++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/not-and.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
5
0	ANDGate 		
1	NOTGate 		
2	INPUT 			
3	INPUT 			
4	OUTPUT 			
0 4  UNKNOWN 
1 0  UNKNOWN 
2 1  UNKNOWN 
3 0  UNKNOWN 
39
0	INPUT 			
1	INPUT 			
2	SELECTOR 		OUTPUT 			
3	SELECTOR 		Protein		
4	LigandProteinComplex		
5	mRNA		
6	Protein		
7	mRNA		
8	mRNA		
9	Protein		
10	mRNA		
11	mRNA		
12	Protein		
13	LigandProteinComplex		
14	mRNA		
15	SELECTOR 		mRNA		
16	SELECTOR 		tRNA		
17	RNAComplex		
18	Protein		
19	mRNA		
20	SELECTOR 		Protein		
21	SELECTOR 		Protein		
22	ProteinComplex		
23	mRNA		
24	SELECTOR 		Protein		
25	Ligand		
26	SELECTOR 		Protein		
27	LigandProteinComplex		
28	mRNA		
29	SELECTOR 		Protein		
30	mRNA		
31	Protein		
32	mRNA		
33	mRNA		
34	Protein		
35	LigandProteinComplex		
36	mRNA		
37	SELECTOR 		Protein		
38	mRNA		
0 7  REP 
0 31  REP 
0 35  ACT 
1 4  ACT 
1 9  REP 
1 13  ACT 
3 4  ACT 
4 5  ACT 
5 6  ACT 
6 2  UNKNOWN 
7 3  ACT 
7 15  ACT 
7 20  ACT 
7 24  ACT 
8 9  ACT 
9 10  REP 
10 16  ACT 
10 21  ACT 
10 26  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 16  ACT 
14 21  ACT 
14 26  ACT 
15 17  ACT 
16 17  ACT 
17 18  ACT 
18 19  ACT 
19 29  ACT 
20 22  ACT 
21 22  ACT 
22 23  ACT 
23 29  ACT 
24 25  ACT 
25 27  ACT 
26 27  ACT 
27 28  ACT 
28 29  ACT 
29 2  UNKNOWN 
30 31  ACT 
31 32  REP 
32 37  ACT 
33 34  ACT 
34 35  ACT 
35 36  ACT 
36 37  ACT 
37 38  REP 
38 3  ACT 
38 15  ACT 
38 20  ACT 
38 24  ACT 
Number of parts: 102 Number of modules: 300
TOTAL 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 
No solution
5.13 seconds 	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/2-cascade.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
4
0	NOTGate 		
1	NOTGate 		
2	INPUT 			
3	OUTPUT 			
0 1  UNKNOWN 
1 3  UNKNOWN 
2 0  UNKNOWN 
15
0	INPUT 			
1	OUTPUT 			
2	mRNA		
3	mRNA		
4	Protein		
5	mRNA		
6	mRNA		
7	Protein		
8	LigandProteinComplex		
9	mRNA		
10	SELECTOR 		Protein		
11	mRNA		
12	SELECTOR 		Protein		
13	mRNA		
14	Protein		
0 2  REP 
0 4  REP 
0 8  ACT 
2 12  ACT 
3 4  ACT 
4 5  REP 
5 10  ACT 
6 7  ACT 
7 8  ACT 
8 9  ACT 
9 10  ACT 
10 11  REP 
11 12  ACT 
12 13  REP 
13 14  ACT 
14 1  UNKNOWN 
Number of parts: 102 Number of modules: 300
TOTAL COST: 1
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 
No solution
1.08 seconds 	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/3-cascade.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
5
0	NOTGate 		
1	NOTGate 		
2	NOTGate 		
3	INPUT 			
4	OUTPUT 			
0 1  UNKNOWN 
1 2  UNKNOWN 
2 4  UNKNOWN 
3 0  UNKNOWN 
17
0	INPUT 			
1	OUTPUT 			
2	mRNA		
3	SELECTOR 		Protein		
4	mRNA		
5	mRNA		
6	Protein		
7	mRNA		
8	mRNA		
9	Protein		
10	LigandProteinComplex		
11	mRNA		
12	SELECTOR 		Protein		
13	mRNA		
14	Protein		
15	mRNA		
16	Protein		
0 2  REP 
0 6  REP 
0 10  ACT 
2 3  ACT 
3 4  REP 
4 14  ACT 
5 6  ACT 
6 7  REP 
7 12  ACT 
8 9  ACT 
9 10  ACT 
10 11  ACT 
11 12  ACT 
12 13  REP 
13 3  ACT 
14 15  REP 
15 16  ACT 
16 1  UNKNOWN 
Number of parts: 102 Number of modules: 300
TOTAL 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 
No solution
1.38 seconds 	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/4-cascade.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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 
19
0	INPUT 			
1	OUTPUT 			
2	mRNA		
3	SELECTOR 		Protein		
4	mRNA		
5	Protein		
6	mRNA		
7	mRNA		
