR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
12	Protein	tetR	pIKE108-110: gfp+pTET<+pLAC>+tetR
13	mRNA	pTET	pIKE108-110: gfp+pTET<+pLAC>+tetR
14	Protein	gfp	pIKE108-110: gfp+pTET<+pLAC>+tetR
0 8  ACT 
2 3  REP 
3 4  ACT 
4 5  REP 
5 12  ACT 
6 7  ACT 
7 8  ACT 
8 9  ACT 
9 10  ACT 
10 11  REP 
11 2  UNKNOWN 
12 13  REP 
13 14  ACT 
14 1  UNKNOWN 
Running time: 0.61
--------------------------------
6
0	NOTGate 		
1	NOTGate 		
2	NOTGate 		
3	NOTGate 		
4	INPUT 			
5	OUTPUT 			
0 1  UNKNOWN 
1 2  UNKNOWN 
2 3  UNKNOWN 
3 5  UNKNOWN 
4 0  UNKNOWN 
Expanded topology size: 19
COST = 3
10
0	INPUT 	Mg2+	Ligand	Mg2+	Module pmgrB
1	OUTPUT 	yfp	Protein	yfp	Module yfp(output)
2	mRNA	pmgrB	Module pmgrB
3	SELECTOR 	lacI	Protein	lacI	pCRT3: lacI+pLAC>+cI+pLAMBDA>
4	mRNA	pLAC	pCRT3: lacI+pLAC>+cI+pLAMBDA>
5	Protein	cI	pCRT3: lacI+pLAC>+cI+pLAMBDA>
6	mRNA	pLAMBDA	pCRT3: lacI+pLAC>+cI+pLAMBDA>
7	Protein	mcbR	pTACsym-McbR-pMcbR-yfp: mcbR+pMCBR>+yfp
8	mRNA	pMCBR	pTACsym-McbR-pMcbR-yfp: mcbR+pMCBR>+yfp
9	Protein	yfp	pTACsym-McbR-pMcbR-yfp: mcbR+pMCBR>+yfp
0 2  REP 
2 3  ACT 
3 4  REP 
4 5  ACT 
5 6  REP 
6 7  ACT 
7 8  REP 
8 9  ACT 
9 1  UNKNOWN 
Running time: 0.12
--------------------------------
6
0	NOTGate 		
1	NOTGate 		
2	NOTGate 		
3	NOTGate 		
4	INPUT 			
5	OUTPUT 			
0 1  UNKNOWN 
1 2  UNKNOWN 
2 3  UNKNOWN 
3 5  UNKNOWN 
4 0  UNKNOWN 
Expanded topology size: 19
COST = 2.95
10
0	INPUT 	Mg2+	Ligand	Mg2+	Module pmgrB
1	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
2	mRNA	pmgrB	Module pmgrB
3	SELECTOR 	cI	Protein	cI	pLD: cI+pLAMBDA>+lacI
4	mRNA	pLAMBDA	pLD: cI+pLAMBDA>+lacI
5	Protein	lacI	pLD: cI+pLAMBDA>+lacI
6	mRNA	pLAC	pIKE108-110: gfp+pTET<+pLAC>+tetR
7	Protein	tetR	pIKE108-110: gfp+pTET<+pLAC>+tetR
8	mRNA	pTET	pIKE108-110: gfp+pTET<+pLAC>+tetR
9	Protein	gfp	pIKE108-110: gfp+pTET<+pLAC>+tetR
0 2  REP 
2 3  ACT 
3 4  REP 
4 5  ACT 
5 6  REP 
6 7  ACT 
7 8  REP 
8 9  ACT 
9 1  UNKNOWN 
Running time: 0.25
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/band-detector.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Number of possible topologies: 6
COST = 5
19
0	INPUT 	Sal	Ligand	Sal	pSal-R73delta-pMcbR-yfp: nahR+pCONST<+pSAL>+R73delta
1	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
2	mRNA	pCONST	pSal-R73delta-pMcbR-yfp: nahR+pCONST<+pSAL>+R73delta
3	Protein	nahR	pSal-R73delta-pMcbR-yfp: nahR+pCONST<+pSAL>+R73delta
4	LigandProteinComplex	Sal-nahR	pSal-R73delta-pMcbR-yfp: nahR+pCONST<+pSAL>+R73delta
5	mRNA	pSAL	pSal-R73delta-pMcbR-yfp: nahR+pCONST<+pSAL>+R73delta
6	mRNA	pCONST	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
7	Protein	nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
8	LigandProteinComplex	Sal-nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
9	mRNA	pSAL	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
10	Protein	mcbR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
11	mRNA	pMCBR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
12	Protein	R73delta	pSal-R73delta-pMcbR-yfp: nahR+pCONST<+pSAL>+R73delta
13	Protein	R73delta	Module R73delta
14	POOL 	R73delta	Protein		
15	mRNA	pF	Module pF
16	Protein	cI	PBW12xlac-cIgfp: cI+pLAMBDA>+gfp
17	mRNA	pLAMBDA	PBW12xlac-cIgfp: cI+pLAMBDA>+gfp
18	Protein	gfp	PBW12xlac-cIgfp: cI+pLAMBDA>+gfp
0 4  ACT 
0 8  ACT 
2 3  ACT 
3 4  ACT 
4 5  ACT 
5 12  ACT 
6 7  ACT 
7 8  ACT 
8 9  ACT 
9 10  ACT 
10 11  REP 
11 13  ACT 
12 14  ACT 
13 14  ACT 
14 15  ACT 
15 16  ACT 
16 17  REP 
17 18  ACT 
18 1  UNKNOWN 
Running time: 4.39
--------------------------------
5
0	YESGate 		
1	NOTGate 		
2	NORGate 		
3	INPUT 			
4	OUTPUT 			
0 2  UNKNOWN 
1 2  UNKNOWN 
2 4  UNKNOWN 
3 0  UNKNOWN 
3 1  UNKNOWN 
Expanded topology size: 26
COST = 6
17
0	INPUT 	aTc	Ligand	aTc	pCRT1: pCONST>+tetR+pTET>
1	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
2	mRNA	pCONST	pCRT1: pCONST>+tetR+pTET>
3	Protein	tetR	pCRT1: pCONST>+tetR+pTET>
4	mRNA	pTET	pCRT1: pCONST>+tetR+pTET>
5	mRNA	pCONST	pCRT2: pCONST>+tetR+pTET>+lacI
6	Protein	tetR	pCRT2: pCONST>+tetR+pTET>+lacI
7	mRNA	pTET	pCRT2: pCONST>+tetR+pTET>+lacI
8	SELECTOR 	lacI	Protein	lacI	pCRT2: pCONST>+tetR+pTET>+lacI
9	mRNA	pTAC	pTACsym-R73delta-pMcbR-yfp: pTAC>+R73delta
10	SELECTOR 	R73delta	Protein	R73delta	Module R73delta
11	SELECTOR 	R73delta	Protein	R73delta	pTACsym-R73delta-pMcbR-yfp: pTAC>+R73delta
12	POOL 	R73delta	Protein		
13	mRNA	pF	Module pF
14	Protein	cI	PBW12xlac-cIgfp: cI+pLAMBDA>+gfp
15	mRNA	pLAMBDA	PBW12xlac-cIgfp: cI+pLAMBDA>+gfp
16	Protein	gfp	PBW12xlac-cIgfp: cI+pLAMBDA>+gfp
0 3  REP 
0 6  REP 
2 3  ACT 
3 4  REP 
4 10  ACT 
5 6  ACT 
6 7  REP 
7 8  ACT 
8 9  REP 
9 11  ACT 
10 12  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 15  REP 
15 16  ACT 
16 1  UNKNOWN 
Running time: 0.15
--------------------------------
5
0	YESGate 		
1	NOTGate 		
2	NORGate 		
3	INPUT 			
4	OUTPUT 			
0 2  UNKNOWN 
1 2  UNKNOWN 
2 4  UNKNOWN 
3 0  UNKNOWN 
3 1  UNKNOWN 
Expanded topology size: 26
COST = 5
17
0	INPUT 	IPTG	Ligand	IPTG	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta
1	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
2	mRNA	pCONST	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta
3	Protein	lacI	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta
4	mRNA	pTAC	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta
5	mRNA	pCONST	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
6	Protein	lacI	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
7	mRNA	pTAC	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
8	SELECTOR 	mcbR	Protein	mcbR	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
9	mRNA	pMCBR	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
10	SELECTOR 	R73delta	Protein	R73delta	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta
11	SELECTOR 	R73delta	Protein	R73delta	Module R73delta
12	POOL 	R73delta	Protein		
13	mRNA	pF	Module pF
14	Protein	cI	PBW12xlac-cIgfp: cI+pLAMBDA>+gfp
15	mRNA	pLAMBDA	PBW12xlac-cIgfp: cI+pLAMBDA>+gfp
16	Protein	gfp	PBW12xlac-cIgfp: cI+pLAMBDA>+gfp
0 3  REP 
0 6  REP 
2 3  ACT 
3 4  REP 
4 10  ACT 
5 6  ACT 
6 7  REP 
7 8  ACT 
8 9  REP 
9 11  ACT 
10 12  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 15  REP 
15 16  ACT 
16 1  UNKNOWN 
Running time: 0.34
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/feed-forward.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Number of possible topologies: 18
COST = 3.9
15
0	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
1	INPUT 	IPTG	Ligand	IPTG	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
2	Protein	R73delta	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
3	mRNA	pF	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
4	mRNA	pCONST	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
5	Protein	lacI	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
6	mRNA	pTAC	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
7	mRNA	pCONST	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
8	Protein	lacI	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
9	mRNA	pLAC	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
10	Protein	hrpS	Module hrpS
11	Protein	hrpR	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
12	ProteinComplex	hrpR-hrpS	Module hrpR-hrpS
13	mRNA	phrpL	pBW400hrpL-gfp: phrpL>+gfp
14	Protein	gfp	pBW400hrpL-gfp: phrpL>+gfp
1 5  REP 
1 8  REP 
2 3  ACT 
3 10  ACT 
4 5  ACT 
5 6  REP 
6 2  UNKNOWN 
7 8  ACT 
8 9  REP 
9 11  ACT 
10 12  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 0  UNKNOWN 
Running time: 10.94
--------------------------------
5
0	ANDGate 		
1	OUTPUT 			
2	INPUT 			
3	YESGate 		
4	YESGate 		
0 1  UNKNOWN 
2 0  UNKNOWN 
2 4  UNKNOWN 
3 0  UNKNOWN 
4 3  UNKNOWN 
Expanded topology size: 42
COST = 3.9
15
0	SELECTOR 	gfp	Protein	gfp	Module gfp(output)
1	INPUT 	IPTG	Ligand	IPTG	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
2	SELECTOR 	R73delta	Protein	R73delta	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
3	mRNA	pF	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
4	mRNA	pCONST	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
5	Protein	lacI	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
6	mRNA	pTAC	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
7	mRNA	pCONST	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
8	Protein	lacI	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
9	mRNA	pLAC	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
10	Protein	hrpS	Module hrpS
11	SELECTOR 	hrpR	Protein	hrpR	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
12	ProteinComplex	hrpR-hrpS	Module hrpR-hrpS
13	mRNA	phrpL	pBW400hrpL-gfp: phrpL>+gfp
14	SELECTOR 	gfp	Protein	gfp	pBW400hrpL-gfp: phrpL>+gfp
1 5  REP 
1 8  REP 
2 3  ACT 
3 10  ACT 
4 5  ACT 
5 6  REP 
6 2  ACT 
7 8  ACT 
8 9  REP 
9 11  ACT 
10 12  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 0  UNKNOWN 
Running time: 0.26
--------------------------------
5
0	ANDGate 		
1	OUTPUT 			
2	INPUT 			
3	YESGate 		
4	YESGate 		
0 1  UNKNOWN 
2 0  UNKNOWN 
2 4  UNKNOWN 
3 0  UNKNOWN 
4 3  UNKNOWN 
Expanded topology size: 42
COST = 3.9
15
0	SELECTOR 	gfp	Protein	gfp	Module gfp(output)
1	INPUT 	IPTG	Ligand	IPTG	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
2	SELECTOR 	R73delta	Protein	R73delta	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
3	mRNA	pF	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
4	mRNA	pCONST	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
5	Protein	lacI	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
6	mRNA	pTAC	pTACsym-R73delta-pMcbR-yfp: lacI+pCONST<+pTAC>+R73delta+pF>
7	mRNA	pCONST	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
8	Protein	lacI	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
9	mRNA	pLAC	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
10	Protein	hrpS	Module hrpS
11	SELECTOR 	hrpR	Protein	hrpR	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
12	ProteinComplex	hrpR-hrpS	Module hrpR-hrpS
13	mRNA	phrpL	pBW400hrpL-gfp: phrpL>+gfp
14	SELECTOR 	gfp	Protein	gfp	pBW400hrpL-gfp: phrpL>+gfp
1 5  REP 
1 8  REP 
2 3  ACT 
3 10  ACT 
4 5  ACT 
5 6  REP 
6 2  ACT 
7 8  ACT 
8 9  REP 
9 11  ACT 
10 12  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 0  UNKNOWN 
Running time: 0.63
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/not-and.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Number of possible topologies: 27
COST = 2
13
0	INPUT 	Sal	Ligand	Sal	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
1	INPUT 	AHL	Ligand	AHL	pBW30xlux-gfp: luxR+pLUX>+gfp
2	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
3	Protein	luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
