recombinase2input5state.eug

// Part properties

Property SEQUENCE(txt);

// Part types

PartType Promoter(SEQUENCE);

PartType RecombinaseRecognitionSite(SEQUENCE);

PartType CDS(SEQUENCE);

PartType Terminator(SEQUENCE);

// Parts

// Coding sequences

CDS GFPmut3b("atgagtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgatctctacaaataa");

CDS mTagBFP("atgagcgagctgattaaggagaacatgcacatgaagctgtacatggagggcaccgtggacaaccatcacttcaagtgcacatccgagggcgaaggcaagccctacgagggcacccagaccatgagaatcaaggtggtcgagggcggccctctccccttcgccttcgacatcctggctactagcttcctctacggcagcaagaccttcatcaaccacacccagggcatccccgacttcttcaagcagtccttccctgagggcttcacatgggagagagtcaccacatacgaagacgggggcgtgctgaccgctacccaggacaccagcctccaggacggctgcctcatctacaacgtcaagatcagaggggtgaacttcacatccaacggccctgtgatgcagaagaaaacactcggctgggaggccttcaccgagacgctgtaccccgctgacggcggcctggaaggcagaaacgacatggccctgaagctcgtgggcgggagccatctgatcgcaaacatcaagaccacatatagatccaagaaacccgctaagaacctcaagatgcctggcgtctactatgtggactacagactggaaagaatcaaggaggccaacaacgagacctacgtcgagcagcacgaggtggcagtggccagatactgcgacctccctagcaaactggggcactaa");

CDS mRFP("atgtccagattagataaaagtaaagttgcgagctctgaagacgttatcaaagagttcatgcgtttcaaagttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaaggtgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactgaaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgtccccgcagttccagtacggttccaaagcttacgttaaacacccggctgacatcccggactacctgaaactgtccttcccggaaggtttcaaatgggaacgtgttatgaacttcgaagacggtggtgttgttaccgttacccaggactcctccctgcaagacggtgagttcatctacaaagttaaactgcgtggtaccaacttcccgtccgacggtccggttatgcagaaaaaaaccatgggttgggaagcttccaccgaacgtatgtacccggaagacggtgctctgaaaggtgaaatcaaaatgcgtctaaaactgaaagacggtggtcactacgacgctgaagttaaaaccacctacatggctaaaaaaccggttcagctgccgggtgcttacaaaaccgacatcaaactggacatcacctcccacaacgaagactacaccatcgttgaacagtacgaacgtgctgaaggtcgtcactccaccggtgcttaataa");

// Promoters

Promoter proD("cacagctaacaccacgtcgtccctatctgctgccctaggtctatgagtggttgctggataactttacgggcatgcataaggctcgtataatatattcagggagaccacaacggtttccctctacaaataattttgtttaacttt");

Promoter proNR3("taacaccgtgcgtttgactattttacctctggcggtgataatggttgcatatagtgaacaaggattaa");

Promoter proNR4("ccgtgacggatcctggtgcaaaacctttcgcggtatggcatgatagcgccataggttaaaagccagacat");

// Recombinase recognition sites

RecombinaseRecognitionSite BxbIB_CA("cggccggcttgtcgacgacggcgcactccgtcgtcaggatcatccgggc");

RecombinaseRecognitionSite BxbIP_CA("gtcgtggtttgtctggtcaaccaccgcgcactcagtggtgtacggtacaaaccccgac");

RecombinaseRecognitionSite BxbIB_GT("cggccggcttgtcgacgacggcggtctccgtcgtcaggatcatccgggc");

RecombinaseRecognitionSite BxbIP_GT("gtcgtggtttgtctggtcaaccaccgcggtctcagtggtgtacggtacaaaccccgac");

RecombinaseRecognitionSite TP901B_AG("atgccaacacaattaacatcagaatcaaggtaaatgctttttgctttttttgc");