8	Protein		
9	mRNA		
10	mRNA		
11	Protein		
12	LigandProteinComplex		
13	mRNA		
14	SELECTOR 		Protein		
15	mRNA		
16	Protein		
17	mRNA		
18	Protein		
0 2  REP 
0 8  REP 
0 12  ACT 
2 3  ACT 
3 4  REP 
4 5  ACT 
5 6  REP 
6 16  ACT 
7 8  ACT 
8 9  REP 
9 14  ACT 
10 11  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 15  REP 
15 3  ACT 
16 17  REP 
17 18  ACT 
18 1  UNKNOWN 
Number of parts: 102 Number of modules: 300
TOTAL COST: 3
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 
No solution
1.64 seconds 	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/3-input-and.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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 
61
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	SELECTOR 		OUTPUT 			
4	SELECTOR 		Protein		
5	LigandProteinComplex		
6	mRNA		
7	Protein		
8	mRNA		
9	Protein		
10	mRNA		
11	mRNA		
12	Protein		
13	LigandProteinComplex		
14	mRNA		
15	SELECTOR 		Protein		
16	LigandProteinComplex		
17	mRNA		
18	mRNA		
19	Protein		
20	mRNA		
21	mRNA		
22	Protein		
23	LigandProteinComplex		
24	mRNA		
25	SELECTOR 		mRNA		
26	SELECTOR 		tRNA		
27	RNAComplex		
28	Protein		
29	mRNA		
30	SELECTOR 		Protein		
31	SELECTOR 		Protein		
32	ProteinComplex		
33	mRNA		
34	SELECTOR 		Protein		
35	Ligand		
36	SELECTOR 		Protein		
37	LigandProteinComplex		
38	mRNA		
39	SELECTOR 		Protein		
40	mRNA		
41	Protein		
42	mRNA		
43	mRNA		
44	Protein		
45	LigandProteinComplex		
46	mRNA		
47	SELECTOR 		mRNA		
48	SELECTOR 		tRNA		
49	RNAComplex		
50	Protein		
51	mRNA		
52	SELECTOR 		Protein		
53	SELECTOR 		Protein		
54	ProteinComplex		
55	mRNA		
56	SELECTOR 		Protein		
57	Ligand		
58	SELECTOR 		Protein		
59	LigandProteinComplex		
60	mRNA		
0 9  REP 
0 13  ACT 
1 16  ACT 
1 41  REP 
1 45  ACT 
2 5  ACT 
2 19  REP 
2 23  ACT 
4 5  ACT 
5 6  ACT 
6 7  ACT 
7 3  UNKNOWN 
8 9  ACT 
9 10  REP 
10 15  ACT 
10 47  ACT 
10 52  ACT 
10 56  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 15  ACT 
14 47  ACT 
14 52  ACT 
14 56  ACT 
15 16  ACT 
16 17  ACT 
17 4  ACT 
17 25  ACT 
17 30  ACT 
17 34  ACT 
18 19  ACT 
19 20  REP 
20 26  ACT 
20 31  ACT 
20 36  ACT 
21 22  ACT 
22 23  ACT 
23 24  ACT 
24 26  ACT 
24 31  ACT 
24 36  ACT 
25 27  ACT 
26 27  ACT 
27 28  ACT 
28 29  ACT 
29 39  ACT 
30 32  ACT 
31 32  ACT 
32 33  ACT 
33 39  ACT 
34 35  ACT 
35 37  ACT 
36 37  ACT 
37 38  ACT 
38 39  ACT 
39 3  UNKNOWN 
40 41  ACT 
41 42  REP 
42 48  ACT 
42 53  ACT 
42 58  ACT 
43 44  ACT 
44 45  ACT 
45 46  ACT 
46 48  ACT 
46 53  ACT 
46 58  ACT 
47 49  ACT 
48 49  ACT 
49 50  ACT 
50 51  ACT 
51 4  ACT 
51 25  ACT 
51 30  ACT 
51 34  ACT 
52 54  ACT 
53 54  ACT 
54 55  ACT 
55 4  ACT 
55 25  ACT 
55 30  ACT 
55 34  ACT 
56 57  ACT 
57 59  ACT 
58 59  ACT 
59 60  ACT 
60 4  ACT 
60 25  ACT 
60 30  ACT 
60 34  ACT 
Number of parts: 102 Number of modules: 300
TOTAL COST: 3
19
0	INPUT 	Lara	Ligand	Lara	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
1	INPUT 	IPTG	Ligand	IPTG	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
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: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
9	Protein	araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
10	LigandProteinComplex	Lara-araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
11	mRNA	pBAD	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
12	mRNA	pCONST	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