4	LigandProteinComplex	AHL-luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
5	mRNA	pLUX	pBW30xlux-gfp: luxR+pLUX>+gfp
6	Protein	gfp	pBW30xlux-gfp: luxR+pLUX>+gfp
7	mRNA	pCONST	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
8	Protein	nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
9	LigandProteinComplex	Sal-nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
10	mRNA	pSAL	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
11	Protein	mcbR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
12	mRNA	pMCBR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
0 9  ACT 
1 4  ACT 
3 4  ACT 
4 5  ACT 
5 6  ACT 
6 2  UNKNOWN 
7 8  ACT 
8 9  ACT 
9 10  ACT 
10 11  ACT 
11 12  REP 
12 3  UNKNOWN 
Running time: 6.04
--------------------------------
5
0	ANDGate 		
1	NOTGate 		
2	INPUT 			
3	INPUT 			
4	OUTPUT 			
0 4  UNKNOWN 
1 0  UNKNOWN 
2 1  UNKNOWN 
3 0  UNKNOWN 
Expanded topology size: 44
COST = 2
8
0	INPUT 	Mg2+	Ligand	Mg2+	Module pmgrB
1	INPUT 	AHL	Ligand	AHL	pBW30xlux-gfp: luxR+pLUX>+gfp
2	SELECTOR 	gfp	Protein	gfp	Module gfp(output)
3	SELECTOR 	luxR	Protein	luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
4	LigandProteinComplex	AHL-luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
5	mRNA	pLUX	pBW30xlux-gfp: luxR+pLUX>+gfp
6	Protein	gfp	pBW30xlux-gfp: luxR+pLUX>+gfp
7	mRNA	pmgrB	Module pmgrB
0 7  REP 
1 4  ACT 
3 4  ACT 
4 5  ACT 
5 6  ACT 
6 2  UNKNOWN 
7 3  ACT 
Running time: 0.31
--------------------------------
5
0	ANDGate 		
1	NOTGate 		
2	INPUT 			
3	INPUT 			
4	OUTPUT 			
0 4  UNKNOWN 
1 0  UNKNOWN 
2 1  UNKNOWN 
3 0  UNKNOWN 
Expanded topology size: 44
COST = 2
8
0	INPUT 	Mg2+	Ligand	Mg2+	Module pmgrB
1	INPUT 	AHL	Ligand	AHL	pBW30xlux-gfp: luxR+pLUX>+gfp
2	SELECTOR 	gfp	Protein	gfp	Module gfp(output)
3	SELECTOR 	luxR	Protein	luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
4	LigandProteinComplex	AHL-luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
5	mRNA	pLUX	pBW30xlux-gfp: luxR+pLUX>+gfp
6	Protein	gfp	pBW30xlux-gfp: luxR+pLUX>+gfp
7	mRNA	pmgrB	Module pmgrB
0 7  REP 
1 4  ACT 
3 4  ACT 
4 5  ACT 
5 6  ACT 
6 2  UNKNOWN 
7 3  ACT 
Running time: 0.64
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/3-input-and.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Number of possible topologies: 324
COST = 2.85
24
0	INPUT 	aTc	Ligand	aTc	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
1	INPUT 	AHL	Ligand	AHL	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
2	INPUT 	Lara	Ligand	Lara	pBAD-sicA: araC+pCONST<+pBAD>+sicA
3	OUTPUT 	rfp	Protein	rfp	Module rfp(output)
4	mRNA	pCONST	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
5	Protein	luxR	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
6	LigandProteinComplex	AHL-luxR	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
7	mRNA	pLUX	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
8	mRNA	pCONST	pBAD-sicA: araC+pCONST<+pBAD>+sicA
9	Protein	araC	pBAD-sicA: araC+pCONST<+pBAD>+sicA
10	LigandProteinComplex	Lara-araC	pBAD-sicA: araC+pCONST<+pBAD>+sicA
11	mRNA	pBAD	pBAD-sicA: araC+pCONST<+pBAD>+sicA
12	Protein	invF	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
13	Protein	sicA	pBAD-sicA: araC+pCONST<+pBAD>+sicA
14	ProteinComplex	sicA-invF	Module sicA-invF
15	mRNA	psicA	psicA-rfp: psicA>+rfp
16	Protein	rfp	psicA-rfp: psicA>+rfp
17	mRNA	pCONST	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
18	Protein	tetR	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
19	mRNA	pTET	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
20	Protein	exsC	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
21	Protein	exsDA	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
22	ProteinComplex	exsC-exsDA	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
23	mRNA	pexsC	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
0 18  REP 
1 6  ACT 
2 10  ACT 
4 5  ACT 
5 6  ACT 
6 7  ACT 
7 20  ACT 
8 9  ACT 
9 10  ACT 
10 11  ACT 
11 13  ACT 
12 14  ACT 
13 14  ACT 
14 15  ACT 
15 16  ACT 
16 3  UNKNOWN 
17 18  ACT 
18 19  REP 
19 21  ACT 
20 22  ACT 
21 22  ACT 
22 23  ACT 
23 12  UNKNOWN 
Running time: 247.92
--------------------------------
6
0	ANDGate 		
1	ANDGate 		
2	INPUT 			
3	INPUT 			
4	INPUT 			
5	OUTPUT 			
0 1  UNKNOWN 
1 5  UNKNOWN 
2 0  UNKNOWN 
3 0  UNKNOWN 
4 1  UNKNOWN 
Expanded topology size: 71
COST = 3
19
0	INPUT 	IPTG	Ligand	IPTG	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
1	INPUT 	Lara	Ligand	Lara	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
2	INPUT 	AHL	Ligand	AHL	pBW30xlux-gfp: luxR+pLUX>+gfp
3	SELECTOR 	gfp	Protein	gfp	Module gfp(output)
4	SELECTOR 	luxR	Protein	luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
5	LigandProteinComplex	AHL-luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
6	mRNA	pLUX	pBW30xlux-gfp: luxR+pLUX>+gfp
7	Protein	gfp	pBW30xlux-gfp: luxR+pLUX>+gfp
8	mRNA	pCONST	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
9	Protein	lacI	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
10	mRNA	pTAC	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
11	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
12	Protein	araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
13	LigandProteinComplex	Lara-araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
14	mRNA	pBAD	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
