From f5b664422ecb051f244724289e33bb596817c278 Mon Sep 17 00:00:00 2001 From: chris-krenz Date: Sun, 15 Sep 2024 21:47:34 -0400 Subject: [PATCH] Removed Eco6 --- library/constraints/Eco2C1G6T1.UCF.json | 110334 ------------------ library/constraints/Eco2C1G6T1.input.json | 575 - library/constraints/Eco2C1G6T1.output.json | 696 - 3 files changed, 111605 deletions(-) delete mode 100644 library/constraints/Eco2C1G6T1.UCF.json delete mode 100644 library/constraints/Eco2C1G6T1.input.json delete mode 100644 library/constraints/Eco2C1G6T1.output.json diff --git a/library/constraints/Eco2C1G6T1.UCF.json b/library/constraints/Eco2C1G6T1.UCF.json deleted file mode 100644 index 04e40f2..0000000 --- a/library/constraints/Eco2C1G6T1.UCF.json +++ /dev/null @@ -1,110334 +0,0 @@ -[ - { - "collection": "header", - "description": "cI homologs: lambda, P22, TP901, r1t, Tuc2009, phage186, 933W, L5, P2hd, P2, VP585, Wphi", - "version": "Eco2C1G6T1", - "date": "Tue January 31 23:01:11 EDT 2023", - "author": [ - "Jai Padmakumar", - "Alexander J. Triassi", - "Hamid Doosthosseini", - "Samuel M.D. Oliveira" - ], - "organism": "Escherichia coli MG1655 (Extended #Gates))", - "genome": "Wildtype (NCBI RefSeq: CP007799) with three landing pads integrated", - "media": "M9 minimal media composed of M9 media salts (6.78 g/L Na2HPO4, 3 g/L KH2PO4, 1 g/L NH4Cl, 0.5 g/L NaCl, 0.34 g/L thiamine hydrochloride, 0.4% D-glucose, 0.2% Casamino acids, 2 mM MgSO4, and 0.1 mM CaCl2", - "temperature": "37", - "growth": "Inoculation: Individual colonies into M9 media, 16 hours overnight in plate shaker.\tDilution: Next day, cells diluted 150-fold into M9 media without antibiotics, growth for 1.5 hours.\tInduction: Cells diluted into M9 media without antibiotics (starting OD600 = 0.0033).\tGrowth: shaking incubator for 5 hours.\tArrest protein production: PBS and 1 mg/ml kanamycin. Measurement: flow cytometry, data processing for RPU normalization." - }, - { - "collection": "measurement_std", - "signal_carrier_units": "RPUG", - "normalization_instructions": "The following equation converts the median YFP fluorescence to RPU. RPU = (YFP - YFP0)/(YFPRPUG - YFP0), where YFP is the median fluorescence of the cells of interest, YFP0 is the median fluorescence of the cells containing full sensor array with two other landing pads empty, and YFPRPUG is the median fluorescence of the cells containing the measurement standard on the genome landing pad", - "plasmid_description": "Genome integrated RPU standard where YFP fluorescent protein is driven by J23101 promoter and B0034 RBS. RiboJ was used as a ribozyme insulator. A bidirectional terminator DT3 was used to insulate YFP from the genome. The insertion is in the landing pad #2, at the position of 4633382" - }, - { - "collection": "input_composition", - "signal_carrier_units": "RPUG", - "normalization_instructions": "The following equation converts the median YFP fluorescence to RPU. RPU = (YFP - YFP0)/(YFPRPUG - YFP0), where YFP is the median fluorescence of the cells of interest, YFP0 is the median fluorescence of the cells containing full sensor array with two other landing pads empty, and YFPRPUG is the median fluorescence of the cells containing the measurement standard on the genome landing pad.", - "plasmid_description": "We used the pRpa*A (pC-HSL inducer) sensor cassette, which was cloned alongside the circuit. 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] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr206-r1t-R4_a AFTER L2", - "Pr206-r1t-R4_a BEFORE L3", - "Pr206-r1t-R4_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr206-r1t-R4_a AFTER L2", - "Pr206-r1t-R4_a BEFORE L3", - "Pr206-r1t-R4_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr206-r1t-R4_b AFTER L2", - "Pr206-r1t-R4_b BEFORE L3", - "Pr206-r1t-R4_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr206-r1t-R4_b AFTER L2", - "Pr206-r1t-R4_b BEFORE L3", - "Pr206-r1t-R4_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr208-Tuc2009-R3_a AFTER L2", - "Pr208-Tuc2009-R3_a BEFORE L3", - "Pr208-Tuc2009-R3_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr208-Tuc2009-R3_a AFTER L2", - "Pr208-Tuc2009-R3_a BEFORE L3", - "Pr208-Tuc2009-R3_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr208-Tuc2009-R3_b AFTER L2", - "Pr208-Tuc2009-R3_b BEFORE L3", - "Pr208-Tuc2009-R3_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr208-Tuc2009-R3_b AFTER L2", - "Pr208-Tuc2009-R3_b BEFORE L3", - "Pr208-Tuc2009-R3_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr210-phage186-RBS50_a AFTER L2", - "Pr210-phage186-RBS50_a BEFORE L3", - "Pr210-phage186-RBS50_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr210-phage186-RBS50_a AFTER L2", - "Pr210-phage186-RBS50_a BEFORE L3", - "Pr210-phage186-RBS50_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr210-phage186-RBS50_b AFTER L2", - "Pr210-phage186-RBS50_b BEFORE L3", - "Pr210-phage186-RBS50_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr210-phage186-RBS50_b AFTER L2", - "Pr210-phage186-RBS50_b BEFORE L3", - "Pr210-phage186-RBS50_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr211-933W-R1_a AFTER L2", - "Pr211-933W-R1_a BEFORE L3", - "Pr211-933W-R1_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr211-933W-R1_a AFTER L2", - "Pr211-933W-R1_a BEFORE L3", - "Pr211-933W-R1_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr211-933W-R1_b AFTER L2", - "Pr211-933W-R1_b BEFORE L3", - "Pr211-933W-R1_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr211-933W-R1_b AFTER L2", - "Pr211-933W-R1_b BEFORE L3", - "Pr211-933W-R1_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr211-933W-R2_a AFTER L2", - "Pr211-933W-R2_a BEFORE L3", - "Pr211-933W-R2_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr211-933W-R2_a AFTER L2", - "Pr211-933W-R2_a BEFORE L3", - "Pr211-933W-R2_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr211-933W-R2_b AFTER L2", - "Pr211-933W-R2_b BEFORE L3", - "Pr211-933W-R2_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr211-933W-R2_b AFTER L2", - "Pr211-933W-R2_b BEFORE L3", - "Pr211-933W-R2_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr212-L5-R1_a AFTER L2", - "Pr212-L5-R1_a BEFORE L3", - "Pr212-L5-R1_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr212-L5-R1_a AFTER L2", - "Pr212-L5-R1_a BEFORE L3", - "Pr212-L5-R1_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr212-L5-R1_b AFTER L2", - "Pr212-L5-R1_b BEFORE L3", - "Pr212-L5-R1_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr212-L5-R1_b AFTER L2", - "Pr212-L5-R1_b BEFORE L3", - "Pr212-L5-R1_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr214-P2hd-R1_a AFTER L2", - "Pr214-P2hd-R1_a BEFORE L3", - "Pr214-P2hd-R1_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr214-P2hd-R1_a AFTER L2", - "Pr214-P2hd-R1_a BEFORE L3", - "Pr214-P2hd-R1_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr214-P2hd-R1_b AFTER L2", - "Pr214-P2hd-R1_b BEFORE L3", - "Pr214-P2hd-R1_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr214-P2hd-R1_b AFTER L2", - "Pr214-P2hd-R1_b BEFORE L3", - "Pr214-P2hd-R1_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr215-P2-R1_a AFTER L2", - "Pr215-P2-R1_a BEFORE