RecombinaseRecognitionSite TP901P_AG("gcgagtttttatttcgtttattagaattaaggtaactaaaaaactccttt");

RecombinaseRecognitionSite TP901B_TC("atgccaacacaattaacatctcaatcaaggtaaatgctttttgctttttttgc");

RecombinaseRecognitionSite TP901P_TC("gcgagtttttatttcgtttatttcaattaaggtaactaaaaaactccttt");

RecombinaseRecognitionSite A118B_AA("aacttttcggatcaagctatgaaaaacgcaaagagggaactaaacactt");

RecombinaseRecognitionSite A118P_AA("ttagttcctcgttttctctcgttaaaagaagaagaaacgagaaactaaa");

RecombinaseRecognitionSite A118B_GG("aacttttcggatcaagctatgaaggacgcaaagagggaactaaacactt");

RecombinaseRecognitionSite A118P_GG("ttagttcctcgttttctctcgttggaagaagaagaaacgagaaactaaa");

// Terminators

Terminator B0062_R("cagataaaaaaaatccttagctttcgctaaggatgatttct");

Terminator ECK120010850("agttaaccaaaaaggggggattttatctcccctttaatttttcct");

Terminator ECK120010825("atctcctttcacggcccattcctcatggatgggccgtttatttccc");

Terminator ECK120030221("cccgcacttaacccgcttcggcgggtttttgttttt");

Terminator ECK120010799("gttatgagtcaggaaaaaaggcgacagagtaatctgtcgccttttttctttgcttgcttt");

Terminator ECK120010818("gtcagtttcacctgttttacgtaaaaacccgcttcggcgggtttttacttttgg");

Terminator ECK120033737("ggaaacacagaaaaaagcccgcacctgacagtgcgggctttttttttcgaccaaagg");

Terminator B0010("ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc");

Terminator ECK120029600("ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa");

Terminator ECK120033736("aacgcatgagaaagcccccggaagatcaccttccgggggcttttttattgcgc");

Terminator ECK120016586("aagaacgagtaaaaggtcggtttaaccggcctttttattttgtga");

Terminator ilvBN("aagacccccgcaccgaaaggtccgggggtttttttt");

Terminator ECK120010782("acctgtaaaaaaggcagccatctggctgccttagtctcccca");

Terminator ECK120015440("tccggcaattaaaaaagcggctaaccacgccgctttttttacgtctgca");

Terminator ECK120010876("taaggttgaaaaataaaaacggcgctaaaaagcgccgttttttttgacggtggta");

Terminator ECK120015170("acaattttcgaaaaaacccgcttcggcgggtttttttatagctaaaa");

Terminator pyrBI("agcccctcaatcgaggggcttttttttgc");

Terminator ECK120026481("taccaccgtcaaaaaaaacggcgctttttagcgccgtttttatttttcaacctt");

Terminator ECK120015444("acatttaataaaaaaagggcggtcgcaagatcgcccttttttacgtatgaca");

Terminator ECK120016882("tgtgaaaaagcccgcgcaagcgggtttttttatg");

// Devices

// 2 inputs, 5 states, length 12
Device rsmOutput160(B0062_R, ECK120010850, ECK120010825, TP901B_TC, TP901B_AG, BxbIB_GT, TP901P_AG, BxbIP_GT, TP901P_TC, ECK120030221, ECK120010799, ECK120010818);

// 2 inputs, 5 states, length 19
Device rsmOutput163(B0062_R, ECK120010850, ECK120010825, proNR3, TP901B_TC, ECK120033737, GFPmut3b, TP901B_AG, BxbIB_GT, TP901P_AG, proD, B0010, ECK120029600, ECK120033736, BxbIP_GT, TP901P_TC, ECK120030221, ECK120010799, ECK120010818);