15	SELECTOR 	mxiE	Protein	mxiE	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
16	SELECTOR 	ipgC	Protein	ipgC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
17	ProteinComplex	ipgC-mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
18	mRNA	pipaH	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
0 9  REP 
1 13  ACT 
2 5  ACT 
4 5  ACT 
5 6  ACT 
6 7  ACT 
7 3  UNKNOWN 
8 9  ACT 
9 10  REP 
10 15  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 16  ACT 
15 17  ACT 
16 17  ACT 
17 18  ACT 
18 4  ACT 
Running time: 0.69
--------------------------------
6
0	ANDGate 		
1	ANDGate 		
2	INPUT 			
3	INPUT 			
4	INPUT 			
5	OUTPUT 			
0 1  UNKNOWN 
1 5  UNKNOWN 
2 0  UNKNOWN 
3 0  UNKNOWN 
4 1  UNKNOWN 
Expanded topology size: 71
COST = 2.85
23
0	INPUT 	Lara	Ligand	Lara	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
1	INPUT 	IPTG	Ligand	IPTG	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
2	INPUT 	aTc	Ligand	aTc	pTET-invF: tetR+pCONST<+pTET>+invF
3	SELECTOR 	rfp	Protein	rfp	Module rfp(output)
4	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
5	Protein	araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
6	LigandProteinComplex	Lara-araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
7	mRNA	pBAD	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
8	mRNA	pCONST	pTET-invF: tetR+pCONST<+pTET>+invF
9	Protein	tetR	pTET-invF: tetR+pCONST<+pTET>+invF
10	mRNA	pTET	pTET-invF: tetR+pCONST<+pTET>+invF
11	SELECTOR 	sicA	Protein	sicA	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
12	SELECTOR 	invF	Protein	invF	pTET-invF: tetR+pCONST<+pTET>+invF
13	ProteinComplex	sicA-invF	Module sicA-invF
14	mRNA	psicA	psicA-rfp: psicA>+rfp
15	SELECTOR 	rfp	Protein	rfp	psicA-rfp: psicA>+rfp
16	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
17	Protein	lacI	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
18	mRNA	pTAC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
19	SELECTOR 	ipgC	Protein	ipgC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
20	SELECTOR 	mxiE	Protein	mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
21	ProteinComplex	ipgC-mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
22	mRNA	pipaH	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
0 6  ACT 
1 17  REP 
2 9  REP 
4 5  ACT 
5 6  ACT 
6 7  ACT 
7 19  ACT 
8 9  ACT 
9 10  REP 
10 12  ACT 
11 13  ACT 
12 13  ACT 
13 14  ACT 
14 15  ACT 
15 3  UNKNOWN 
16 17  ACT 
17 18  REP 
18 20  ACT 
19 21  ACT 
20 21  ACT 
21 22  ACT 
22 11  ACT 
Running time: 2.33
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/3-input-not-and.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Number of possible topologies: 432
COST = 3.9
26
0	INPUT 	aTc	Ligand	aTc	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
1	INPUT 	AHL	Ligand	AHL	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
2	INPUT 	Sal	Ligand	Sal	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
3	OUTPUT 	rfp	Protein	rfp	Module rfp(output)
4	mRNA	pCONST	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
5	Protein	luxR	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
6	LigandProteinComplex	AHL-luxR	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
7	mRNA	pLUX	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
8	Protein	sicA	Module sicA
9	Protein	invF	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
10	ProteinComplex	sicA-invF	Module sicA-invF
11	mRNA	psicA	psicA-rfp: psicA>+rfp
12	Protein	rfp	psicA-rfp: psicA>+rfp
13	mRNA	pCONST	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
14	Protein	nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
15	LigandProteinComplex	Sal-nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
16	mRNA	pSAL	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
17	Protein	mcbR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
18	mRNA	pMCBR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
19	mRNA	pCONST	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
20	Protein	tetR	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
21	mRNA	pTET	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
22	Protein	exsC	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
23	Protein	exsDA	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
24	ProteinComplex	exsC-exsDA	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
25	mRNA	pexsC	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
0 20  REP 
1 6  ACT 
2 15  ACT 
4 5  ACT 
5 6  ACT 
6 7  ACT 
7 22  ACT 
8 10  ACT 
9 10  ACT 
10 11  ACT 
11 12  ACT 
12 3  UNKNOWN 
13 14  ACT 
14 15  ACT 
15 16  ACT 
16 17  ACT 
17 18  REP 
18 8  UNKNOWN 
19 20  ACT 
20 21  REP 
21 23  ACT 
22 24  ACT 
23 24  ACT 
24 25  ACT 
25 9  UNKNOWN 
Running time: 578.76
--------------------------------
7
0	ANDGate 		
1	ANDGate 		
2	INPUT 			
3	INPUT 			
4	INPUT 			
5	OUTPUT 			
6	NOTGate 		
0 1  UNKNOWN 
1 5  UNKNOWN 
2 0  UNKNOWN 
3 0  UNKNOWN 
4 6  UNKNOWN 
6 1  UNKNOWN 
Expanded topology size: 70
COST = 4.95
16
0	INPUT 	IPTG	Ligand	IPTG	pCFP: lacI+pCONST<+pLAC>
1	INPUT 	AHL	Ligand	AHL	pBW313lux-hrpR: luxR+pLUX>+hrpR
2	INPUT 	Mg2+	Ligand	Mg2+	Module pmgrB
3	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
4	mRNA	pmgrB	Module pmgrB
5	mRNA	pCONST	pCFP: lacI+pCONST<+pLAC>
6	Protein	lacI	pCFP: lacI+pCONST<+pLAC>
7	mRNA	pLAC	pCFP: lacI+pCONST<+pLAC>