13	Protein	lacI	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
14	mRNA	pTAC	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
15	SELECTOR 	ipgC	Protein	ipgC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
16	SELECTOR 	mxiE	Protein	mxiE	pXCPi-sicA: TTT+lacI+pCONST<+pTAC>+mxiE
17	ProteinComplex	ipgC-mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
18	mRNA	pipaH	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>
0 10  ACT 
1 13  REP 
2 5  ACT 
4 5  ACT 
5 6  ACT 
6 7  ACT 
7 3  UNKNOWN 
8 9  ACT 
9 10  ACT 
10 11  ACT 
11 15  ACT 
12 13  ACT 
13 14  REP 
14 16  ACT 
15 17  ACT 
16 17  ACT 
17 18  ACT 
18 4  ACT 
No solution
19.05 seconds 	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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 
72
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	OUTPUT 			
4	mRNA		
5	SELECTOR 		Protein		
6	LigandProteinComplex		
7	mRNA		
8	SELECTOR 		Protein		
9	SELECTOR 		Protein		
10	POOL 		Protein		
11	mRNA		
12	Protein		
13	mRNA		
14	mRNA		
15	Protein		
16	LigandProteinComplex		
17	mRNA		
18	SELECTOR 		Protein		
19	mRNA		
20	mRNA		
21	Protein		
22	mRNA		
23	mRNA		
24	Protein		
25	LigandProteinComplex		
26	mRNA		
27	SELECTOR 		mRNA		
28	SELECTOR 		tRNA		
29	RNAComplex		
30	Protein		
31	mRNA		
32	SELECTOR 		Protein		
33	SELECTOR 		Protein		
34	ProteinComplex		
35	mRNA		
36	SELECTOR 		Protein		
37	Ligand		
38	SELECTOR 		Protein		
39	LigandProteinComplex		
40	mRNA		
41	mRNA		
42	Protein		
43	mRNA		
44	mRNA		
45	Protein		
46	LigandProteinComplex		
47	mRNA		
48	SELECTOR 		Protein		
49	LigandProteinComplex		
50	mRNA		
51	mRNA		
52	Protein		
53	mRNA		
54	mRNA		
55	Protein		
56	LigandProteinComplex		
57	mRNA		
58	SELECTOR 		mRNA		
59	SELECTOR 		tRNA		
60	RNAComplex		
61	Protein		
62	mRNA		
63	SELECTOR 		Protein		
64	SELECTOR 		Protein		
65	ProteinComplex		
66	mRNA		
67	SELECTOR 		Protein		
68	Ligand		
69	SELECTOR 		Protein		
70	LigandProteinComplex		
71	mRNA		
0 6  ACT 
0 21  REP 
0 25  ACT 
1 4  REP 
1 12  REP 
1 16  ACT 
1 42  REP 
1 46  ACT 
2 49  ACT 
2 52  REP 
2 56  ACT 
4 5  ACT 
4 27  ACT 
4 32  ACT 
4 36  ACT 
5 6  ACT 
6 7  ACT 
7 8  ACT 
8 10  ACT 
9 10  ACT 
10 3  UNKNOWN 
11 12  ACT 
12 13  REP 
13 18  ACT 
14 15  ACT 
15 16  ACT 
16 17  ACT 
17 18  ACT 
18 19  REP 
19 5  ACT 
19 27  ACT 
19 32  ACT 
19 36  ACT 
20 21  ACT 
21 22  REP 
22 28  ACT 
22 33  ACT 
22 38  ACT 
23 24  ACT 
24 25  ACT 
25 26  ACT 
26 28  ACT 
26 33  ACT 
26 38  ACT 
27 29  ACT 
28 29  ACT 
29 30  ACT 
30 31  ACT 
31 8  ACT 
32 34  ACT 
33 34  ACT 
34 35  ACT 
35 8  ACT 
36 37  ACT 
37 39  ACT 
38 39  ACT 
39 40  ACT 
40 8  ACT 
41 42  ACT 
42 43  REP 
43 48  ACT 
43 58  ACT 
43 63  ACT 
43 67  ACT 
44 45  ACT 
45 46  ACT 
46 47  ACT 
47 48  ACT 
47 58  ACT 
47 63  ACT 
47 67  ACT 
48 49  ACT 
49 50  ACT 
50 9  ACT 
51 52  ACT 
52 53  REP 
53 59  ACT 
53 64  ACT 
53 69  ACT 
54 55  ACT 
55 56  ACT 
56 57  ACT 
57 59  ACT 
57 64  ACT 
57 69  ACT 
58 60  ACT 
59 60  ACT 
60 61  ACT 
61 62  ACT 
62 9  ACT 
63 65  ACT 
64 65  ACT 
65 66  ACT 
66 9  ACT 
67 68  ACT 
68 70  ACT 
69 70  ACT 
70 71  ACT 
71 9  ACT 
Number of parts: 102 Number of modules: 300
TOTAL COST: 5
21
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	Module Lara-araC
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	pBW20xara-gfp: pBAD>+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 Lara-araC
20	mRNA	pBAD	pBW20xara-gfp: pBAD>+gfp