L3", - "Pr215-P2-R1_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr215-P2-R1_a AFTER L2", - "Pr215-P2-R1_a BEFORE L3", - "Pr215-P2-R1_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr215-P2-R1_b AFTER L2", - "Pr215-P2-R1_b BEFORE L3", - "Pr215-P2-R1_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr215-P2-R1_b AFTER L2", - "Pr215-P2-R1_b BEFORE L3", - "Pr215-P2-R1_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr215-P2-R3_a AFTER L2", - "Pr215-P2-R3_a BEFORE L3", - "Pr215-P2-R3_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr215-P2-R3_a AFTER L2", - "Pr215-P2-R3_a BEFORE L3", - "Pr215-P2-R3_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr215-P2-R3_b AFTER L2", - "Pr215-P2-R3_b BEFORE L3", - "Pr215-P2-R3_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr215-P2-R3_b AFTER L2", - "Pr215-P2-R3_b BEFORE L3", - "Pr215-P2-R3_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr215-P2-R4_a AFTER L2", - "Pr215-P2-R4_a BEFORE L3", - "Pr215-P2-R4_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr215-P2-R4_a AFTER L2", - "Pr215-P2-R4_a BEFORE L3", - "Pr215-P2-R4_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr215-P2-R4_b AFTER L2", - "Pr215-P2-R4_b BEFORE L3", - "Pr215-P2-R4_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr215-P2-R4_b AFTER L2", - "Pr215-P2-R4_b BEFORE L3", - "Pr215-P2-R4_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr217-VP585-R1_a AFTER L2", - "Pr217-VP585-R1_a BEFORE L3", - "Pr217-VP585-R1_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr217-VP585-R1_a AFTER L2", - "Pr217-VP585-R1_a BEFORE L3", - "Pr217-VP585-R1_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr217-VP585-R1_b AFTER L2", - "Pr217-VP585-R1_b BEFORE L3", - "Pr217-VP585-R1_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr217-VP585-R1_b AFTER L2", - "Pr217-VP585-R1_b BEFORE L3", - "Pr217-VP585-R1_a BEFORE L2" - ] - } - ] - }, - { - "function": "OR", - "rules": [ - { - "function": "AND", - "rules": [ - "Pr218-Wphi-R1_a AFTER L2", - "Pr218-Wphi-R1_a BEFORE L3", - "Pr218-Wphi-R1_b AFTER L3" - ] - }, - { - "function": "AND", - "rules": [ - "Pr218-Wphi-R1_a AFTER L2", - "Pr218-Wphi-R1_a BEFORE L3", - "Pr218-Wphi-R1_b BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr218-Wphi-R1_b AFTER L2", - "Pr218-Wphi-R1_b BEFORE L3", - "Pr218-Wphi-R1_a BEFORE L2" - ] - }, - { - "function": "AND", - "rules": [ - "Pr218-Wphi-R1_b AFTER L2", - "Pr218-Wphi-R1_b BEFORE L3", - "Pr218-Wphi-R1_a BEFORE L2" - ] - } - ] - } - ] - } - }, - { - "collection": "device_rules", - "rules": { - "function": "AND", - "rules": [ - "ALL_FORWARD" - ] - } - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr203", - "dnasequence": "TTCTTTCAGGCCGGGtaacaccgtgcgtgttgactattttacctctggcggtgataatAGCT" - }, - { - "collection": "parts", - "type": "cds", - "name": "Lambda", - "dnasequence": "atgagcacaaaaaagaaaccattaacacaagagcagcttgaggacgcacgtcgccttaaagcaatttatgaaaaaaagaaaaatgaacttggcttatcccaggaatctgtcgcagacaagatggggatggggcagtcaggcgttggtgctttatttaatggcatcaatgcattaaatgcttataacgccgcattgcttgcaaaaattctcaaagttagcgttgaagaatttagcccttcaatcgccagagaaatctacgagatgtatgaagcggttagtatgcagccgtcacttagaagtgagtatgagtaccctgttttttctcatgttcaggcagggatgttctcacctgagcttagaacctttaccaaaggtgatgcggagagatgggtaagcacaaccaaaaaagccagtgattctgcattctggcttgaggttgaaggtaattccatgaccgcaccaacaggctccaagccaagctttcctgacggaatgttaattctcgttgaccctgagcaggctgttgagccaggtgatttctgcatagccagacttgggggtgatgagtttaccttcaagaaactgatcagggatagcggtcaggtgtttttacaaccactaaacccacagtacccaatgatcccatgcaatgagagttgttccgttgtggggaaagttatcgctagtcagtggcctgaagagacgtttggcTGA" - }, - { - "collection": "parts", - "type": "rbs", - "name": "lambda-R3", - "dnasequence": "AACATCACACGTTAGCCTCTAC" - }, - { - "collection": "parts", - "type": "rbs", - "name": "lambda-R4", - "dnasequence": "AACATCCCTCGTTAGCCTCTTC" - }, - { - "collection": "parts", - "type": "ribozyme", - "name": "RiboJ54", - "dnasequence": "aggggtcagttgatgtgctttcaactctgatgagtcagtgatgacgaaaccccctctacaaataattttgtttaa" - }, - { - "collection": "parts", - "type": "terminator", - "name": "Ret0", - "dnasequence": "GCAGACAAAAAAAATGGCGCACAATGTGCGCCATTTTTCACTTCACAGGTACTATTGTTTTGAATTGAAAAGGGCGCTTCGGCGCCCTTTTTGCATTTGTTGACGGCATATATTTGTATATCGAAGCGCCCTGATGGGCGCTTTTTTTATTTAATCGATAACCAGA" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr204", - "dnasequence": "GATGAGGCGGTCAGGaataaacttgactaaagattcctttagtagataatttaagtgttctttaatttc" - }, - { - "collection": "parts", - "type": "cds", - "name": "P22", - "dnasequence": "ATGGGAGAGCGTATCCGTGCGCGCCGTAAAAAATTAAAAATCCGCCAGGCAGCGTTAGGCAAGATGGTCGGTGTTTCGAATGTAGCGATCTCTCAGTGGGAGCGTAGCGAAACTGAACCGAATGGAGAAAATTTATTGGCTTTATCTAAGGCACTGCAGTGTAGTCCGGACTACTTGTTGAAAGGTGATCTGAGTCAAACAAACGTCGCGTACCATTCTCGCCATGAACCACGTGGCTCTTATCCTCTGATTAGCTGGGTGTCTGCGGGGCAGTGGATGGAGGCGGTCGAACCGTATCACAAGCGTGCAATCGAGAATTGGCATGATACGACTGTAGACTGTAGCGAGGATTCGTTCTGGTTGGATGTTCAAGGGGATAGCATGACCGCACCCGCCGGATTAAGCATCCCCGAAGGCATGATTATTTTGGTCGATCCGGAAGTGGAGCCTCGCAACGGCAAACTTGTCGTGGCTAAGTTGGAAGGCGAGAATGAGGCGACGTTTAAGAAACTTGTCATGGATGCCGGACGTAAGTTTTTGAAACCCTTAAATCCGCAATATCCGATGATCGAGATCAATGGAAACTGCAAAATTATCGGTGTAGTAGTTGATGCCAAGCTGGCTAACTTACCGTAG" - }, - { - "collection": "parts", - "type": "rbs", - "name": "P22-R3", - "dnasequence": "ACTTTTAGCTAAAGGAATGATTG" - }, - { - "collection": "parts", - "type": "ribozyme", - "name": "RiboJ71", - "dnasequence": "AGTTGTCAGCCACTGTGCTTGTGGCTCTGATGAGACGGTGACGTCGAAACAACCTCTACAAATAATTTTGTTTAA" - }, - { - "collection": "parts", - "type": "terminator", - "name": "IlvGEDA", - "dnasequence": "TAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACA" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr253", - "dnasequence": "GCCACAAGCTCGAAAagttcatgaaacgtgaacttgacagctagctcagtcctaggtataaagttcatgaaacgtgaact" - }, - { - "collection": "parts", - "type": "cds", - "name": "TP901", - "dnasequence": "ATGAAGACTGACACATCAAATCGCTTAAAGCAGATCATGGCTGAGCGCAACCTTAAACAAGTGGATATCCTGAATCTTAGCATCCCTTTTCAAAAAAAATTCGGGATCAAATTGAGCAAGTCCACCCTTTCGCAATACGTCAACTCGGTACAATCCCCAGACCAGAACCGTATTTACCTGTTAGCCAAGACCTTGGGGGTAAGTGAAGCATGGTTGATGGGATTCGACGTTCCAATGGTGGAATCCTCGAAGATTGAGAATGATTCAGAGAACATTGAGGAGACGATCACCGTCATGAAGAAGCTGGAAGAGCCGCGTCAGAAAGTGGTCTTGGATACAGCAAAAATTCAGTTAAAGGAGCAGGATGAACAGAATAAGGTAAAGCAGATCGAGGACTATCGCTTATCCGACGAATATTTGGAGGAGCAGATCAGCAAGGCGTCGGCTTACGGAGGGGGGCAACTTAACGATAATGATAAGGAATTTTTCAAACGTCTGCTGAAAAACACCCTTAAGGAGAAAATTGACAAAGGCGATCTTTGA" - }, - { - "collection": "parts", - "type": "rbs", - "name": "TP901-R2", - "dnasequence": "GCTGGTACTGCTCGAGTATCTT" - }, - { - "collection": "parts", - "type": "ribozyme", - "name": "RiboJ69", - "dnasequence": "AGCTGTCAAGGCGTGTGCTTCGCCTTCTGATGAGCCCGTGAGGGCGAAACAGCCTCTACAAATAATTTTGTTTAA" - }, - { - "collection": "parts", - "type": "terminator", - "name": "RpoC", - "dnasequence": "GTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGCGGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCA" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr206", - "dnasequence": "GAGAGCTAACTTTATaacttgacaaattggatagttttaggtataataacttgacaaattggatagtt" - }, - { - "collection": "parts", - "type": "cds", - "name": "R1t", - "dnasequence": "ATGAAGAAGATTCGCCTTCCCGAAATGATTGACTACTTCCGTAAGGAAAACGGCTGGACTATGAAAGAGTTTGGTGAAAAATTAGGGAAGAGTGAGAGCGCTATTAGCAAGTGGATCAAGGGGGTACGCTCCCCTATGGTAGAGGATTTTGACAAGATGGTGAATTTATTTAACACTGACCCAGAAACCCTGATGTATGGTGCGTCAGATTTATCTACGACGTTGAGCGAAATCAATAAGATTTCGAGCCAACTTGAGGAACCGCGCCAGAAGGTTGTACTGAATACGGCAAATAATCAGCTTGACGAACAAAATCAGGAAAAGAAAAAGGAATCTAAAGTCATCCCTATTAACAAAATCCCAGATGACTTACCACCCTACATTAGTCGCAAAATTCTGGAAAATTTTGTAATGCCGACTAACACTATGGAATACGAAGCTGATGAAGATATGGTGGACGTACCCATCCTTGGGCGCATCGCGGCGGGCCTTCCGCTTGACGCGGTAGAAAACTTTGATGGAACGCGCCCAGTCCCTGCACATTTCCTTTCGAGTGCCCGTGATTACTATTGGCTTATGGTGGACGGCCATTCTATGGAACCTAAGATTCCGTACGGAGCATACGTCTTGATCGAAGCCGTCCCCGATGTGAGCGATGGGACCATTGGTGCCGTCTTATTCCATGATGATTGTCAGGCGACGCTGAAAAAGGTATATCACGAGATCGACTGTTTGCGCTTAGTCTCAATTAACAAAGAATTTAAGGACCAATTCGCCACGCAAGATAATCCAGCTGCAGTGATTGGTCAAGCAGTTAAGGTTGAAATCGACTTGTAA" - }, - { - "collection": "parts", - "type": "rbs", - "name": "r1t-R4", - "dnasequence": "TATTTTTAATAAATAGGGTT" - }, - { - "collection": "parts", - "type": "ribozyme", - "name": "BydvJ", - "dnasequence": "agggtgtctcaaggtgcgtaccttgactgatgagtccgaaaggacgaaacacccctctacaaataattttgtttaa" - }, - { - "collection": "parts", - "type": "terminator", - "name": "ECK120029600", - "dnasequence": "TTCAGCCAAAAAACTTAAGACCGCCGGTCTTGTCCACTACCTTGCAGTAATGCGGTGGACAGGATCGGCGGTTTTCTTTTCTCTTCTCAA" - }, - { - "collection": "parts", - "type": "ribozyme", - "name": "ElvJ", - "dnasequence": "agccccatagggtggtgtgtaccacccctgatgagtccaaaaggacgaaatggggcctctacaaataattttgtttaa" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr208", - "dnasequence": "AGTCTGGGAGGTACTtttcttgacaaaccacgaaaagtggactataattaAG" - }, - { - "collection": "parts", - "type": "cds", - "name": "Tuc2009", - "dnasequence": "ATGGTTATCGAACAAATCAACAAGTACGTTGGAAGCAAGATTAAGGATTATCGTAAATCATTTGGACTTTCCCAGGAAGAATTGGCTAAAAAAATTGGAGTCGGCAAAACCACTATCTCTAATTATGAAGTAGGGATCCGCTCACCAAAAAAGCCTCAGCTTATTAAATTATCCGAGGTGTTCGATGTAGCAATTGATGATTTTTTTCCTCAGACTGATAGTACACGCATGAACGTGTCTAGCATCCTGTCCGAAATCAACAAGATTTCCTCCCAGCTTGAAGAACCGCGCCAAAAGATCGTGCTTAATACCGCTACCAACCAACTTGATGAGCAGAATCAAGAAAAGAAAAAGGAAAGTAAGGTCATTCCTATCAATAAGATCCCTGACGATCTTCCACCTTACATTTCCCGCAAAATTTTAGAGAATTTTATTATGCCTTCCAATACGATGGAATATGAACCCGACGAGGACATGGTAGACGTTCCGATTTTGGGGCGTATTGCCGCCGGGTTACCACTGGATGCGGTCGAAAACTTCGATGGAACCCGTCCCGTACCAGCCCATTTCTTATCAAGTGCCCGTGATTACTACTGGTTAATGGTAGACGGTCACAGTATGGAACCGAAGATTCCTTATGGAGCCTACGTGCTGATTGAGGCGGTTCCCGATGTGTCAGACGGTACTATTGGTGCTGTACTTTTCCAAGATGACTGCCAGGCCACGTTAAAGAAGGTATATCACGAGATCGACTGTTTACGCCTGGTGTCCATTAACAAAGAGTTTAAGGATCAGTTTGCCACGCAAGACAATCCTGCTGCTGTTATCGGGCAGGCAGTGAAAGTAGAAATCGATTTGTAA" - }, - { - "collection": "parts", - "type": "rbs", - "name": "Tuc2009-R3", - "dnasequence": "AGAATATTATTGAAGATAATAGGA" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr217", - "dnasequence": "GGTGCAGTTTTGTGCgattgcaaaatttgcatttacttttattatcttttttgataaaaact" - }, - { - "collection": "parts", - "type": "cds", - "name": "VP585", - "dnasequence": "atgaaggaaaataagaggatgatagaaatagatattggcccggtattaaagcgcatccgttatgagcgagggctaacgctacaaaagctgtcacggcttacggatgacaaagtgctaccaagcaacatttcccgcatcgagagtgcgggcgctggcgctacgcttaaaaccttgaccaccttggcgaatgcgctggggacttctccttctgacattcttcgtgaagctgagggcggtgataaggtgatcaccaagccgcagcaagtcctttatgtacctgttttgtcttgggttcaggctggcacctggactgaatcaccagagcagcctgccgatggtgactatgatgaatgggtagaggcaccaagaggcgcatccaggaaggctttcggccttcgagttcaaggggatagtatgcaagcccctatcggcaagtcgttcccggaaggatgctgcatagttgttgacccaaccaaacaagcagataaccgctcgtttgttgttgctcgcctggcagacacaggagagcacacgttcaagcagctgatcattgacgggccgcaccaatatctaaagccgctaaacccaagttaccgaaccatagaagtgaacagcgaagtacacgtctgcggggtcgttttagcatggggtgaagggtacacggtgaacggtatttaa" - }, - { - "collection": "parts", - "type": "rbs", - "name": "VP585-R1", - "dnasequence": "CGGATCTAGTAGGTACAGTGCAATC" - }, - { - "collection": "parts", - "type": "ribozyme", - "name": "SarJ", - "dnasequence": "gactgtcgccggatgtgtatccgacctgacgatggcccaaaagggccgaaacagtcctctacaaataattttgtttaa" - }, - { - "collection": "parts", - "type": "terminator", - "name": "DT19", - "dnasequence": "TTCAGCCAAAAAACTTAAGACCGCCGGTCTTGTCCACTACCTTGCAGTAATGCGGTGGACAGGATCGGCGGTTTTCTTTTCTCTTCTCAACTCGGTACCAAAGACGAACAATAAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCC" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr210", - "dnasequence": "TTGTTACCCATACTGtttcgataaaacctatttactatctctcaattgggagatatattttggctaaaccca" - }, - { - "collection": "parts", - "type": "cds", - "name": "Phage186", - "dnasequence": "atgagaatagattctttaggatggagcaacgtggatgtacttgaccgcatctgcgaggcgtacggattttcgcagaaaattcaattagctaaccacttcgatatcgcgtccagctcattgtcaaacaggtacacccgaggcgctatctcctatgactttgcggctcactgtgcccttgaaacaggtgctaatctccagtggttacttaccggagaaggagaagcatttgtaaataacagagaatcgagcgacgcaaaaaggattgagggattcacattaagtgaagaaatcctcaaatccgataaacaattgagtgttgatgcccaatttttcacaaaaccgctcacagatgggatggctatccgttccgaggggaaaatttattttgtggacaagcaagcatcattgtctgacggcttatggctagtcgacattgagggagcaataagcattcgagagttaacaaaactaccgggtagaaaactacatgttgcaggcgggaaggttcctttcgaatgcggcattgatgatattaaaacgttggggcgtgtggtgggtgtatacagcgaggttaactaa" - }, - { - "collection": "parts", - "type": "rbs", - "name": "phage186-RBS50", - "dnasequence": "AAGAGGCGACGTAACATCCTGGAGGCAAGTAATAACT" - }, - { - "collection": "parts", - "type": "ribozyme", - "name": "RiboJ10", - "dnasequence": "agcgctcaacgggtgtgcttcccgttctgatgagtccgtgaggacgaaagcgcctctacaaataattttgtttaa" - }, - { - "collection": "parts", - "type": "terminator", - "name": "DT83", - "dnasequence": "AGCGTCAAAAGGCCGGATTTTCCGGCCTTTTTTATTAGGCAGCATGCTGCCAGGTGATCCCCCTGGCCACCTCTTTT" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr211", - "dnasequence": "ATTGTCAGAAATGGCacttgcaaaaactttcagttcaaccataatacgtactgaaagtacgaaaaagg" - }, - { - "collection": "parts", - "type": "cds", - "name": "933W", - "dnasequence": "atggttcagaatgaaaaagtgcgcaaagaattcgcccagcggctagcgcaagcctgtaaagaagctggtcttgatgaacatggtaggggaatggctatagcccgtgccctttctctttcgtccaaaggcgttagcaaatggtttaatgctgagtctttaccgcgtcaggaaaaaatgaatgcgcttgcgaaatttctaaacgttgatgttgtttggcttcagcacggcacttcgttaaatggagcgaatgatgaagatactctttcatttgttggcaaattaaaaaaagggttagtgcgcgtggttggtgaggcaattcttggtgttgatggtgccatcgagatgaccgaagaacgcgatgggtggctcaaaatttatagcgatgatccagatgcctttggtctgcgtgtgaaaggagacagcatgtggcccagaataaaatcaggagaatatgtactcattgagcctaacaccaaagtattcccgggtgatgaggtgtttgtcagaaccgttgaaggacacaacatgattaaggttcttggctatgacagagatggagaataccaatttacaagcattaaccaggatcacaggcctataacgttgccttatcatcaagtagcaaaggtggagtatgtagctggtattctgaagcaatctcgccatctggatgacatcgaggcaagggagtggctgaaaagttcgtga" - }, - { - "collection": "parts", - "type": "rbs", - "name": "933W-R1", - "dnasequence": "GCACTACGGAATTAAGCGCTCAA" - }, - { - "collection": "parts", - "type": "rbs", - "name": "933W-R2", - "dnasequence": "GCACTACGGCATTAAGCGCTCAA" - }, - { - "collection": "parts", - "type": "ribozyme", - "name": "PlmJ", - "dnasequence": "agtcataagtctgggctaagcccactgatgagtcgctgaaatgcgacgaaacttatgacctctacaaataattttgtttaa" - }, - { - "collection": "parts", - "type": "terminator", - "name": "DT36", - "dnasequence": "GATCTAACTAAAAAGGCCGCTCTGCGGCCTTTTTTCTTTTCACTGTAACAACGGAAACCGGCCATTGCGCCGGTTTTTTTTGGCCT" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr212", - "dnasequence": "TGTTAATGTAATCTGcttgacagccacctcagtcctaggtactgtgctagcttgacagccacc" - }, - { - "collection": "parts", - "type": "cds", - "name": "L5", - "dnasequence": "atgagcggcaaaatccaacacaaagcagtggttccggcccctagccgaataccactcactctcagcgagatcgaagatcttcgcaggaaggggtttaatcagaccgaaatcgcagagctgtatggcgtgactcgacaagcggtgtcgtggcacaagaaaacctacggaggacggttgaccaccaggcagatcgtccagcagaactggccgtgggacacgcggaaacctcacgataagtcgaaggcttttcagaggctccgggatcacggcgagtacatgcgagtgggtagcttccgcacgatgtccgaagataagaagaagcgcctattgtcgtggtggaagatgctccgcgacgacgacttagtgctcgagttcgacccatccatcgagccctacgaaggtatggccggcggcgggttcaggtacgtcccccgaggcatcgaggatgacgatctcctgatccgggtgaacgagcacaccaacctcaccgccgagggtgaactcctctggtcgtggccagacgacatcgaggagcttctctcggagccctaa" - }, - { - "collection": "parts", - "type": "rbs", - "name": "L5-R1", - "dnasequence": "CAATTATAAGGCCTGACGCGT" - }, - { - "collection": "parts", - "type": "ribozyme", - "name": "RiboJ60", - "dnasequence": "ctgaagtcgtcaagtgctgtgcttgcacttctgatgaggcagtgatgccgaaacgacctctacaaataattttgtttaa" - }, - { - "collection": "parts", - "type": "terminator", - "name": "L3S2P11", - "dnasequence": "ctcggtaccaaattccagaaaagagacgctttcgagcgtcttttttcgttttggtcc" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr214", - "dnasequence": "AACTACTACGCAAAAttcaacttctccgaaacgtctattgacataattactccgattgcgtaatttcttg" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr215", - "dnasequence": "ATGATTGGCGACTCGgtttagatctcattgacatggtgtttagatctcaagtactgttagtttagatgtacaattttgttagtttagat" - }, - { - "collection": "parts", - "type": "promoter", - "name": "Pr218", - "dnasequence": "TCCTATAAGGACACGcatttgacagtaacctattggtgacttatattcccgtcaaaaggttgtgtattggtgacctt" - }, - { - "collection": "parts", - "type": "cds", - "name": "P2hd", - "dnasequence": "atgtcaatagacgtttcggagaagttgaagctaatccgtgaatctgaaaggttaaaccgtaaagaattcagtgaattaactggtgtagcctacagctcactttcgagctatgagagccggtcaaaaaacgctggagttgaagccataatgaaggtcttacaacatcctagatttactaaatatactttgtggttcatgactgatcaggtagctccagaagccgggcaaattgcgcccgctctcgcacactttgggcaaaacgaaacaacgtcgccccactccggtcaaaagactggttaa" - }, - { - "collection": "parts", - "type": "cds", - "name": "P2", - "dnasequence": "atgtcaaacacgataagcgagaagatagtcttaatgcgaaaatcagagtatttgagcagacaacaacttgctgatttaacaggggttccgtatggcacgctgagttactatgaaagtggtcgttcaacacctccaacagatgtcatgatgaacatcctgcagaccccacaattcaccaaatacactttatggttcatgaccaatcagatcgctcctgagtccgggcaaattgcgcccgctctcgcacactttgggcaaaacgaaacaacgtcgccccactccggtcaaaagactggttaa" - }, - { - "collection": "parts", - "type": "cds", - "name": "Wphi", - "dnasequence": "atgcagacattcgaaaaactgaaagcgattaggaaagcagaaggcttaacacaggcgaaattcagcgaaattagcgggatagctctaggaacagtcaaaaattacgaaagtgggcataaagaccctggtctgagcatcgttatgcgagtcacaaatacgcctttatttaaaaaatatacgctctggttaatgactggtgatacgtcaccacaagctggtcagatcgcgccggctctcgcacacattgggcaaaaaccaacagaatcagaccactccgaaaaacagactggttaa" - }, - { - "collection": "parts", - "type": "rbs", - "name": "P2hd-R1", - "dnasequence": "TTATCTTAGGTACAGGGCACATAA" - }, - { - "collection": "parts", - "type": "rbs", - "name": "P2-R1", - "dnasequence": "CAGGTTATAAGGCCTGCAGCGT" - }, - { - "collection": "parts", - "type": "rbs", - "name": "P2-R3", - "dnasequence": "TTTTTCTCCACTACGATGGTAAT" - }, - { - "collection": "parts", - "type": "rbs", - "name": "P2-R4", - "dnasequence": "TTTGTCCCTTCCACTAGGCTGGTAAT" - }, - { - "collection": "parts", - "type": "rbs", - "name": "Wphi-R1", - "dnasequence": "TGCCACTTACATTAGCGTTTTTGA" - }, - { - "collection": "parts", - "type": "ribozyme", - "name": "RiboJ64", - "dnasequence": "aggagtcaattaatgtgcttttaattctgatgagacggtgacgtcgaaactccctctacaaataattttgtttaa" - }, - { - "collection": "parts", - "type": "terminator", - "name": "DT56", - "dnasequence": "TACCACCGTCAAAAAAAACGGCGCTTTTTAGCGCCGTTTTTATTTTTCAACCTTCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTC" - }, - { - "collection": "parts", - "type": "terminator", - "name": "DT86", - "dnasequence": "TAATCATTCTTAGCGTGACCGGGAAGTCGGTCACGCTACCTCTTCTGAAGAAACAGCAAACAATCCAAAACGCCGCGTTCAGCGGCGTTTTTTCTGCTTTTCT" - }, - { - "collection": "parts", - "type": "scar", - "name": "F_scar", - "dnasequence": "CGCT" - }, - { - "collection": "parts", - "type": "scar", - "name": "E_scar", - "dnasequence": "GCTT" - }, - { - "collection": "parts", - "type": "scar", - "name": "D_scar", - "dnasequence": "AGGT" - }, - { - "collection": "parts", - "type": "scar", - "name": "C_scar", - "dnasequence": "AATG" - }, - { - "collection": "parts", - "type": "scar", - "name": "B_scar", - "dnasequence": "TACG" - }, - { - "collection": "parts", - "type": "scar", - "name": "A_scar", - "dnasequence": "GGAG" - }, - { - "collection": "parts", - "type": "scar", - "name": "Y_scar", - "dnasequence": "ATTG" - }, - { - "collection": "parts", - "type": "scar", - "name": "X_scar", - "dnasequence": "TGTC" - }, - { - "collection": "parts", - "type": "scar", - "name": "V_scar", - "dnasequence": "TCTG" - }, - { - "collection": "parts", - "type": "scar", - "name": "U_scar", - "dnasequence": "GGGC" - }, - { - "collection": "parts", - "type": "scar", - "name": "R_scar", - "dnasequence": "GTAA" - }, - { - "collection": "parts", - "type": "scar", - "name": "Q_scar", - "dnasequence": "GAGT" - }, - { - "collection": "parts", - "type": "scar", - "name": "P_scar", - "dnasequence": "CCTA" - }, - { - "collection": "parts", - "type": "scar", - "name": "O_scar", - "dnasequence": "ATGC" - }, - { - "collection": "parts", - "type": "scar", - "name": "G_scar", - "dnasequence": "ATAG" - }, - { - "collection": "functions", - "name": "Pr203-cI-R3_v2_toxicity", - "variables": [ - { - "name": "x", - "map": "#//model/functions/input_composition" - } - ], - "table": { - "x": [ - 0.013914542, - 0.030185553, - 0.058391454, - 0.093907232, - 0.14300548, - 0.202310877, - 0.353791451, - 0.625141869, - 1.184715283, - 1.801997992, - 3.241444823, - 4.620927241 - ], - "output": [ - 1.0, - 1.023474178, - 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"description": "Minimal transcription" - } - ] - }, - { - "collection": "structures", - "name": "RpaR-AM2_sensor_structure", - "outputs": [ - "PRpa_A" - ], - "inputs": [ - { - "name": "in1", - "part_type": "promoter" - } - ], - "devices": [ - { - "name": "PRpa_A_RiboRpa_RpaR-AM2_TerRpa", - "components": [ - "#in1", - "PRpa_A_RiboRpa_RpaR-AM2_TerRpa_cassette" - ] - }, - { - "name": "PRpa_A_RiboRpa_RpaR-AM2_TerRpa_cassette", - "components": [ - "RiboRpa_RpaR-AM2_TerRpa" - ] - } - ] - }, - { - "collection": "parts", - "type": "cassette", - "name": "RiboRpa_RpaR-AM2_TerRpa", - "dnasequence": "AAAAAAAAAGGCTCCAAAAGGAGCCttgacggctagctcagtcctaggtacagtgctagctactAGATGCTGTAGTGGGATGTGTGTCTCACCTGAAGAGTACAAAAGTCCGAAACGGTATCCTCTACAAATAATTTTGTTTAAaAGCGATACTTAGGGTAACAGtAATGattgtgggtgaagatcagctgtggggtcgtcgtacactggaatttgttgatagcgttgaacgtctggaagcaccggcactgattagccgttttgaaagcctgattgcaagctgtggttttaccgcctatatcatggcaggtctgccgagccgtaatgccggtctgccggaactgaccctggcaaatggttggcctcgtgattggtttgatctgtatgttagcgaaaactttagcgcagttgatccggttccgcgttatggtgcaaccactgttcatccgtttgtttggagtgatgcaccgtatgatcgtgaccgtgatcaggcagcacatcgtgttatgacccgtgcagcagaatttggtctggttgaaggttattgtattccgctgcattacgatgatggtagcgcagcaattagtatggcaggtgaagatcctgatctgagtccggcagcccgtggtgtaatgcagctggttagcatttatgcacatagccgtctgcgtgtactgagccgtccgaaaccgattcgtcgtaatcgtctgacaccgcgtgaatgtgaaattctgcagtgggcagcacagggtaaaaccgcatgggaaattagcgttattctgtgtattaccgaacgcaccgttaaatttcatctgattgaagcagcacgtaaactggatgcagcaaatcgtaccgcagcagttgcaaaagcactgacactgggtctgattcgtctgtaatagagttaaccaaAAAGGGGGGATTTTATCTCCCCTTTaatttttcct" - }, - - - - - - - - - - - - - - - - - { - "collection": "input_sensors", - "name": "OC6_in", - "model": "OC6_in_model", - "structure": "OC6_in_structure", - "description": "comms_device" - }, - { - "collection": "models", - "name": "OC6_in_model", - "functions": { - "response_function": "sensor_response" - }, - "parameters": [ - { - "name": "ymax", - "value": 7.5, - "description": "Maximal transcription" - }, - { - "name": "ymin", - "value": 0.06, - "description": "Minimal transcription" - } - ] - }, - { - "collection": "structures", - "name": "OC6_in_structure", - "outputs": [ - "pLuxB" - ] - }, - { - "collection": "parts", - "type": "promoter", - "name": "pLuxB", - "dnasequence": "ACCTGTAGGATCGTACAGGTTTACGCAAGAAAATGGTTTGTTACAGTCGAATAAAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAG" - }, - - - - - - { - "collection": "input_sensors", - "name": "OHC12_in", - "model": "OHC12_in_model", - "structure": "OHC12_in_structure", - "description": "comms_device" - }, - { - "collection": "models", - "name": "OHC12_in_model", - "functions": { - "response_function": "sensor_response" - }, - "parameters": [ - { - "name": "ymax", - "value": 3.4, - "description": "Maximal transcription" - }, - { - "name": "ymin", - "value": 0.01, - "description": "Minimal transcription" - } - ] - }, - { - "collection": "structures", - "name": "OHC12_in_structure", - "outputs": [ - "pCin" - ] - }, - { - "collection": "parts", - "type": "promoter", - "name": "pCin", - "dnasequence": "CGTAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAG" - }, - - - - - - { - "collection": "input_sensors", - "name": "pC-HSL_in", - "model": "pC-HSL_in_model", - "structure": "pC-HSL_in_structure", - "description": "comms_device" - }, - { - "collection": "models", - "name": "pC-HSL_in_model", - "functions": { - "response_function": "sensor_response" - }, - "parameters": [ - { - "name": "ymax", - "value": 6, - "description": "Maximal transcription" - }, - { - "name": "ymin", - "value": 0.02, - "description": "Minimal transcription" - } - ] - }, - { - "collection": "structures", - "name": "pC-HSL_in_structure", - "outputs": [ - "pRpa" - ] - }, - { - "collection": "parts", - "type": "promoter", - "name": "pRpa", - "dnasequence": "CGTAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAG" - }, - - - - - - { - "collection": "input_sensors", - "name": "DAPG_in", - "model": "DAPG_in_model", - "structure": "DAPG_in_structure", - "description": "comms_device" - }, - { - "collection": "models", - "name": "DAPG_in_model", - "functions": { - "response_function": "sensor_response" - }, - "parameters": [ - { - "name": "ymax", - "value": 3.4, - "description": "Maximal transcription" - }, - { - "name": "ymin", - "value": 0.02, - "description": "Minimal transcription" - } - ] - }, - { - "collection": "structures", - "name": "DAPG_in_structure", - "inputs": [ - { - "name": "in1", - "part_type": "promoter" - } - ], - "outputs": [ - "pPhlF" - ] - }, - { - "collection": "parts", - "type": "promoter", - "name": "pPhlF", - "dnasequence": "AGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAG" - }, - - - - - - { - "collection": "functions", - "name": "sensor_response", - "equation": "$STATE * (ymax - ymin) + ymin", - "parameters": [ - { - "name": "ymax", - "map": "#//model/parameters/ymax" - }, - { - "name": "ymin", - "map": "#//model/parameters/ymin" - } - ] - } -] diff --git a/library/constraints/Eco2C1G6T1.output.json b/library/constraints/Eco2C1G6T1.output.json deleted file mode 100644 index 622dc84..0000000 --- a/library/constraints/Eco2C1G6T1.output.json +++ /dev/null @@ -1,696 +0,0 @@ -[ - { - "collection": "measurement_std", - "signal_carrier_units": "RNAP/s", - "normalization_instructions": "The values are converted from RPUG (from the Eco2C1G6T1 UCF) to RNAP/s with the following conversion factor: RPU = 0.019 RNAP/s (see 10.15252/msb.20209584). The same factor has also been applied to the ymax an ymin values of the communication molecule outputs (OC6, OHC12, pC-HSL, DAPG). Note: change unit conversion factors accordingly if using a different or modified UCF." - }, - - - - - - { - "collection": "output_devices", - "name": "BFP_reporter", - "model": "BFP_reporter_model", - "structure": "BFP_reporter_structure" - }, - { - "collection": "models", - "name": "BFP_reporter_model", - "functions": { - "response_function": "linear_response", - "input_composition": "linear_input_composition" - }, - "parameters": [ - { - "name": "unit_conversion", - "value": 0.019, - "description": "Unit conversion" - } - ] - }, - { - "collection": "structures", - "name": "BFP_reporter_structure", - "inputs": [ - { - "name": "in1", - "part_type": "promoter" - }, - { - "name": "in2", - "part_type": "promoter" - } - ], - "devices": [ - { - "name": "BFP_reporter_a", - "components": [ - "#in1", - "BFP_reporter_cassette" - ] - }, - { - "name": "BFP_reporter_b", - "components": [ - "#in2", - "BFP_reporter_cassette" - ] - } - ] - }, - { - "collection": "parts", - "name": "BFP_reporter_cassette", - "type": "cassette", - "dnasequence": "GCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGaaagaggagaaaTACTAGATGGTGTCTAAGGGCGAAGAGCTGATTAAGGAGAACATGCACATGAAGCTGTACATGGAGGGCACCGTGGACAACCATCACTTCAAGTGCACATCCGAGGGCGAAGGCAAGCCCTACGAGGGCACCCAGACCATGCGCATCAAGGTGGTCGAGGGCGGCCCTCTCCCCTTCGCCTTCGACATCCTGGCTACTAGCTTCCTCTACGGCAGCAAGACCTTCATCAACCACACCCAGGGCATCCCCGACTTCTTCAAGCAGTCCTTCCCTGAGGGCTTCACATGGGAGCGCGTCACCACATACGAGGACGGGGGCGTGCTGACCGCTACCCAGGACACCAGCCTCCAGGACGGCTGCCTCATCTACAACGTCAAGATCCGGGGGGTGAACTTCACATCCAACGGCCCTGTGATGCAGAAGAAAACACTCGGCTGGGAGGCCTTCACCGAAACCCTGTACCCCGCTGACGGCGGCCTGGAAGGCCGTAACGACATGGCCCTGAAGCTCGTGGGCGGGAGCCATCTGATCGCAAACGCCAAGACCACATATCGTTCCAAGAAACCCGCTAAGAACCTCAAGATGCCTGGCGTCTACTATGTGGACTACCGCCTGGAACGTATCAAGGAGGCCAACAACGAAACGTACGTCGAGCAGCACGAGGTGGCAGTGGCCCGGTACTGCGACCTCCCTAGCAAACTGGGGCACAAGCTTAATTAAAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGG" - }, - - - - - - { - "collection": "output_devices", - "name": "RFP_reporter", - "model": "RFP_reporter_model", - "structure": "RFP_reporter_structure" - }, - { - "collection": "models", - "name": "RFP_reporter_model", - "functions": { - "response_function": "linear_response", - "input_composition": "linear_input_composition" - }, - "parameters": [ - { - "name": "unit_conversion", - "value": 0.019, - "description": "Unit conversion" - } - ] - }, - { - "collection": "structures", - "name": "RFP_reporter_structure", - "inputs": [ - { - "name": "in1", - "part_type": "promoter" - }, - { - "name": "in2", - "part_type": "promoter" - } - ], - "devices": [ - { - "name": "RFP_reporter_a", - "components": [ - "#in1", - "RFP_reporter_cassette" - ] - }, - { - "name": "RFP_reporter_b", - "components": [ - "#in2", - "RFP_reporter_cassette" - ] - } - ] - }, - { - "collection": "parts", - "name": "RFP_reporter_cassette", - "type": "cassette", - "dnasequence": "agaagtcaattaatgtgcttttaattctgatgagtcggtgacgacgaaacttcctctacaaataattttgtttaaTACTAGAGAAAGAGGGGAAATACTAGATGGCTTCCTCCGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGAAGGTTCCGTTAACGGTCACGAGTTCGAAATCGAAGGTGAAGGTGAAGGTCGTCCGTACGAAGGTACCCAGACCGCTAAACTGAAAGTTACCAAAGGTGGTCCGCTGCCGTTCGCTTGGGACATCCTGTCCCCGCAGTTCCAGTACGGTTCCAAAGCTTACGTTAAACACCCGGCTGACATCCCGGACTACCTGAAACTGTCCTTCCCGGAAGGTTTCAAATGGGAACGTGTTATGAACTTCGAAGACGGTGGTGTTGTTACCGTTACCCAGGACTCCTCCCTGCAAGACGGTGAGTTCATCTACAAAGTTAAACTGCGTGGTACCAACTTCCCGTCCGACGGTCCGGTTATGCAGAAAAAAACCATGGGTTGGGAAGCTTCCACCGAACGTATGTACCCGGAAGACGGTGCTCTGAAAGGTGAAATCAAAATGCGTCTGAAACTGAAAGACGGTGGTCACTACGACGCTGAAGTTAAAACCACCTACATGGCTAAAAAACCGGTTCAGCTGCCGGGTGCTTACAAAACCGACATCAAACTGGACATCACCTCCCACAACGAAGACTACACCATCGTTGAACAGTACGAACGTGCTGAAGGTCGTCACTCCACCGGTGCTTAAGATGTGGGGTCCGATCTAACTAAAAAGGCCgctCTGCGGCCTTTTTTCTTTTCACT" - }, - - - - - - { - "collection": "output_devices", - "name": "YFP_reporter", - "model": "YFP_reporter_model", - "structure": "YFP_reporter_structure" - }, - { - "collection": "models", - "name": "YFP_reporter_model", - "functions": { - "response_function": "linear_response", - "input_composition": "linear_input_composition" - }, - "parameters": [ - { - "name": "unit_conversion", - "value": 0.019, - "description": "Unit conversion" - } - ] - }, - { - "collection": "structures", - "name": "YFP_reporter_structure", - "inputs": [ - { - "name": "in1", - "part_type": "promoter" - }, - { - "name": "in2", - "part_type": "promoter" - } - ], - "devices": [ - { - "name": "YFP_reporter_a", - "components": [ - "#in1", - "YFP_reporter_cassette" - ] - }, - { - "name": "YFP_reporter_b", - "components": [ - "#in2", - "YFP_reporter_cassette" - ] - } - ] - }, - { - "collection": "parts", - "name": "YFP_reporter_cassette", - "type": "cassette", - "dnasequence": "AGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGAGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAAGCTCATGTATGTGTCTACGCGAGATTCTCGCCCGAGAACTTCTGCAAGGCACTGCTCTTGGCT" - }, - - - - - - { - "collection": "output_devices", - "name": "YFP_reporter_2", - "model": "YFP_reporter_2_model", - "structure": "YFP_reporter_2_structure" - }, - { - "collection": "models", - "name": "YFP_reporter_2_model", - "functions": { - "response_function": "linear_response", - "input_composition": "linear_input_composition" - }, - "parameters": [ - { - "name": "unit_conversion", - "value": 0.019 - } - ] - }, - { - "collection": "structures", - "name": "YFP_reporter_2_structure", - "inputs": [ - { - "name": "in1", - "part_type": "promoter" - }, - { - "name": "in2", - "part_type": "promoter" - } - ], - "devices": [ - { - "name": "YFP_reporter_2", - "components": [ - "#in1", - "#in2", - "YFP_cassette" - ] - } - ] - }, - { - "collection": "parts", - "type": "cassette", - "name": "YFP_cassette", - "dnasequence": "CTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCC" - }, - - - - - { - "collection": "functions", - "name": "linear_response", - "equation": "c * x", - "variables": [ - { - "name": "x", - "map": "#//model/functions/input_composition" - } - ], - "parameters": [ - { - "name": "c", - "map": "#//model/parameters/unit_conversion" - } - ] - }, - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - { - "collection": "output_devices", - "name": "OC6_out", - "model": "OC6_out_model", - "structure": "OC6_out_structure", - "description": "comms_device" - }, - { - "collection": "models", - "name": "OC6_out_model", - "functions": { - "response_function": "Hill_response", - "input_composition": "linear_input_composition" - }, - "parameters": [ - { - "name": "ymax", - "value": 0.1425, - "description": "Maximal transcription (7.5 RPU * 0.019 for conversion to RNAP/s)" - }, - { - "name": "ymin", - "value": 0.00114, - "description": "Minimal transcription (0.06 RPU * 0.019 for conversion to RNAP/s)" - }, - { - "name": "kd", - "value": 0.1, - "description": "Dissociation equilibrium constant" - }, - { - "name": "n", - "value": 1.9, - "description": "Cooperativety" - } - ] - }, - { - "collection": "structures", - "name": "OC6_out_structure", - "inputs": [ - { - "name": "in1", - "part_type": "promoter" - }, - { - "name": "in2", - "part_type": "promoter" - } - ], - "devices": [ - { - "name": "OC6_out_a", - "components": [ - "#in1", - "#in2", - "sLux_cassette" - ] - } - ] - }, - { - "collection": "parts", - "type": "cassette", - "name": "sLux_cassette", - "dnasequence": "agcgctcaacgggtgtgcttcccgttctgatgagtccgtgaggacgaaagcgcctctacaaataattttgtttaacggttccaaagccagatactaaggaggtcccAcATGactataatgataaaaaaatcggattttttggcaattccatcggaggagtataaaggtattctaagccttcgttatcaagtgtttaagcaaagacttgagtgggacttagttgtagaaaataaccttgaatcagatgagtatgataactcaaatgcagaatatatttatgcttgtgatgatactgaaaatgtaagtggatgctggcgtttattacctacaacaggtgattatatgctgaaaagtgtttttcctgaattgcttggtcaacagagtgctcccaaagatcctaatatagtcgaattaagtcgttttgctgtaggtaaaaatagctcaaagataaataactctgctagtgaaattacaatgaaactatttgaagctatatataaacacgctgttagtcaaggtattacagaatatgtaacagtaacatcaacagcaatagagcgatttttaaagcgtattaaagttccttgtcatcgtattggagacaaagaaattcatgtattaggtgatactaaatcggttgtattgtctatgcctattaatgaacagtttaaaaaagcagtcttaaattaatagCTTATTCCATAACAAAGCCGGGTAATTCCCGGCTTTGTTGTATCTGAACAATAAATGGATGCCCTGCGTAAGCGGGGCATTTTTCTTCCT" - }, - - - - - - { - "collection": "output_devices", - "name": "OHC12_out", - "model": "OHC12_out_model", - "structure": "OHC12_out_structure", - "description": "comms_device" - }, - { - "collection": "models", - "name": "OHC12_out_model", - "functions": { - "response_function": "Hill_response", - "input_composition": "linear_input_composition" - }, - "parameters": [ - { - "name": "ymax", - "value": 0.0646, - "description": "Maximal transcription (3.4 RPU * 0.019 for conversion to RNAP/s)" - }, - { - "name": "ymin", - "value": 0.00019, - "description": "Minimal transcription (0.01 RPU * 0.019 for conversion to RNAP/s)" - }, - { - "name": "kd", - "value": 0.3, - "description": "Dissociation equilibrium constant" - }, - { - "name": "n", - "value": 3.9, - "description": "Cooperativety" - } - ] - }, - { - "collection": "structures", - "name": "OHC12_out_structure", - "inputs": [ - { - "name": "in1", - "part_type": "promoter" - }, - { - "name": "in2", - "part_type": "promoter" - } - ], - "devices": [ - { - "name": "OHC12_out_a", - "components": [ - "#in1", - "#in2", - "sCin_cassette" - ] - } - ] - }, - { - "collection": "parts", - "type": "cassette", - "name": "sCin_cassette", - "dnasequence": "gctgtcaccggatgtgctttccggtctgatgagtccgtgaggacgaaacagcctctacaaataattttgtttaatggttccaaagccagatactaaggaggtcccAATGttcgttatcatccaggctcacgaataccagaaatacgctgctgttctggaccagatgttccgtctgcgtaaaaaagttttcgctgacaccctgtgctgggacgttccggttatcggtccgtacgaacgtgactcctacgactccctggctccggcttacctggtttggtgcaacgactcccgtacccgtctgtacggtggtatgcgtctgatgccgaccaccggtccgaccctgctgtacgacgttttccgtgaaaccttcccggacgctgctgacctgatcgctccgggtatctgggaaggtacccgtatgtgcatcgacgaagaagctatcgctaaagacttcccggaaatcgacgctggtcgtgctttctccatgatgctgctggctctgtgcgaatgcgctctggaccacggtatccacaccatgatctccaactacgaaccgtacctgaaacgtgtttacaaacgtgctggtgctgaagttgaagaactgggtcgtgctgacggttacggtaaatacccggtttgctgcggtgctttcgaagtttccgaccgtgttctgcgtaaaatgcgtgctgctctgggtctgaccctgccgctgtacgttcgtcacgttccggctcgttccgttgttacccagttcctggaaatggctgcttaatagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata" - }, - - - - - - { - "collection": "output_devices", - "name": "pC-HSL_out", - "model": "pC-HSL_out_model", - "structure": "pC-HSL_out_structure", - "description": "comms_device" - }, - { - "collection": "models", - "name": "pC-HSL_out_model", - "functions": { - "response_function": "Hill_response", - "input_composition": "linear_input_composition" - }, - "parameters": [ - { - "name": "ymax", - "value": 0.114, - "description": "Maximal transcription (6 RPU * 0.019 for conversion to RNAP/s)" - }, - { - "name": "ymin", - "value": 0.00038, - "description": "Minimal transcription (0.02 RPU * 0.019 for conversion to RNAP/s)" - }, - { - "name": "kd", - "value": 0.2, - "description": "Dissociation equilibrium constant" - - }, - { - "name": "n", - "value": 2, - "description": "Cooperativety" - } - ] - }, - { - "collection": "structures", - "name": "pC-HSL_out_structure", - "inputs": [ - { - "name": "in1", - "part_type": "promoter" - }, - { - "name": "in2", - "part_type": "promoter" - } - ], - "devices": [ - { - "name": "pC-HSL_out_a", - "components": [ - "#in1", - "#in2", - "sRpa_cassette" - ] - } - ] - }, - { - "collection": "parts", - "type": "cassette", - "name": "sRpa_cassette", - "dnasequence": "AGTGGTCGTGATCTGAAACTCGATCACCTGATGAGCTCAAGGCAGAGCGAAACCACCTCTACAAATAATTTTGTTTAAtggttccaaagccagatactaaggaggtcccAATGcaggttcatgttattcgtcgtgaaaatcgtgcactgtatgcaggtctgctggaaaaatactttcgtattcgccatcagatctatgttgttgaacgtggttggaaagaactggatcgtccggatggtcgtgaaattgatcagtttgataccgaagatgcagtttatctgctgggtgttgataacgatgatattgttgcaggtatgcgtatggttccgaccaccagtccgaccctgctgagtgatgtttttccgcagctggcactggcaggtccggttcgtcgtcctgatgcatatgaactgagccgtatttttgttgttccgcgtaaacgtggtgaacatggtggtccgcgtgcagaagcagttattcaggcagcagcaatggaatatggtctgagcattggtctgagtgcatttaccattgttctggaaacctggtggctgcctcgtctggttgatcagggctggaaagcaaaaccgctgggtctgccgcaggatattaatggttttagcaccaccgcagttattgtggatgttgatgatgatgcatgggtgggtatttgtaatcgtcgtagcgttccgggtccgacactggaatggcgtggtctggaagcaattcgtcgtcatagcctgccggaatttcaggttattagcTAAAGTCGCGGCAGCAGCACAAGAAGATGGAGAAGGACACGAAACAAGTCGACATCATTTTTCGTTCGAAGCTCCCCGACATTTACATCCCCAACCATCTTCCGCTTCACTCGTACTGTTTTGAAAACATTTCCGAATTCAGCAGCCGGCCCTGTCTCATTAACGGCGCAAATAAGCAGATTTACACCTACGCGGATGTTGAACTTAATTCGCGCAAAGTCGCCGCCGGCCTCCATAAGCAGGGTATCCAGCCCAAAGATACGATCATGATCCTGCTTCCCAACTCGCCCGAATTCGTTTTCGCGTTTATTGGCGCGTCGTACCTGGGCGCAATCAGCACGATGGCCAACCCCCTTTTTACCCCCGCCGAGGTGGTTAAGCAAGCCAAGGCGAGCTCCGCCAAGATTATTGTCACGCAGGCATGCCACGTCAATAAAGTTAAGGATTACGCATTTGAAAATGATGTGAAGATTATCTGCATCGACAGCGCCCCCGAGGGCTGCCTGCACTTCTCGGTCCTTACGCAGGCCAATGAGCACGACATTCCCGAGGTGGAGATTCAGCCCGATGACGTCGTCGCGCTCCCCTATAGCAGCGGCACCACGGGTCTGCCCAAAGGTGTCATGCTCACCCACAAAGGCCTCGTGACCAGCGTGGCACAACAGGTGGACGGCGAAAACCCCAACCTTTACATCCATTCCGAGGACGTTATGCTGTGTGTGCTCCCCCTGTTTCACATTTACTCCCTTAACTCGGTCCTTCTTTGCGGCCTCCGTGTTGGCGCAGCAATCCTTATTATGCAAAAGTTCGATATTGTCAGCTTCCTGGAGCTCATTCAACGCTACAAAGTCACGATTGGCCCCTTCGTCCCCCCGATTGTGCTCGCGATTGCGAAGTCCCCCATGGTGGATGACTACGATCTCAGCAGCGTCCGTACGGTCATGTCCGGCGCGGCACCGCTCGGTAAAGAACTGGAGGATACGGTCCGGGCCAAATTCCCGAATGCGAAGCTGGGTCAGGGTTACGGCATGACCGAGGCAGGTCCCGTGCTCGCCATGTGCCTGGCATTCGCGAAGGAGCCCTTCGAGATCAAGAGCGGTGCGTGCGGCACGGTCGTTCGGAACGCGGAAATGAAAATCGTGGACCCCAAAACCGGCAATTCCCTTCCCCGCAACCAATCCGGCGAAATTTGCATCCGGGGTGACCAGATTATGAAGGGCTATCTTAATGACCCGGAAGCCACGGCGCGGACGATTGACAAAGAAGGTTGGCTGTATACCGGTGACATTGGTTACATCGACGATGACGACGAGCTTTTTATTGTGGACCGGCTCAAAGAACTCATCAAATATAAAGGCTTTCAAGTTGCGCCCGCGGAGCTGGAGGCACTGCTTCTTAACCATCCCAACATCTCGGATGCCGCGGTCGTGCCGATGAAGGATGAACAAGCGGGTGAAGTGCCGGTCGCGTTTGTGGTTCGGAGCAACGGCTCCACGATTACGGAGGATGAGGTTAAGGATTTTATTTCCAAGCAGGTTATCTTTTATAAACGGATTAAACGCGTTTTCTTCGTCGATGCCATCCCCAAATCCCCCAGCGGCAAGATCCTTCGGAAAGATCTTCGTGCGAAACTGGCAGCAGGcCTTCCGAATTAAAAGAGGAGAAAGGTACCATGCTGGCCATGAGCCCGCCGAAACCGGCAGTGGAACTGGATCGTCATATTGATCTGGACCAGGCACACGCTGTTGCAAGCGGCGGTGCACGTATCGTCCTGGCACCTCCGGCCCGTGATCGCTGCCGTGCATCCGAAGCTCGTCTGGGTGCAGTCATTCGTGAAGCTCGCCATGTGTATGGCCTGACCACGGGTTTTGGTCCGCTGGCAAACCGTCTGATCAGCGGTGAAAATGTGCGCACCCTGCAAGCTAACCTGGTTCATCACCTGGCCAGCGGCGTGGGTCCGGTTCTGGATTGGACCACGGCACGTGCAATGGTCCTGGCACGCCTGGTGAGCATTGCACAAGGTGCCAGCGGTGCATCCGAAGGCACCATTGCGCGTCTGATCGATCTGCTGAACAGCGAACTGGCTCCTGCGGTGCCGAGCCGCGGTACCGTTGGTGCAAGCGGCGACCTGACGCCGCTGGCACATATGGTGCTGTGTCTGCAAGGCCGCGGTGATTTCCTGGATCGTGACGGTACCCGCCTGGACGGTGCAGAAGGCCTGCGTCGCGGCCGTCTGCAACCGCTGGATCTGAGCCACCGCGACGCCCTGGCACTGGTGAACGGTACCAGCGCGATGACGGGCATCGCCCTGGTTAATGCTCATGCGTGCCGTCACCTGGGTAACTGGGCAGTTGCACTGACCGCTCTGCTGGCAGAATGTCTGCGTGGTCGTACGGAAGCATGGGCGGCCGCACTGAGCGATCTGCGCCCGCATCCGGGTCAGAAAGACGCTGCGGCCCGCCTGCGTGCACGTGTTGATGGCTCCGCTCGTGTGGTTCGCCACGTCATTGCGGAACGTCGCCTGGATGCCGGTGACATCGGCACCGAACCGGAAGCCGGTCAGGATGCATACAGCCTGCGTTGCGCACCGCAAGTGCTGGGTGCTGGTTTTGATACCCTGGCGTGGCATGACCGCGTTCTGACCATTGAACTGAACGCGGTTACGGATAATCCGGTCTTTCCGCCGGACGGTAGCGTCCCGGCACTGCATGGCGGTAATTTCATGGGCCAGCACGTTGCACTGACCTCGGATGCTCTGGCAACCGCCGTTACGGTCCTGGCAGGTCTGGCAGAACGTCAAATCGCGCGCCTGACGGACGAACGTCTGAATCGCGGCCTGCCGCCGTTTCTGCATCGTGGTCCGGCGGGCCTGAACAGCGGTTTCATGGGTGCACAGGTGACCGCAACGGCTCTGCTGGCTGAAATGCGTGCAACCGGTCCGGCAAGCATTCACAGCATCAGCACGAACGCAGCTAATCAAGATGTCGTGTCGCTGGGCACCATTGCGGCCCGTCTGTGTCGCGAAAAAATCGACCGTTGGGCAGAAATTCTGGCTATCCTGGCACTGTGCCTGGCACAGGCAGCTGAACTGCGCTGTGGCAGCGGTCTGGATGGTGTCTCGCCGGCAGGCAAAAAACTGGTGCAGGCGCTGCGTGAACAATTCCCGCCGCTGGAAACCGATCGTCCGCTGGGTCAGGAAATTGCAGCACTGGCGACGCATCTGCTGCAACAAAGCCCGGTGTAaGGCTCCTTTTGGAGCCTTTTTTTTT" - }, - - - - - - { - "collection": "output_devices", - "name": "DAPG_out", - "model": "DAPG_out_model", - "structure": "DAPG_out_structure", - "description": "comms_device" - }, - { - "collection": "models", - "name": "DAPG_out_model", - "functions": { - "response_function": "Hill_response", - "input_composition": "linear_input_composition" - }, - "parameters": [ - { - "name": "ymax", - "value": 0.0646, - "description": "Maximal transcription (3.4 RPU * 0.019 for conversion to RNAP/s)" - }, - { - "name": "ymin", - "value": 0.00038, - "description": "Minimal transcription (0.02 RPU * 0.019 for conversion to RNAP/s)" - }, - { - "name": "kd", - "value": 0.15, - "description": "Dissociation equilibrium constant" - }, - { - "name": "n", - "value": 4, - "description": "Cooperativety" - } - ] - }, - { - "collection": "structures", - "name": "DAPG_out_structure", - "inputs": [ - { - "name": "in1", - "part_type": "promoter" - }, - { - "name": "in2", - "part_type": "promoter" - } - ], - "devices": [ - { - "name": "DAPG_out_a", - "components": [ - "#in1", - "#in2", - "sPhl_cassette" - ] - } - ] - }, - { - "collection": "parts", - "type": "cassette", - "name": "sPhl_cassette", - "dnasequence": "actcttcctttttcaatattattgaagcatttatcagggttattgtctcatgagcggatacatatttgaatgtatttagaaaaataaacaaataggggttccgcgTACATCAGAGATTTTGAGACACAaGTACNNNNNNNNNNNNNNNNNNNNCGTAagctgtcaccggatgtgctttccggtctgatgagtccgtgaggacgaaacagcctctacaaataattttgtttaaGTGAAAGAACGGAATCTGGAGGATGTACACATGAATAAGGTAGGAATTGTGAGCTATGGCGCGGGTATCCCGGTCTGCCGGCTCAAGGTGGACGACGTGATCCAGGTGTGGAAAAACACCGATCTGAGTTTGGTAAAGGGCCAATTGGGCGTTATTGAAAGGGCCGTCCTGCAACCCGACGAAGATGTCATAACCTTGGGTGTCCTCGCCGCCCAACGCGCGCTGGACAAGGCACCACCTTGTTCCCTCGAAGCGCTTTATCTCGGCACCTGCACCAATCCTTATGACTCCCGGGCCTCGGCCGCAATCATCCTGGAAATGCTCGGCTGCGGCTATGACGCCTTTTGCGCAGACGTGCAGTTTGCCGGCAAATCAGGCACCAGCGCCCTCCAGATCGCATACGCCTTGGTAGCGTCGGGCATGGTGGGCAACGCTTTGGCGGTGGGTGCCGATACGATCAACCGCAACACCGCCCCCGGTGACTTGACGGAGTCCTATGCCGGAGCCGGGGCCGCGGCCTTGCTGTTGGGGACAGAAAATGTGATCGCGCATTTTGACGCAAGTTTTTCTTGCGCGGCGGATGTCGCTGACAACATCAGGCCTCAAGGGGACCGCTATATCCGCTCGGGAATGGGATTGGGCTCGGACAAGAACAGTATCGGCCTCGAGGACCAGACTCGCCGCGCCGCCTCGGGATTGATGGCCAAGATCCATGCGCAAGCCGATGATTTCGATTACGTCGTTTTCCAACAAAACCTGGTGTCGACCCCCTACTCTCTCGGCAAGCACCTGGGATTCACGAAGGCCCAAATCGAACCTGGCATCTACGCCCAGAGTGTCGGCGATGCTGGAGCCGCGAGTCCTTTACTGGGCTTGGTCAACGTACTCGATCAAGCGCGTCCTGGCGAAAGAATCCTGGTGGTTTCCTATGGCTTCGGTGCGGGCAGCGATGCCATCGCCTTGACCGTCACCGATGCCATCGAAGCCTATCAAAAGACCAACGTTCCGCTGCGCACGCAGCTGGAGGATAAGTACTACGTGGATTACGGGACGTCGATCAAGTACGAGTTCAAATACTTGCGGCCCGACTATGCCCTGACGGCCTATCTCTGATTCCAATCATCCAGCAAGGAGCACCTTTTTATGTGCGCACGACGCGTTGCTATCGTTTCGGCTGCCTATACCCCTAAACCTGGCAGTTCCAGAGTTCGCCAGACTTTCAAGGAGATGATCGTCGAGTCCGCCTACCAGGCACTCAACGCCATCAAGATGCACCCTCGCGAACTTCAGGCAGTTGCCTATGGGTACCATGGTGAAGGTATTTCTGAATACGGAGGTCTGGGCCCAACCATCTCCGATGCCTTGGGGATCAGCCCTGCCCCCACGTTCATGAGTACGGCCAACTGCACCAGCAGTTCGGTGTCTTTCCAGATGGCTCACCAAATGGTCGCCTCAGGTGAATACGACATCGTTCTGTGTGGCGGCTTTGAAAAAATGACCGATCACTTCAACTATGCCGAGTACATTGGCTCGAGCACTGAATGTGAATACGATTATTTTCTAGGCATCTCTCACACAGACGCCTTCGCCCTGGCGACCGCCGAATATTTTGAAAAGTACGGCTATGCAGGACGCGAAGCGGATGTATTGGCCACTTTCGGGCGGCAGATGCGCATTTATGCCCATAACACTCCCACGGCTACCCGTTATGGCGTGCCGATCCCGTCTCTCGAAACACTCAAAAGCAGCGAAGCATGCGGCTCCATGCTGGCCTGGGGTGAAGCCAGCGGTTGCGCCATCCTGGTTGCCGAACACCTTGTGCACCGCTACACGACCCAACCGGTATTTGTCCGTGGCTGTGCCTACACCGGTGTGTCGCATTATTTCGGCACGCGCTATCACAACCCGACGTTGCAATTTCCGGGGCTGCCAAAAGATGTCGGCATGGCGGTTTCCGCCAACTCGCTGGCCTGCGCCGAAATCGCCTACAAAAAAGCCGGTATCACCGCAAAGGATATCGATGTGGCGCAAGTCTACGACTTGCTGGGCGCCGGGTTGATTCAAATGGAGTCCATGGGCGTATGTGGTCCAGGCCAGGCAGGCGACTTTGTATTGGAAGGCGGCATAGCCCTTGATGGGCAACTTCCCCTGAACACTGACGGCGGCAACATCGGACGCGGCCACGCTTCCGGTTGCGATGGGATTTTGCACATTACTGAATTGTTCCGGCAGCTTCGCGGCGAGTCCAACAATCAAGTCAAAGGCGCGCGTATTGGCGTCTCGCAAAACCTGGGCGGTTACGCCGCGCACAACAGCGTCATTGTGCTTTCCAACGATTAAGGAGCCGACCATGTCCCTTTACCCTGAACAAATTCACCGCATGACCACCGCCAGCATGTTGCGCGAATGGCGCGAACACGGTGGCAAATACCGCCTCGAAGGCAGCCGATGCCAGGACTGCGAAGAAATCTTCTTCCCTCGGCGCACAGTTTGCGGTGCGTGCAACTCGTTGAATGTAGAACCGTATCGCTGCGCGCGCACCGGCACTATCCAGGTCAGCGCACACGCCGAGAACCCCATTCTTGCGGCCATGGGCTACGGCGAAACCGTGCCCCGCTTCATGGCGATGGTGCGCCTGGATGATGGTCTGGTGATTGCCTCGGAAATAGTTGACGTCATCGATCCGCGACAAGTCGTCAGCGGTGCGCCCGTGCGCATGGTCATTCGAAAACATGTCCGGGAAAGTAACTTGGCCTGGCAATATGCCTATAAGTTTGTATTGGTGAAATAACAAACTTAGACGCCGCCATACCCCGCGTTATCGATAACAACAGTCAAGTTTTTGGCCTCCAAGCCCGTTGCTTTGATTCTGTCTTTCAGAGTCCAGCTTTGCTGTTATTGCCTTAAACATGTTTCTAACTTTATTGGCTTTTAGCCGAGGACTTGTCATGTCTACTCTTTGCAAACCCAGTCTGCTGTTCCCGCAATATAAGATCACCCAGCAACAAATGATCGAGCATCTAGAGCAGTTGCATGATGATCACCCGAGAATGGCTCTTGCCAAACGCATGATTCAAAACACACAGGTGAACGAACGATACTTGGTCCTGCCCATTGATGAACTGGCGGTGCATACCGGCTTCACCCATCGCAGCATTGTTTATGAGCGCGAGGCCCGCCGCATGTCATCCATCGCGGCGCGCCAAGCCATCGAGAATGCCGGGCTGACCACCGACGACATTCGAATGGTCGCTGTGACATCGTGCACGGGTTTCATGATGCCTTCGCTGACGGCCCACTTGATCAACGACCTGGGCCTGCGAACATCGACCGTACAACTGCCTATCGCTCAATTGGGATGCGTGGCAGGCGCTGCGGCGATCAATCGAGCCAATGACTTCGCCAGCCTGGCGCCGGACAACCATGTGCTCATCGTCTCCCTGGAGTTCTCGTCGCTCTGCTATCAACCCCAGGACACCAAGTTGCACGCATTCATCTCAGCGGCATTATTCGGCGATGCGGTATCAGCCTGCGTAATGCGAGCCGACGATCAGGCGTCTGGTTTCAAGATCGCCAAGACGGGGTCTTACTTCCTGCCTGATAGCGAGCACTATATTAAATACGACGTCAAAGACAGTGGCTTTCACTTCACCCTGGACAAGGCGGTCATGAACTCCATTAAAGATGTCGCACCCATGATGGAGGAATTGAACTACGAAACCTTCAATCAACATTGCGCTCAAAATGACTTTTTCATCTTCCATACAGGCGGACGGAAAATTCTTGATGAACTGGTCCTGCAATTGGACTTGGAACCCGGCAGGGTCGCGCAATCCCGCGACAGTTTGAGCGAAGCCGGGAACATCGCCAGCGTGGTGGTTTTCGATGTGCTCAAGCGCCAGTTCGACAGCGGACCTGTCAATGGCGCGACGGGCATGTTGGCGGCCTTCGGCCCGGGTTTCACCGCTGAAATGGCCGTGGGCAAGTGGGTCGCCTGAcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttataAGGTGCTTCCTCGCTCACTGactcgctgcacgaggcagacctcagcgctagcggagtgtatactggcttactatgttggcactgatgagggtgtcagtgaagtgcttcatgtggcaggagaaaaaaggctgcaccggtgcgtcagcagaatatgtgatacaggatatattccgcttcctcgctcactgactcgctacgctcggtcgttcgactgcggcgagcggaaatggcttacgaacggggcggagatttcctggaagatgccaggaagatacttaacagggaagtgagagggccgcggcaaagccgtttttccataggctccgcccccctgacaagcatcacgaaatctgacgctcaaatcagtggtggcgaaacccgacaggactataaagataccaggcgtttccccCtggcggctccctcgtgcgctctcctgttcctgcctttcggtttaccggtgtcattccgctgttatggccgcgtttgtctcattccacgcctgacactcagttccgggtaggcagttcgctccaagctggactgtatgcacgaaccccccgttcagtccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggaaagacatgcaaaagcaccactggcagcagccactggtaattgatttagaggagttagtcttgaagtcatgcgccggttaaggctaaactgaaaggacaagttttggtgactgcgctcctccaagccagttacctcggttcaaagagttggtagctcagagaaccttcgaaaaaccgccctgcaaggcggttttttcgttttcagagcaagagattacgcgcagaccaaaacgatctcaagaagatcatcttattaaATTCTCACCAATAAAAAACGCCCGGCGGCAACCGAGCGTTCTGAACAAATCCAGATGGAGTTCTGAGGTCATTACTGGATCTATCAACAGGAGTCCAAGCGAGCTTTAGAAAAACTCATCGAGgttaggtggcggtacttgggtcgatatcaaagtgcatcacttcttcccgtatgcccaactttgtatagagagccactgcgggatcgtcaccgtaatctgcttgcacgtagatcacataagcaccaagcgcgttggcctcatgcttgaggagattgatgagcgcggtggcaatgccctgcctccggtgctcgccggagactgcgagatcatagatatagatctcactacgcggctgctcaaacttgggcagaacgtaagccgcgagagcgccaacaaccgcttcttggtcgaaggcagcaagcgcgatgaatgtcttactacggagcaagttcccgaggtaatcggagtccggctgatgttgggagtaggtggctacgtctccgaactcacgaccgaaaagatcaagagcagtccgcatggatttgacttggtcagggccgagcctacatgtgcgaatgatgcccatacttgagccacctaactttgttttagggcgactgccctgctgcgtaacatcgttgctgctgcgtaacatcgttgctgctccataacatcaaacatcgacccacggcgtaacgcgcttgctgcttggatgcccgaggcatagactgtacaaaaaaacagtcataacaagccatgaaaaccgccactgcgccgttaccaccgctgcgttcggtcaaggttctggaccagttgcgtgagcgcatacgctacttgcattacagtttacgaaccgaacaggcttatgtcaattcggttgaatactcat" - }, - - - - - - { - "collection": "functions", - "name": "Hill_response", - "equation": "ymin + (ymax - ymin) / (1.0 + (kd / x)^n)", - "variables": [ - { - "name": "x", - "map": "#//model/functions/input_composition" - } - ], - "parameters": [ - { - "name": "ymax", - "map": "#//model/parameters/ymax" - }, - { - "name": "ymin", - "map": "#//model/parameters/ymin" - }, - { - "name": "kd", - "map": "#//model/parameters/kd" - }, - { - "name": "n", - "map": "#//model/parameters/n" - } - ] - }, - { - "collection": "functions", - "name": "linear_input_composition", - "equation": "x", - "variables": [ - { - "name": "x", - "map": "#//structure/inputs/in1/model/functions/response_function" - } - ] - }, - - - - - - - { - "collection": "circuit_rules", - "rules": { - "function": "AND", - "rules": [ - "YFP_reporter_a AFTER L3", - "YFP_reporter_b BEFORE L3", - - "YFP_reporter_a BEFORE attB2", - "attB2 AFTER L3", - "OC6_out_a AFTER attB2", - "OHC12_out_a AFTER attB2", - "DAPG_out_a AFTER attB2", - "pC-HSL_out_a AFTER attB2", - - "attB2 AFTER Pr203-cI-R3_v2_a", - "attB2 AFTER Pr203-cI-R4_v2_a", - "attB2 AFTER Pr204-P22-R3_a", - "attB2 AFTER Pr253-TP901-R2_a", - "attB2 AFTER Pr206-r1t-R4_a", - "attB2 AFTER Pr208-Tuc2009-R3_a", - "attB2 AFTER Pr210-phage186-RBS50_a", - "attB2 AFTER Pr211-933W-R1_a", - "attB2 AFTER Pr211-933W-R2_a", - "attB2 AFTER Pr212-L5-R1_a", - "attB2 AFTER Pr214-P2hd-R1_a", - "attB2 AFTER Pr215-P2-R1_a", - "attB2 AFTER Pr215-P2-R3_a", - "attB2 AFTER Pr215-P2-R4_a", - "attB2 AFTER Pr218-Wphi-R1_a", - "attB2 AFTER Pr217-VP585-R1_a", - - "attB2 AFTER Pr203-cI-R3_v2_b", - "attB2 AFTER Pr203-cI-R4_v2_b", - "attB2 AFTER Pr204-P22-R3_b", - "attB2 AFTER Pr253-TP901-R2_b", - "attB2 AFTER Pr206-r1t-R4_b", - "attB2 AFTER Pr208-Tuc2009-R3_b", - "attB2 AFTER Pr210-phage186-RBS50_b", - "attB2 AFTER Pr211-933W-R1_b", - "attB2 AFTER Pr211-933W-R2_b", - "attB2 AFTER Pr212-L5-R1_b", - "attB2 AFTER Pr214-P2hd-R1_b", - "attB2 AFTER Pr215-P2-R1_b", - "attB2 AFTER Pr215-P2-R3_b", - "attB2 AFTER Pr215-P2-R4_b", - "attB2 AFTER Pr218-Wphi-R1_b", - "attB2 AFTER Pr217-VP585-R1_b" - ] - } - }, - { - "collection": "device_rules", - "rules": { - "function": "AND", - "rules": [ - "ALL_FORWARD" - ] - } - } -]