8	SELECTOR 	luxR	Protein	luxR	pBW313lux-hrpR: luxR+pLUX>+hrpR
9	LigandProteinComplex	AHL-luxR	pBW313lux-hrpR: luxR+pLUX>+hrpR
10	mRNA	pLUX	pBW313lux-hrpR: luxR+pLUX>+hrpR
11	SELECTOR 	hrpS	Protein	hrpS	Module hrpS
12	SELECTOR 	hrpR	Protein	hrpR	pBW313lux-hrpR: luxR+pLUX>+hrpR
13	ProteinComplex	hrpR-hrpS	Module hrpR-hrpS
14	mRNA	phrpL	pBW400hrpL-gfp: phrpL>+gfp
15	SELECTOR 	gfp	Protein	gfp	pBW400hrpL-gfp: phrpL>+gfp
0 6  REP 
1 9  ACT 
2 4  REP 
4 11  ACT 
5 6  ACT 
6 7  REP 
7 8  ACT 
8 9  ACT 
9 10  ACT 
10 12  ACT 
11 13  ACT 
12 13  ACT 
13 14  ACT 
14 15  ACT 
15 3  UNKNOWN 
Running time: 0.67
--------------------------------
7
0	ANDGate 		
1	ANDGate 		
2	INPUT 			
3	INPUT 			
4	INPUT 			
5	OUTPUT 			
6	NOTGate 		
0 1  UNKNOWN 
1 5  UNKNOWN 
2 0  UNKNOWN 
3 0  UNKNOWN 
4 6  UNKNOWN 
6 1  UNKNOWN 
Expanded topology size: 70
COST = 3.9
21
0	INPUT 	AHL	Ligand	AHL	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
1	INPUT 	aTc	Ligand	aTc	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
2	INPUT 	Mg2+	Ligand	Mg2+	Module pmgrB
3	OUTPUT 	rfp	Protein	rfp	Module rfp(output)
4	mRNA	pmgrB	Module pmgrB
5	mRNA	pCONST	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
6	Protein	luxR	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
7	LigandProteinComplex	AHL-luxR	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
8	mRNA	pLUX	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
9	SELECTOR 	sicA	Protein	sicA	Module sicA
10	SELECTOR 	invF	Protein	invF	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
11	ProteinComplex	sicA-invF	Module sicA-invF
12	mRNA	psicA	psicA-rfp: psicA>+rfp
13	SELECTOR 	rfp	Protein	rfp	psicA-rfp: psicA>+rfp
14	mRNA	pCONST	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
15	Protein	tetR	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
16	mRNA	pTET	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
17	SELECTOR 	exsC	Protein	exsC	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
18	SELECTOR 	exsDA	Protein	exsDA	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
19	ProteinComplex	exsC-exsDA	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
20	mRNA	pexsC	pACPc-invF: tetR+pCONST<+pTET>+exsDA+XXX+exsC+pLUX<+pCONST>+luxR+TTT+invF+pexsC<
0 7  ACT 
1 15  REP 
2 4  REP 
4 9  ACT 
5 6  ACT 
6 7  ACT 
7 8  ACT 
8 17  ACT 
9 11  ACT 
10 11  ACT 
11 12  ACT 
12 13  ACT 
13 3  UNKNOWN 
14 15  ACT 
15 16  REP 
16 18  ACT 
17 19  ACT 
18 19  ACT 
19 20  ACT 
20 10  ACT 
Running time: 36.34
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/2-to-1-multiplexer-1.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
8
0	NOTGate 		
1	ANDGate 		
2	ANDGate 		
3	ORGate 		
4	INPUT 			
5	INPUT 			
6	INPUT 			
7	OUTPUT 			
0 1  UNKNOWN 
1 3  UNKNOWN 
2 3  UNKNOWN 
3 7  UNKNOWN 
4 1  UNKNOWN 
5 0  UNKNOWN 
5 2  UNKNOWN 
6 2  UNKNOWN 
Number of possible topologies: 972
Overtime
COST = 10
35
0	INPUT 	C4HSL	Ligand	C4HSL	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
1	INPUT 	Sal	Ligand	Sal	pAC-SalSer914: nahR+pCONST<+pSAL>
2	INPUT 	Lara	Ligand	Lara	pBW20xara-gfp: araC+pCONST<+pBAD>
3	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
4	Protein	gfp	Module gfp
5	Protein	gfp	pBW30xlux-gfp: luxR+pLUX>+gfp
6	POOL 	gfp	Protein		
7	mRNA	pCONST	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
8	Protein	nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
9	LigandProteinComplex	Sal-nahR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
10	mRNA	pSAL	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
11	Protein	mcbR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
12	mRNA	pMCBR	pSal-McbR-pMcbR-yfp: nahR+pCONST<+pSAL>+mcbR+pMCBR>
13	mRNA	pCONST	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
14	Protein	rhlR	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
15	LigandProteinComplex	C4HSL-rhlR	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
16	mRNA	pRHL	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
17	Protein	lasI	Module lasI
18	Ligand	HSL	Module lasI
19	Protein	lasR	Module lasR
20	LigandProteinComplex	HSL-lasR	Module pLAS
21	mRNA	pLAS	Module pLAS
22	mRNA	pCONST	pBW20xara-gfp: araC+pCONST<+pBAD>
23	Protein	araC	pBW20xara-gfp: araC+pCONST<+pBAD>
24	LigandProteinComplex	Lara-araC	pBW20xara-gfp: araC+pCONST<+pBAD>
25	mRNA	pBAD	pBW20xara-gfp: araC+pCONST<+pBAD>
26	mRNA	pCONST	pAC-SalSer914: nahR+pCONST<+pSAL>
27	Protein	nahR	pAC-SalSer914: nahR+pCONST<+pSAL>
28	LigandProteinComplex	Sal-nahR	pAC-SalSer914: nahR+pCONST<+pSAL>
29	mRNA	pSAL	pAC-SalSer914: nahR+pCONST<+pSAL>
30	Protein	luxI	Module luxI
31	Ligand	AHL	Module luxI
32	Protein	luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
33	LigandProteinComplex	AHL-luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
34	mRNA	pLUX	pBW30xlux-gfp: luxR+pLUX>+gfp
0 15  ACT 
1 9  ACT 
1 28  ACT 
2 24  ACT 
4 6  ACT 
5 6  ACT 
6 3  UNKNOWN 
7 8  ACT 
8 9  ACT 
9 10  ACT 
10 11  ACT 
11 12  REP 
12 19  ACT 
13 14  ACT 
14 15  ACT 
15 16  ACT 
16 17  ACT 
17 18  ACT 
18 20  ACT 
19 20  ACT 
20 21  ACT 
21 4  UNKNOWN 
22 23  ACT 
23 24  ACT 
24 25  ACT 
25 32  ACT 
26 27  ACT 
27 28  ACT 
28 29  ACT 
29 30  ACT 
30 31  ACT 
31 33  ACT 
32 33  ACT 
33 34  ACT 
34 5  UNKNOWN 
Running time: 2877.12
--------------------------------
8
0	NOTGate 		
1	ANDGate 		
2	ANDGate 		
3	ORGate 		
4	INPUT 			
5	INPUT 			