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 
No solution
56.33 seconds 	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/3-input-not-and.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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 
60
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	OUTPUT 			
4	mRNA		
5	mRNA		
6	Protein		
7	mRNA		
8	mRNA		
9	Protein		
10	LigandProteinComplex		
11	mRNA		
12	SELECTOR 		Protein		
13	LigandProteinComplex		
14	mRNA		
15	SELECTOR 		mRNA		
16	SELECTOR 		tRNA		
17	RNAComplex		
18	Protein		
19	mRNA		
20	SELECTOR 		Protein		
21	SELECTOR 		Protein		
22	ProteinComplex		
23	mRNA		
24	SELECTOR 		Protein		
25	Ligand		
26	SELECTOR 		Protein		
27	LigandProteinComplex		
28	mRNA		
29	SELECTOR 		Protein		
30	mRNA		
31	Protein		
32	mRNA		
33	mRNA		
34	Protein		
35	LigandProteinComplex		
36	mRNA		
37	SELECTOR 		Protein		
38	mRNA		
39	mRNA		
40	Protein		
41	mRNA		
42	mRNA		
43	Protein		
44	LigandProteinComplex		
45	mRNA		
46	SELECTOR 		mRNA		
47	SELECTOR 		tRNA		
48	RNAComplex		
49	Protein		
50	mRNA		
51	SELECTOR 		Protein		
52	SELECTOR 		Protein		
53	ProteinComplex		
54	mRNA		
55	SELECTOR 		Protein		
56	Ligand		
57	SELECTOR 		Protein		
58	LigandProteinComplex		
59	mRNA		
0 6  REP 
0 10  ACT 
1 13  ACT 
1 40  REP 
1 44  ACT 
2 4  REP 
2 31  REP 
2 35  ACT 
4 15  ACT 
4 20  ACT 
4 24  ACT 
5 6  ACT 
6 7  REP 
7 12  ACT 
7 46  ACT 
7 51  ACT 
7 55  ACT 
8 9  ACT 
9 10  ACT 
10 11  ACT 
11 12  ACT 
11 46  ACT 
11 51  ACT 
11 55  ACT 
12 13  ACT 
13 14  ACT 
14 16  ACT 
14 21  ACT 
14 26  ACT 
15 17  ACT 
16 17  ACT 
17 18  ACT 
18 19  ACT 
19 29  ACT 
20 22  ACT 
21 22  ACT 
22 23  ACT 
23 29  ACT 
24 25  ACT 
25 27  ACT 
26 27  ACT 
27 28  ACT 
28 29  ACT 
29 3  UNKNOWN 
30 31  ACT 
31 32  REP 
32 37  ACT 
33 34  ACT 
34 35  ACT 
35 36  ACT 
36 37  ACT 
37 38  REP 
38 15  ACT 
38 20  ACT 
38 24  ACT 
39 40  ACT 
40 41  REP 
41 47  ACT 
41 52  ACT 
41 57  ACT 
42 43  ACT 
43 44  ACT 
44 45  ACT 
45 47  ACT 
45 52  ACT 
45 57  ACT 
46 48  ACT 
47 48  ACT 
48 49  ACT 
49 50  ACT 
50 16  ACT 
50 21  ACT 
50 26  ACT 
51 53  ACT 
52 53  ACT 
53 54  ACT 
54 16  ACT 
54 21  ACT 
54 26  ACT 
55 56  ACT 
56 58  ACT 
57 58  ACT 
58 59  ACT 
59 16  ACT 
59 21  ACT 
59 26  ACT 
Number of parts: 102 Number of modules: 300
TOTAL COST: 4
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 
No solution
47.96 seconds 	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/band-detector.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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 
26
0	INPUT 			
1	OUTPUT 			
2	mRNA		
3	Protein		
4	mRNA		
5	mRNA		
6	Protein		
7	LigandProteinComplex		
8	mRNA		
9	mRNA		
10	mRNA		
11	Protein		
12	mRNA		
13	mRNA		
14	Protein		
15	LigandProteinComplex		
16	mRNA		
17	SELECTOR 		Protein		
18	mRNA		
19	SELECTOR 		Protein		
20	SELECTOR 		Protein		
21	POOL 		Protein		
22	mRNA		
23	Protein		
24	mRNA		
25	Protein		
0 3  REP 
0 7  ACT 
0 9  REP 
0 11  REP 
0 15  ACT 
2 3  ACT 
3 4  REP 
4 19  ACT 
5 6  ACT 
6 7  ACT 
7 8  ACT 
8 19  ACT 
9 20  ACT 
10 11  ACT 
11 12  REP 
12 17  ACT 
13 14  ACT 
14 15  ACT 
15 16  ACT 
16 17  ACT 
17 18  REP 
18 20  ACT 
19 21  ACT 
20 21  ACT 
21 22  ACT 
22 23  ACT 
23 24  REP 
24 25  ACT 
25 1  UNKNOWN 
Number of parts: 102 Number of modules: 300
TOTAL 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 
No solution