// 2 inputs, 5 states, length 22
Device rsmOutput186(B0062_R, ECK120010850, ECK120010825, TP901B_TC, TP901B_AG, proNR3, proD, BxbIB_GT, TP901P_AG, ECK120016586, ilvBN, ECK120010782, BxbIP_GT, ECK120015440, ECK120010876, ECK120015170, TP901P_TC, GFPmut3b, ECK120033737, ECK120030221, ECK120010799, ECK120010818);

// 2 inputs, 5 states, length 16
Device rsmOutput165(B0062_R, ECK120010850, ECK120010825, ECK120033737, GFPmut3b, TP901B_TC, proNR3, TP901B_AG, BxbIB_GT, TP901P_AG, proD, BxbIP_GT, TP901P_TC, ECK120030221, ECK120010799, ECK120010818);

// 2 inputs, 5 states, length 19
Device rsmOutput164(B0062_R, ECK120010850, ECK120010825, proNR3, TP901B_TC, TP901B_AG, BxbIB_GT, TP901P_AG, proD, B0010, ECK120029600, ECK120033736, BxbIP_GT, GFPmut3b, ECK120033737, TP901P_TC, ECK120030221, ECK120010799, ECK120010818);

// 2 inputs, 5 states, length 26
Device rsmOutput291(B0062_R, ECK120010850, ECK120010825, ECK120033737, GFPmut3b, TP901B_TC, pyrBI, ECK120026481, ECK120015444, proNR4, TP901B_AG, mTagBFP, ECK120016882, proNR3, BxbIB_GT, ECK120010782, ilvBN, ECK120016586, mRFP, TP901P_AG, BxbIP_GT, TP901P_TC, proD, ECK120030221, ECK120010799, ECK120010818);

// 2 inputs, 5 states, length 19
Device rsmOutput166(B0062_R, ECK120010850, ECK120010825, TP901B_TC, TP901B_AG, GFPmut3b, ECK120033737, BxbIB_GT, ECK120033736, ECK120029600, B0010, TP901P_AG, BxbIP_GT, proNR3, TP901P_TC, proD, ECK120030221, ECK120010799, ECK120010818);

// 2 inputs, 5 states, length 21
Device rsmOutput187(B0062_R, ECK120010850, ECK120010825, ECK120033737, GFPmut3b, TP901B_TC, ECK120033736, ECK120029600, B0010, proD, TP901B_AG, BxbIB_GT, ECK120015170, ECK120010876, ECK120015440, TP901P_AG, BxbIP_GT, TP901P_TC, ECK120030221, ECK120010799, ECK120010818);

// Rules

Rule rsmOutput160Rules(ON rsmOutput160:
	ALL_FORWARD
);

Rule rsmOutput163Rules(ON rsmOutput163:
	ALL_FORWARD
);

Rule rsmOutput186Rules(ON rsmOutput186:
	ALL_FORWARD
);

Rule rsmOutput165ules(ON rsmOutput165:
	ALL_FORWARD
);

Rule rsmOutput164Rules(ON rsmOutput164:
	ALL_FORWARD
);

Rule rsmOutput291Rules(ON rsmOutput291:
	ALL_FORWARD
);

Rule rsmOutput166Rules(ON rsmOutput166:
	ALL_FORWARD
);

Rule rsmOutput187Rules(ON rsmOutput187:
	ALL_FORWARD
);

// Enumerate devices

result = product(rsmOutput160);

result = result + product(rsmOutput163);

result = result + product(rsmOutput186);

result = result + product(rsmOutput165);

result = result + product(rsmOutput164);

result = result + product(rsmOutput291);

result = result + product(rsmOutput166);

result = result + product(rsmOutput187);

// Print devices

println("Number of devices: " + SIZEOF(result));

println(result);

// Visualize devices

for(num i = 0; i < SIZEOF(result); i = i + 1) {
   SBOL.visualize(result[i]);
}

// Export devices to SBOL

SBOL.export(result, "./sbol/rsmOutput2inputs5states.xml");