6	INPUT 			
7	OUTPUT 			
0 1  UNKNOWN 
1 3  UNKNOWN 
2 3  UNKNOWN 
3 7  UNKNOWN 
4 1  UNKNOWN 
5 0  UNKNOWN 
5 2  UNKNOWN 
6 2  UNKNOWN 
Expanded topology size: 82
Expanded topology size: 82
COST = 7
21
0	INPUT 	AHL	Ligand	AHL	pBW30xlux-gfp: luxR+pLUX>
1	INPUT 	IPTG	Ligand	IPTG	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
2	INPUT 	Lara	Ligand	Lara	Module pBAD(+Lara)
3	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
4	SELECTOR 	luxR	Protein	luxR	pBW30xlux-gfp: luxR+pLUX>
5	LigandProteinComplex	AHL-luxR	pBW30xlux-gfp: luxR+pLUX>
6	mRNA	pLUX	pBW30xlux-gfp: luxR+pLUX>
7	SELECTOR 	gfp	Protein	gfp	Module gfp
8	SELECTOR 	gfp	Protein	gfp	Module gfp
9	POOL 	gfp	Protein		
10	mRNA	pCONST	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
11	Protein	lacI	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
12	mRNA	pTAC	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
13	SELECTOR 	mcbR	Protein	mcbR	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
14	mRNA	pMCBR	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
15	mRNA	pCONST	pCFP: lacI+pCONST<+pLAC>
16	Protein	lacI	pCFP: lacI+pCONST<+pLAC>
17	mRNA	pLAC	pCFP: lacI+pCONST<+pLAC>
18	SELECTOR 	araC	Protein	araC	Module araC
19	LigandProteinComplex	Lara-araC	Module pBAD(+Lara)
20	mRNA	pBAD	Module pBAD(+Lara)
0 5  ACT 
1 11  REP 
1 16  REP 
2 19  ACT 
4 5  ACT 
5 6  ACT 
6 7  ACT 
7 9  ACT 
8 9  ACT 
9 3  UNKNOWN 
10 11  ACT 
11 12  REP 
12 13  ACT 
13 14  REP 
14 4  ACT 
15 16  ACT 
16 17  REP 
17 18  ACT 
18 19  ACT 
19 20  ACT 
20 8  ACT 
Running time: 1.76
--------------------------------
8
0	NOTGate 		
1	ANDGate 		
2	ANDGate 		
3	ORGate 		
4	INPUT 			
5	INPUT 			
6	INPUT 			
7	OUTPUT 			
0 1  UNKNOWN 
1 3  UNKNOWN 
2 3  UNKNOWN 
3 7  UNKNOWN 
4 1  UNKNOWN 
5 0  UNKNOWN 
5 2  UNKNOWN 
6 2  UNKNOWN 
Expanded topology size: 82
COST = 4.85
26
0	INPUT 	AHL	Ligand	AHL	pBW30xlux-gfp: luxR+pLUX>+gfp
1	INPUT 	IPTG	Ligand	IPTG	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
2	INPUT 	Lara	Ligand	Lara	pBW213ara-hrpS: araC+pCONST<+pBAD>+hrpS
3	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
4	SELECTOR 	luxR	Protein	luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
5	LigandProteinComplex	AHL-luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
6	mRNA	pLUX	pBW30xlux-gfp: luxR+pLUX>+gfp
7	SELECTOR 	gfp	Protein	gfp	pBW30xlux-gfp: luxR+pLUX>+gfp
8	SELECTOR 	gfp	Protein	gfp	pBW400hrpL-gfp: phrpL>+gfp
9	POOL 	gfp	Protein		
10	mRNA	pCONST	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
11	Protein	lacI	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
12	mRNA	pTAC	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
13	SELECTOR 	mcbR	Protein	mcbR	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
14	mRNA	pMCBR	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
15	mRNA	pCONST	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
16	Protein	lacI	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
17	mRNA	pLAC	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
18	mRNA	pCONST	pBW213ara-hrpS: araC+pCONST<+pBAD>+hrpS
19	Protein	araC	pBW213ara-hrpS: araC+pCONST<+pBAD>+hrpS
20	LigandProteinComplex	Lara-araC	pBW213ara-hrpS: araC+pCONST<+pBAD>+hrpS
21	mRNA	pBAD	pBW213ara-hrpS: araC+pCONST<+pBAD>+hrpS
22	SELECTOR 	hrpR	Protein	hrpR	pBW115lac-hrpR: pLAC>+hrpR+pCONST>+lacI
23	SELECTOR 	hrpS	Protein	hrpS	pBW213ara-hrpS: araC+pCONST<+pBAD>+hrpS
24	ProteinComplex	hrpR-hrpS	Module hrpR-hrpS
25	mRNA	phrpL	pBW400hrpL-gfp: phrpL>+gfp
0 5  ACT 
1 11  REP 
1 16  REP 
2 20  ACT 
4 5  ACT 
5 6  ACT 
6 7  ACT 
7 9  ACT 
8 9  ACT 
9 3  UNKNOWN 
10 11  ACT 
11 12  REP 
12 13  ACT 
13 14  REP 
14 4  ACT 
15 16  ACT 
16 17  REP 
17 22  ACT 
18 19  ACT 
19 20  ACT 
20 21  ACT 
21 23  ACT 
22 24  ACT 
23 24  ACT 
24 25  ACT 
25 8  ACT 
Running time: 111.73
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/D1_Nat_Biotech.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
10
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	INPUT 			
4	ANDGate 		
5	ANDGate 		
6	ANDGate 		
7	ORGate 		
8	OUTPUT 			
9	INPUT 			
0 4  UNKNOWN 
1 5  UNKNOWN 
2 5  UNKNOWN 
3 6  UNKNOWN 
4 7  UNKNOWN 
5 6  UNKNOWN 
6 7  UNKNOWN 
7 8  UNKNOWN 
9 4  UNKNOWN 
Number of possible topologies: 11664
Overtime
COST = -1
Running time: 361584
--------------------------------
10
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	INPUT 			
4	ANDGate 		
5	ANDGate 		
6	ANDGate 		
7	ORGate 		
8	OUTPUT 			
9	INPUT 			
0 4  UNKNOWN 
1 5  UNKNOWN 
2 5  UNKNOWN 
3 6  UNKNOWN 
4 7  UNKNOWN 
5 6  UNKNOWN 
6 7  UNKNOWN 
7 8  UNKNOWN 
9 4  UNKNOWN 
Expanded topology size: 110
COST = 7
29
0	INPUT 	aTc	Ligand	aTc	pCRT1: pCONST>+tetR+pTET>
1	INPUT 	Lara	Ligand	Lara	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
2	INPUT 	IPTG	Ligand	IPTG	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
3	INPUT 	HSL	Ligand	HSL	Module pLAS
4	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
5	INPUT 	AHL	Ligand	AHL	pBW30xlux-gfp: luxR+pLUX>+gfp
6	SELECTOR 	lasR	Protein	lasR	Module lasR
7	LigandProteinComplex	HSL-lasR	Module pLAS
8	mRNA	pLAS	Module pLAS
9	SELECTOR 	gfp	Protein	gfp	pBW30xlux-gfp: luxR+pLUX>+gfp
10	SELECTOR 	gfp	Protein	gfp	Module gfp
11	POOL 	gfp	Protein		
12	mRNA	pCONST	pCRT1: pCONST>+tetR+pTET>
13	Protein	tetR	pCRT1: pCONST>+tetR+pTET>
14	mRNA	pTET	pCRT1: pCONST>+tetR+pTET>