2.71 seconds 	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/feed-forward.xml
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
4
0	ANDGate 		
1	YESGate 		
2	OUTPUT 			
3	INPUT 			
0 2  UNKNOWN 
1 0  UNKNOWN 
3 0  UNKNOWN 
3 1  UNKNOWN 
35
0	SELECTOR 		OUTPUT 			
1	INPUT 			
2	SELECTOR 		Protein		
3	LigandProteinComplex		
4	mRNA		
5	Protein		
6	mRNA		
7	Protein		
8	mRNA		
9	mRNA		
10	Protein		
11	LigandProteinComplex		
12	mRNA		
13	mRNA		
14	Protein		
15	mRNA		
16	mRNA		
17	Protein		
18	LigandProteinComplex		
19	mRNA		
20	SELECTOR 		mRNA		
21	SELECTOR 		tRNA		
22	RNAComplex		
23	Protein		
24	mRNA		
25	SELECTOR 		Protein		
26	SELECTOR 		Protein		
27	ProteinComplex		
28	mRNA		
29	SELECTOR 		Protein		
30	Ligand		
31	SELECTOR 		Protein		
32	LigandProteinComplex		
33	mRNA		
34	SELECTOR 		Protein		
1 3  ACT 
1 7  REP 
1 11  ACT 
1 14  REP 
1 18  ACT 
2 3  ACT 
3 4  ACT 
4 5  ACT 
5 0  UNKNOWN 
6 7  ACT 
7 8  REP 
8 2  ACT 
8 20  ACT 
8 25  ACT 
8 29  ACT 
9 10  ACT 
10 11  ACT 
11 12  ACT 
12 2  ACT 
12 20  ACT 
12 25  ACT 
12 29  ACT 
13 14  ACT 
14 15  REP 
15 21  ACT 
15 26  ACT 
15 31  ACT 
16 17  ACT 
17 18  ACT 
18 19  ACT 
19 21  ACT 
19 26  ACT 
19 31  ACT 
20 22  ACT 
21 22  ACT 
22 23  ACT 
23 24  ACT 
24 34  ACT 
25 27  ACT 
26 27  ACT 
27 28  ACT 
28 34  ACT 
29 30  ACT 
30 32  ACT 
31 32  ACT 
32 33  ACT 
33 34  ACT 
34 0  UNKNOWN 
Number of parts: 102 Number of modules: 300
TOTAL COST: 3
15
0	SELECTOR 	gfp	Protein	gfp	Module gfp(output)
1	INPUT 	Lara	Ligand	Lara	pTSara-C: araC+pCONST<+pBAD>+T7-C
2	mRNA	pCONST	pTSara-C: araC+pCONST<+pBAD>+T7-C
3	Protein	araC	pTSara-C: araC+pCONST<+pBAD>+T7-C
4	LigandProteinComplex	Lara-araC	pTSara-C: araC+pCONST<+pBAD>+T7-C
5	mRNA	pBAD	pTSara-C: araC+pCONST<+pBAD>+T7-C
6	mRNA	pCONST	pTSara-N: araC+pCONST<+pBAD>+T7-N
7	Protein	araC	pTSara-N: araC+pCONST<+pBAD>+T7-N
8	LigandProteinComplex	Lara-araC	pTSara-N: araC+pCONST<+pBAD>+T7-N
9	mRNA	pBAD	pTSara-N: araC+pCONST<+pBAD>+T7-N
10	SELECTOR 	T7-C	Protein	T7-C	pTSara-C: araC+pCONST<+pBAD>+T7-C
11	SELECTOR 	T7-N	Protein	T7-N	pTSara-N: araC+pCONST<+pBAD>+T7-N
12	ProteinComplex	T7-C-T7-N	Module T7-C-T7-N
13	mRNA	pT7	pET:NNNN:GFP: gfp+pT7<
14	SELECTOR 	gfp	Protein	gfp	pET:NNNN:GFP: gfp+pT7<
1 4  ACT 
1 8  ACT 
2 3  ACT 
3 4  ACT 
4 5  ACT 
5 10  ACT 
6 7  ACT 
7 8  ACT 
8 9  ACT 
9 11  ACT 
10 12  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 0  UNKNOWN 
No solution
4.97 seconds 	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/D1_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 
97
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	INPUT 			
4	OUTPUT 			
5	mRNA		
6	SELECTOR 		Protein		
7	LigandProteinComplex		
8	mRNA		
9	SELECTOR 		Protein		
10	LigandProteinComplex		
11	mRNA		
12	SELECTOR 		Protein		
13	SELECTOR 		Protein		
14	POOL 		Protein		
15	mRNA		
16	Protein		
17	mRNA		
18	mRNA		
19	Protein		
20	LigandProteinComplex		
21	mRNA		
22	SELECTOR 		Protein		
23	mRNA		
24	mRNA		
25	Protein		
26	mRNA		
27	mRNA		
28	Protein		
29	LigandProteinComplex		
30	mRNA		
31	SELECTOR 		mRNA		
32	SELECTOR 		tRNA		
33	RNAComplex		
34	Protein		
35	mRNA		
36	SELECTOR 		Protein		
37	SELECTOR 		Protein		
38	ProteinComplex		
39	mRNA		
40	SELECTOR 		Protein		
41	Ligand		
42	SELECTOR 		Protein		
43	LigandProteinComplex		
44	mRNA		
45	mRNA		
46	Protein		
47	mRNA		
48	mRNA		
49	Protein		
50	LigandProteinComplex		
51	mRNA		
52	SELECTOR 		Protein		
53	LigandProteinComplex		
54	mRNA		
55	mRNA		
56	Protein		
57	mRNA		
58	mRNA		
59	Protein		
60	LigandProteinComplex		
61	mRNA		
62	SELECTOR 		mRNA		
63	SELECTOR 		tRNA		
64	RNAComplex		
65	Protein		
66	mRNA		
67	SELECTOR 		Protein		
68	SELECTOR 		Protein		
69	ProteinComplex		
70	mRNA		
71	SELECTOR 		Protein		
72	Ligand		
73	SELECTOR 		Protein		
74	LigandProteinComplex		
75	mRNA		
76	mRNA		
77	Protein		
78	mRNA		
79	mRNA		
80	Protein		
81	LigandProteinComplex		
82	mRNA		
83	SELECTOR 		mRNA		
84	SELECTOR 		tRNA		
85	RNAComplex		
86	Protein		
87	mRNA		
88	SELECTOR 		Protein		
89	SELECTOR 		Protein		
90	ProteinComplex		
91	mRNA		
92	SELECTOR 		Protein		
93	Ligand		
94	SELECTOR 		Protein		
95	LigandProteinComplex		
96	mRNA		
0 7  ACT 
0 25  REP 
0 29  ACT 
1 5  REP 
1 16  REP 
1 20  ACT 
1 46  REP 
1 50  ACT 
2 53  ACT 
2 77  REP 
2 81  ACT 
3 10  ACT 
3 56  REP 
3 60  ACT 
5 6  ACT 
5 31  ACT 
5 36  ACT 
5 40  ACT 
6 7  ACT 
7 8  ACT 
8 12  ACT 
9 10  ACT 
10 11  ACT 
11 13  ACT 
12 14  ACT 
13 14  ACT 
14 4  UNKNOWN 
15 16  ACT 
16 17  REP 
17 22  ACT 
18 19  ACT 
19 20  ACT 
20 21  ACT 
21 22  ACT 
22 23  REP 
23 6  ACT 
23 31  ACT 
23 36  ACT 
23 40  ACT 
24 25  ACT 
25 26  REP 
26 32  ACT 
26 37  ACT 
26 42  ACT 
27 28  ACT 
28 29  ACT 
29 30  ACT 
30 32  ACT 
30 37  ACT 
30 42  ACT 
31 33  ACT 
32 33  ACT 
33 34  ACT 
34 35  ACT 
35 12  ACT 
36 38  ACT 
37 38  ACT 
38 39  ACT 
39 12  ACT 
40 41  ACT 
41 43  ACT 
42 43  ACT 
43 44  ACT 
44 12  ACT 
45 46  ACT 
46 47  REP 
47 52  ACT 
47 83  ACT 
47 88  ACT 
47 92  ACT 
48 49  ACT 
49 50  ACT 
50 51  ACT 
51 52  ACT 
51 83  ACT 
51 88  ACT 
51 92  ACT 
52 53  ACT 
53 54  ACT 
54 9  ACT 
54 62  ACT 
54 67  ACT 
54 71  ACT 
55 56  ACT 
56 57  REP 
57 63  ACT 
57 68  ACT 
57 73  ACT 
58 59  ACT 
59 60  ACT 
60 61  ACT 
61 63  ACT 
61 68  ACT 
61 73  ACT 
62 64  ACT 
63 64  ACT 
64 65  ACT 
65 66  ACT 
66 13  ACT 
67 69  ACT 
68 69  ACT 
69 70  ACT 
70 13  ACT 
71 72  ACT 
72 74  ACT 
73 74  ACT 
74 75  ACT 
75 13  ACT 
76 77  ACT 
77 78  REP 
78 84  ACT 
78 89  ACT 
78 94  ACT 
79 80  ACT 
80 81  ACT 
81 82  ACT 
82 84  ACT 
82 89  ACT 
82 94  ACT 
83 85  ACT 
84 85  ACT 
85 86  ACT 
86 87  ACT 
87 9  ACT 
87 62  ACT 
87 67  ACT 
87 71  ACT 
88 90  ACT 
89 90  ACT 
90 91  ACT 
91 9  ACT 
91 62  ACT 
91 67  ACT 
91 71  ACT 
92 93  ACT 
93 95  ACT 
94 95  ACT 
95 96  ACT 
96 9  ACT 
96 62  ACT 
96 67  ACT 
96 71  ACT 
Number of parts: 102 Number of modules: 300
TOTAL COST: 6
34
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	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 	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 	gfp	Protein	gfp	pBW30xlux-gfp: luxR+pLUX>+gfp
9	SELECTOR 	gfp	Protein	gfp	Module gfp
10	POOL 	gfp	Protein		
11	mRNA	pCONST	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
12	Protein	lacI	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
13	mRNA	pTAC	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
14	SELECTOR 	mcbR	Protein	mcbR	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
15	mRNA	pMCBR	pTACsym-McbR-pMcbR-yfp: lacI+pCONST<+pTAC>+mcbR+pMCBR>
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	mRNA	pCONST	pTET-invF: tetR+pCONST<+pTET>+invF
20	Protein	tetR	pTET-invF: tetR+pCONST<+pTET>+invF
21	mRNA	pTET	pTET-invF: tetR+pCONST<+pTET>+invF
22	SELECTOR 	sicA	Protein	sicA	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
23	SELECTOR 	invF	Protein	invF	pTET-invF: tetR+pCONST<+pTET>+invF
24	ProteinComplex	sicA-invF	Module psicA
25	mRNA	psicA	Module psicA
26	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
27	Protein	araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
28	LigandProteinComplex	Lara-araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
29	mRNA	pBAD	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
30	SELECTOR 	mxiE	Protein	mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
31	SELECTOR 	ipgC	Protein	ipgC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
32	ProteinComplex	ipgC-mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
33	mRNA	pipaH	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
0 6  ACT 
1 12  REP 
1 17  REP 
2 28  ACT 
3 20  REP 
5 6  ACT 
6 7  ACT 
7 8  ACT 
8 10  ACT 
9 10  ACT 
10 4  UNKNOWN 
11 12  ACT 
12 13  REP 
13 14  ACT 
14 15  REP 
15 5  ACT 
16 17  ACT 
17 18  REP 
18 30  ACT 
19 20  ACT 
20 21  REP 
21 23  ACT 
22 24  ACT 
23 24  ACT 
24 25  ACT 
25 9  ACT 
26 27  ACT 
27 28  ACT 
28 29  ACT 
29 31  ACT 
30 32  ACT 
31 32  ACT 
32 33  ACT 
33 22  ACT 
No solution
667.71 seconds 	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Benchmarks/Bioinformatics/D2_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 
95
0	INPUT 			
1	INPUT 			
2	INPUT 			
3	INPUT 			
4	OUTPUT 			
5	INPUT 			
6	SELECTOR 		Protein		
7	LigandProteinComplex		
8	mRNA		
9	SELECTOR 		Protein		
10	SELECTOR 		Protein		
11	POOL 		Protein		
12	mRNA		
13	Protein		
14	mRNA		
15	mRNA		
16	Protein		
17	LigandProteinComplex		
18	mRNA		
19	SELECTOR 		Protein		
20	LigandProteinComplex		
21	mRNA		
22	mRNA		
23	Protein		
24	mRNA		
25	mRNA		
26	Protein		
27	LigandProteinComplex		
28	mRNA		
29	SELECTOR 		Protein		
30	LigandProteinComplex		
31	mRNA		
32	mRNA		
33	Protein		
34	mRNA		
35	mRNA		
36	Protein		
37	LigandProteinComplex		
38	mRNA		
39	SELECTOR 		mRNA		
40	SELECTOR 		tRNA		
41	RNAComplex		
42	Protein		
43	mRNA		
44	SELECTOR 		Protein		
45	SELECTOR 		Protein		
46	ProteinComplex		
47	mRNA		
48	SELECTOR 		Protein		
49	Ligand		
50	SELECTOR 		Protein		
51	LigandProteinComplex		
52	mRNA		
53	mRNA		
54	Protein		
55	mRNA		
56	mRNA		
57	Protein		
58	LigandProteinComplex		
59	mRNA		
60	SELECTOR 		mRNA		
61	SELECTOR 		tRNA		
62	RNAComplex		
63	Protein		
64	mRNA		
65	SELECTOR 		Protein		
66	SELECTOR 		Protein		
67	ProteinComplex		
68	mRNA		
69	SELECTOR 		Protein		
70	Ligand		
71	SELECTOR 		Protein		
72	LigandProteinComplex		
73	mRNA		
74	mRNA		
75	Protein		
76	mRNA		
77	mRNA		
78	Protein		
79	LigandProteinComplex		
80	mRNA		
81	SELECTOR 		mRNA		
82	SELECTOR 		tRNA		
83	RNAComplex		
84	Protein		
85	mRNA		
86	SELECTOR 		Protein		
87	SELECTOR 		Protein		
88	ProteinComplex		
89	mRNA		
90	SELECTOR 		Protein		
91	Ligand		
92	SELECTOR 		Protein		
93	LigandProteinComplex		
94	mRNA		
0 13  REP 
0 17  ACT 
1 23  REP 
1 27  ACT 
2 30  ACT 
2 75  REP 
2 79  ACT 
3 7  ACT 
3 33  REP 
3 37  ACT 
5 20  ACT 
5 54  REP 
5 58  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 19  ACT 
14 60  ACT 
14 65  ACT 
14 69  ACT 
15 16  ACT 
16 17  ACT 
17 18  ACT 
18 19  ACT 
18 60  ACT 
18 65  ACT 
18 69  ACT 
19 20  ACT 
20 21  ACT 
21 9  ACT 
22 23  ACT 
23 24  REP 
24 29  ACT 
24 81  ACT 
24 86  ACT 
24 90  ACT 
25 26  ACT 
26 27  ACT 
27 28  ACT 
28 29  ACT 
28 81  ACT 
28 86  ACT 
28 90  ACT 
29 30  ACT 
30 31  ACT 
31 6  ACT 
31 39  ACT 
31 44  ACT 
31 48  ACT 
32 33  ACT 
33 34  REP 
34 40  ACT 
34 45  ACT 
34 50  ACT 
35 36  ACT 
36 37  ACT 