15	SELECTOR 	luxR	Protein	luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
16	LigandProteinComplex	AHL-luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
17	mRNA	pLUX	pBW30xlux-gfp: luxR+pLUX>+gfp
18	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
19	Protein	araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
20	LigandProteinComplex	Lara-araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
21	mRNA	pBAD	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
22	mRNA	pCONST	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
23	Protein	lacI	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
24	mRNA	pTAC	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
25	SELECTOR 	ipgC	Protein	ipgC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
26	SELECTOR 	mxiE	Protein	mxiE	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
27	ProteinComplex	ipgC-mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
28	mRNA	pipaH	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
0 13  REP 
1 20  ACT 
2 23  REP 
3 7  ACT 
5 16  ACT 
6 7  ACT 
7 8  ACT 
8 10  ACT 
9 11  ACT 
10 11  ACT 
11 4  UNKNOWN 
12 13  ACT 
13 14  REP 
14 15  ACT 
15 16  ACT 
16 17  ACT 
17 9  ACT 
18 19  ACT 
19 20  ACT 
20 21  ACT 
21 25  ACT 
22 23  ACT 
23 24  REP 
24 26  ACT 
25 27  ACT 
26 27  ACT 
27 28  ACT 
28 6  ACT 
Running time: 1.15
--------------------------------
10
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	INPUT 			
4	ANDGate 		
5	ANDGate 		
6	ANDGate 		
7	ORGate 		
8	OUTPUT 			
9	INPUT 			
0 4  UNKNOWN 
1 5  UNKNOWN 
2 5  UNKNOWN 
3 6  UNKNOWN 
4 7  UNKNOWN 
5 6  UNKNOWN 
6 7  UNKNOWN 
7 8  UNKNOWN 
9 4  UNKNOWN 
Expanded topology size: 110
COST = 5.8
39
0	INPUT 	AHL	Ligand	AHL	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
1	INPUT 	Lara	Ligand	Lara	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
2	INPUT 	IPTG	Ligand	IPTG	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
3	INPUT 	aTc	Ligand	aTc	pTET-invF: tetR+pCONST<+pTET>+invF
4	OUTPUT 	rfp	Protein	rfp	Module rfp(output)
5	INPUT 	C4HSL	Ligand	C4HSL	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
6	SELECTOR 	rfp	Protein	rfp	pexsC-rfp: pexsC>+rfp
7	SELECTOR 	rfp	Protein	rfp	psicA-rfp: psicA>+rfp
8	POOL 	rfp	Protein		
9	mRNA	pCONST	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
10	Protein	luxR	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
11	LigandProteinComplex	AHL-luxR	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
12	mRNA	pLUX	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
13	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
14	Protein	araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
15	LigandProteinComplex	Lara-araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
16	mRNA	pBAD	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
17	mRNA	pCONST	pTET-invF: tetR+pCONST<+pTET>+invF
18	Protein	tetR	pTET-invF: tetR+pCONST<+pTET>+invF
19	mRNA	pTET	pTET-invF: tetR+pCONST<+pTET>+invF
20	SELECTOR 	sicA	Protein	sicA	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
21	SELECTOR 	invF	Protein	invF	pTET-invF: tetR+pCONST<+pTET>+invF
22	ProteinComplex	sicA-invF	Module sicA-invF
23	mRNA	psicA	psicA-rfp: psicA>+rfp
24	mRNA	pCONST	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
25	Protein	rhlR	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
26	LigandProteinComplex	C4HSL-rhlR	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
27	mRNA	pRHL	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
28	SELECTOR 	exsC	Protein	exsC	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
29	SELECTOR 	exsDA	Protein	exsDA	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
30	ProteinComplex	exsC-exsDA	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
31	mRNA	pexsC	pexsC-rfp: pexsC>+rfp
32	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
33	Protein	lacI	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
34	mRNA	pTAC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
35	SELECTOR 	ipgC	Protein	ipgC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
36	SELECTOR 	mxiE	Protein	mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
37	ProteinComplex	ipgC-mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
38	mRNA	pipaH	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
0 11  ACT 
1 15  ACT 
2 33  REP 
3 18  REP 
5 26  ACT 
6 8  ACT 
7 8  ACT 
8 4  UNKNOWN 
9 10  ACT 
10 11  ACT 
11 12  ACT 
12 28  ACT 
13 14  ACT 
14 15  ACT 
15 16  ACT 
16 35  ACT 
17 18  ACT 
18 19  REP 
19 21  ACT 
20 22  ACT 
21 22  ACT 
22 23  ACT 
23 7  ACT 
24 25  ACT 
25 26  ACT 
26 27  ACT 
27 29  ACT 
28 30  ACT 
29 30  ACT 
30 31  ACT 
31 6  ACT 
32 33  ACT 
33 34  REP 
34 36  ACT 
35 37  ACT 
36 37  ACT 
37 38  ACT 
38 20  ACT 
Running time: 1257.1
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/D2_Nat_Biotech.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
10
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	INPUT 			
4	NOTGate 		
5	ANDGate 		
6	ANDGate 		
7	ANDGate 		
8	ORGate 		
9	OUTPUT 			
0 5  UNKNOWN 
1 4  UNKNOWN 
1 6  UNKNOWN 
2 6  UNKNOWN 
3 7  UNKNOWN 
4 5  UNKNOWN 
5 8  UNKNOWN 
6 7  UNKNOWN 
7 8  UNKNOWN 
8 9  UNKNOWN 
Number of possible topologies: 8748
Overtime
COST = -1
Running time: 1.50072e+06
--------------------------------
10
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	INPUT 			
4	NOTGate 		
5	ANDGate 		
6	ANDGate 		
7	ANDGate 		
8	ORGate 		
9	OUTPUT 			
0 5  UNKNOWN 
1 4  UNKNOWN 
1 6  UNKNOWN 
2 6  UNKNOWN 
3 7  UNKNOWN 
4 5  UNKNOWN 
5 8  UNKNOWN 
6 7  UNKNOWN 
7 8  UNKNOWN 
8 9  UNKNOWN 
Expanded topology size: 112
Expanded topology size: 112
COST = 8
25
0	INPUT 	AHL	Ligand	AHL	pBW30xlux-gfp: luxR+pLUX>+gfp
1	INPUT 	aTc	Ligand	aTc	pCRT2: pCONST>+tetR+pTET>+lacI+pLAC>
2	INPUT 	HSL	Ligand	HSL	Module pLAS
3	INPUT 	Lara	Ligand	Lara	Module pBAD(+Lara)
4	OUTPUT 	gfp	Protein	gfp	Module gfp(output)
5	SELECTOR 	luxR	Protein	luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
6	LigandProteinComplex	AHL-luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
7	mRNA	pLUX	pBW30xlux-gfp: luxR+pLUX>+gfp
8	SELECTOR 	araC	Protein	araC	Module araC
9	LigandProteinComplex	Lara-araC	Module pBAD(+Lara)
10	mRNA	pBAD	Module pBAD(+Lara)
11	SELECTOR 	gfp	Protein	gfp	pBW30xlux-gfp: luxR+pLUX>+gfp
12	SELECTOR 	gfp	Protein	gfp	Module gfp
13	POOL 	gfp	Protein		
14	mRNA	pCONST	pCRT2: pCONST>+tetR+pTET>+lacI+pLAC>
15	Protein	tetR	pCRT2: pCONST>+tetR+pTET>+lacI+pLAC>
16	mRNA	pTET	pCRT2: pCONST>+tetR+pTET>+lacI+pLAC>
17	SELECTOR 	lacI	Protein	lacI	pCRT2: pCONST>+tetR+pTET>+lacI+pLAC>
18	mRNA	pLAC	pCRT2: pCONST>+tetR+pTET>+lacI+pLAC>
19	mRNA	pCONST	pCRT1: pCONST>+tetR+pTET>
20	Protein	tetR	pCRT1: pCONST>+tetR+pTET>
21	mRNA	pTET	pCRT1: pCONST>+tetR+pTET>
22	SELECTOR 	lasR	Protein	lasR	Module lasR
23	LigandProteinComplex	HSL-lasR	Module pLAS
24	mRNA	pLAS	Module pLAS
0 6  ACT 
1 15  REP 
1 20  REP 
2 23  ACT 
3 9  ACT 
5 6  ACT 
6 7  ACT 
7 11  ACT 
8 9  ACT 
9 10  ACT 
10 12  ACT 
11 13  ACT 
12 13  ACT 
13 4  UNKNOWN 
14 15  ACT 
15 16  REP 
16 17  ACT 
17 18  REP 
18 5  ACT 
19 20  ACT 
20 21  REP 
21 22  ACT 
22 23  ACT 
23 24  ACT 
24 8  ACT 
Running time: 2.83
--------------------------------
10
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	INPUT 			
4	NOTGate 		
5	ANDGate 		
6	ANDGate 		
7	ANDGate 		
8	ORGate 		
9	OUTPUT 			
0 5  UNKNOWN 
1 4  UNKNOWN 
1 6  UNKNOWN 
2 6  UNKNOWN 
3 7  UNKNOWN 
4 5  UNKNOWN 
5 8  UNKNOWN 
6 7  UNKNOWN 
7 8  UNKNOWN 
8 9  UNKNOWN 
Expanded topology size: 112
COST = 5.8
39
0	INPUT 	AHL	Ligand	AHL	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
1	INPUT 	IPTG	Ligand	IPTG	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
2	INPUT 	Lara	Ligand	Lara	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
3	INPUT 	aTc	Ligand	aTc	pTET-invF: tetR+pCONST<+pTET>+invF
4	OUTPUT 	rfp	Protein	rfp	Module rfp(output)
5	SELECTOR 	rfp	Protein	rfp	pexsC-rfp: pexsC>+rfp
6	SELECTOR 	rfp	Protein	rfp	psicA-rfp: psicA>+rfp
7	POOL 	rfp	Protein		
8	mRNA	pCONST	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
9	Protein	lacI	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
10	mRNA	pTAC	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
11	SELECTOR 	mcbR	Protein	mcbR	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
12	mRNA	pMCBR	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
13	mRNA	pCONST	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
14	Protein	luxR	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
15	LigandProteinComplex	AHL-luxR	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
16	mRNA	pLUX	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
17	SELECTOR 	exsDA	Protein	exsDA	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
18	SELECTOR 	exsC	Protein	exsC	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
19	ProteinComplex	exsC-exsDA	pACPc-invF: exsDA+XXX+exsC+pLUX<+pCONST>+luxR
20	mRNA	pexsC	pexsC-rfp: pexsC>+rfp
21	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
22	Protein	lacI	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
23	mRNA	pTAC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
24	mRNA	pCONST	pTET-invF: tetR+pCONST<+pTET>+invF
25	Protein	tetR	pTET-invF: tetR+pCONST<+pTET>+invF
26	mRNA	pTET	pTET-invF: tetR+pCONST<+pTET>+invF
27	SELECTOR 	sicA	Protein	sicA	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
28	SELECTOR 	invF	Protein	invF	pTET-invF: tetR+pCONST<+pTET>+invF
29	ProteinComplex	sicA-invF	Module sicA-invF
30	mRNA	psicA	psicA-rfp: psicA>+rfp
31	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
32	Protein	araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
33	LigandProteinComplex	Lara-araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
34	mRNA	pBAD	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
35	SELECTOR 	mxiE	Protein	mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
36	SELECTOR 	ipgC	Protein	ipgC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
37	ProteinComplex	ipgC-mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
38	mRNA	pipaH	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
0 15  ACT 
1 9  REP 
1 22  REP 
2 33  ACT 
3 25  REP 
5 7  ACT 
6 7  ACT 
7 4  UNKNOWN 
8 9  ACT 
9 10  REP 
10 11  ACT 
11 12  REP 
12 17  ACT 
13 14  ACT 
14 15  ACT 
15 16  ACT 
16 18  ACT 
17 19  ACT 
18 19  ACT 
19 20  ACT 
20 5  ACT 
21 22  ACT 
22 23  REP 
23 35  ACT 
24 25  ACT 
25 26  REP 
26 28  ACT 
27 29  ACT 
28 29  ACT 
29 30  ACT 
30 6  ACT 
31 32  ACT 
32 33  ACT 
33 34  ACT 
34 36  ACT 
35 37  ACT 
36 37  ACT 
37 38  ACT 
38 27  ACT 
Running time: 2059.84
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