37 38  ACT 
38 40  ACT 
38 45  ACT 
38 50  ACT 
39 41  ACT 
40 41  ACT 
41 42  ACT 
42 43  ACT 
43 10  ACT 
44 46  ACT 
45 46  ACT 
46 47  ACT 
47 10  ACT 
48 49  ACT 
49 51  ACT 
50 51  ACT 
51 52  ACT 
52 10  ACT 
53 54  ACT 
54 55  REP 
55 61  ACT 
55 66  ACT 
55 71  ACT 
56 57  ACT 
57 58  ACT 
58 59  ACT 
59 61  ACT 
59 66  ACT 
59 71  ACT 
60 62  ACT 
61 62  ACT 
62 63  ACT 
63 64  ACT 
64 9  ACT 
65 67  ACT 
66 67  ACT 
67 68  ACT 
68 9  ACT 
69 70  ACT 
70 72  ACT 
71 72  ACT 
72 73  ACT 
73 9  ACT 
74 75  ACT 
75 76  REP 
76 82  ACT 
76 87  ACT 
76 92  ACT 
77 78  ACT 
78 79  ACT 
79 80  ACT 
80 82  ACT 
80 87  ACT 
80 92  ACT 
81 83  ACT 
82 83  ACT 
83 84  ACT 
84 85  ACT 
85 6  ACT 
85 39  ACT 
85 44  ACT 
85 48  ACT 
86 88  ACT 
87 88  ACT 
88 89  ACT 
89 6  ACT 
89 39  ACT 
89 44  ACT 
89 48  ACT 
90 91  ACT 
91 93  ACT 
92 93  ACT 
93 94  ACT 
94 6  ACT 
94 39  ACT 
94 44  ACT 
94 48  ACT 
Number of parts: 102 Number of modules: 300
TOTAL COST: 6
34
0	INPUT 	C4HSL	Ligand	C4HSL	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
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 	gfp	Protein	gfp	Module gfp(output)
5	INPUT 	AHL	Ligand	AHL	pBW30xlux-gfp: luxR+pLUX>+gfp
6	SELECTOR 	gfp	Protein	gfp	pBW30xlux-gfp: luxR+pLUX>+gfp
7	SELECTOR 	gfp	Protein	gfp	Module gfp
8	POOL 	gfp	Protein		
9	mRNA	pCONST	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
10	Protein	rhlR	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
11	LigandProteinComplex	C4HSL-rhlR	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
12	mRNA	pRHL	pFNK-202-eyfp-qscxxx: rhlR+pCONST<+pRHL>
13	SELECTOR 	luxR	Protein	luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
14	LigandProteinComplex	AHL-luxR	pBW30xlux-gfp: luxR+pLUX>+gfp
15	mRNA	pLUX	pBW30xlux-gfp: luxR+pLUX>+gfp
16	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
17	Protein	araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
18	LigandProteinComplex	Lara-araC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
19	mRNA	pBAD	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
20	mRNA	pCONST	pTET-invF: tetR+pCONST<+pTET>+invF
21	Protein	tetR	pTET-invF: tetR+pCONST<+pTET>+invF
22	mRNA	pTET	pTET-invF: tetR+pCONST<+pTET>+invF
23	SELECTOR 	sicA	Protein	sicA	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
24	SELECTOR 	invF	Protein	invF	pTET-invF: tetR+pCONST<+pTET>+invF
25	ProteinComplex	sicA-invF	Module psicA
26	mRNA	psicA	Module psicA
27	mRNA	pCONST	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
28	Protein	lacI	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
29	mRNA	pTAC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
30	SELECTOR 	ipgC	Protein	ipgC	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
31	SELECTOR 	mxiE	Protein	mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
32	ProteinComplex	ipgC-mxiE	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
33	mRNA	pipaH	pXCPi-sicA: ipgC+pBAD<+pCONST>+araC+XXX+pipaH>+sicA+TTT+lacI+pCONST<+pTAC>+mxiE
0 11  ACT 
1 18  ACT 
2 28  REP 
3 21  REP 
5 14  ACT 
6 8  ACT 
7 8  ACT 
8 4  UNKNOWN 
9 10  ACT 
10 11  ACT 
11 12  ACT 
12 13  ACT 
13 14  ACT 
14 15  ACT 
15 6  ACT 
16 17  ACT 
17 18  ACT 
18 19  ACT 
19 30  ACT 
20 21  ACT 
21 22  REP 
22 24  ACT 
23 25  ACT 
24 25  ACT 
25 26  ACT 
26 7  ACT 
27 28  ACT 
28 29  REP 
29 31  ACT 
30 32  ACT 
31 32  ACT 
32 33  ACT 
33 23  ACT 
No solution
397.42 seconds 	
FINISH!
