Update docs
This commit is contained in:
cjmyers
parent
8ce5a5ce01
commit
3495edbc2a
16 changed files with 366 additions and 361 deletions
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@ -2252,138 +2252,20 @@
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</DnaComponent>
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</component>
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</Collection>
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||||
<DnaComponent ns2:about="http://www.async.ece.utah.edu#comp_10_2_2014_15_7_48_611_iBioSim">
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||||
<DnaComponent ns2:about="http://www.async.ece.utah.edu#comp_5_4_2015_20_2_22_118_iBioSim">
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||||
<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000804"/>
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||||
<displayId>MyGeneticToggle</displayId>
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||||
<name>pIKE Genetic Toggle Switch</name>
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||||
<description>Gardner/Collins Genetic Toggle Switch</description>
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||||
<dnaSequence>
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||||
<DnaSequence ns2:about="http://www.async.ece.utah.edu#seq_10_2_2014_15_7_48_611_iBioSim">
|
||||
<nucleotides>ttgagaagagaaaagaaaaccgccgatcctgtccaccgcattactgcaaggtagtggacaagaccggcggtcttaagttttttggctgaattattaagctactaaagcgtagttttcgtcgtttgcagcctgcccgctttccagtcgggaaacctgtcgtgccagctgcattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcgccagggtggtttttcttttcaccagtgagacgggcaacagctgattgcccttcaccgcctggccctgagagagttgcagcaagcggtccacgctggtttgccccagcaggcgaaaatcctgtttgatggtggttaacggcgggatataacatgagctgtcttcggtatcgtcgtatcccactaccgagatatccgcaccaacgcgcagcccggactcggtaatggcgcgcattgcgcccagcgccatctgatcgttggcaaccagcatcgcagtgggaacgatgccctcattcagcatttgcatggtttgttgaaaaccggacatggcactccagtcgccttcccgttccgctatcggctgaatttgattgcgagtgagatatttatgccagccagccagacgcagacgcgccgagacagaacttaatgggcccgctaacagcgcgatttgctggtgacccaatgcgaccagatgctccacgcccagtcgcgtaccgtcttcatgggagaaaataatactgttgatgggtgtctggtcagagacatcaagaaataacgccggaacattagtgcaggcagcttccacagcaatggcatcctggtcatccagcggatagttaatgatcagcccactgacgcgttgcgcgagaagattgtgcaccgccgctttacaggcttcgacgccgcttcgttctaccatcgacaccaccacgctggcacccagttgatcggcgcgagatttaatcgccgcgacaatttgcgacggcgcgtgcagggccagactggaggtggcaacgccaatcagcaacgactgtttgcccgccagttgttgtgccacgcggttgggaatgtaattcagctccgccatcgccgcttccactttttcccgcgttttcgcagaaacgtggctggcctggttcaccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcgtataacgttactggtttcacattcaccatggtcctgtctttgtgctcagtatctctatcactgatagggatgtcaatctctatcactgatagggacaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacacaaaagacgcgagaatgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataaaaagaaacgacaatgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataaaacgcatgagaaagcccccggaagatcaccttccgggggcttttttattgcgc</nucleotides>
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<DnaSequence ns2:about="http://www.async.ece.utah.edu#seq_5_4_2015_20_2_22_118_iBioSim">
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<nucleotides>caatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacacaaaagacgcgagaatgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataaaaagaaacgacaatgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataaaacgcatgagaaagcccccggaagatcaccttccgggggcttttttattgcgcttgagaagagaaaagaaaaccgccgatcctgtccaccgcattactgcaaggtagtggacaagaccggcggtcttaagttttttggctgaattattaagctactaaagcgtagttttcgtcgtttgcagcctgcccgctttccagtcgggaaacctgtcgtgccagctgcattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcgccagggtggtttttcttttcaccagtgagacgggcaacagctgattgcccttcaccgcctggccctgagagagttgcagcaagcggtccacgctggtttgccccagcaggcgaaaatcctgtttgatggtggttaacggcgggatataacatgagctgtcttcggtatcgtcgtatcccactaccgagatatccgcaccaacgcgcagcccggactcggtaatggcgcgcattgcgcccagcgccatctgatcgttggcaaccagcatcgcagtgggaacgatgccctcattcagcatttgcatggtttgttgaaaaccggacatggcactccagtcgccttcccgttccgctatcggctgaatttgattgcgagtgagatatttatgccagccagccagacgcagacgcgccgagacagaacttaatgggcccgctaacagcgcgatttgctggtgacccaatgcgaccagatgctccacgcccagtcgcgtaccgtcttcatgggagaaaataatactgttgatgggtgtctggtcagagacatcaagaaataacgccggaacattagtgcaggcagcttccacagcaatggcatcctggtcatccagcggatagttaatgatcagcccactgacgcgttgcgcgagaagattgtgcaccgccgctttacaggcttcgacgccgcttcgttctaccatcgacaccaccacgctggcacccagttgatcggcgcgagatttaatcgccgcgacaatttgcgacggcgcgtgcagggccagactggaggtggcaacgccaatcagcaacgactgtttgcccgccagttgttgtgccacgcggttgggaatgtaattcagctccgccatcgccgcttccactttttcccgcgttttcgcagaaacgtggctggcctggttcaccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcgtataacgttactggtttcacattcaccatggtcctgtctttgtgctcagtatctctatcactgatagggatgtcaatctctatcactgataggga</nucleotides>
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</DnaSequence>
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</dnaSequence>
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<annotation>
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<SequenceAnnotation ns2:about="http://www.async.ece.utah.edu#anno0_10_2_2014_15_7_48_611_iBioSim">
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||||
<SequenceAnnotation ns2:about="http://www.async.ece.utah.edu#anno0_5_4_2015_20_2_22_118_iBioSim">
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<bioStart>1</bioStart>
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<bioEnd>1284</bioEnd>
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<strand>-</strand>
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<subComponent>
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<DnaComponent ns2:about="http://www.eugenecad.org/pIKELeftCassette_1">
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||||
<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000805"/>
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<displayId>pIKELeftCassette_1</displayId>
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||||
<description>pIKELeftCassette_1</description>
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<dnaSequence>
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<DnaSequence ns2:about="http://www.eugenecad.org/pIKELeftCassette_1_sequence">
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<nucleotides>tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcacaaagacaggaccatggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataattcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa</nucleotides>
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</DnaSequence>
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</dnaSequence>
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<annotation>
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<SequenceAnnotation ns2:about="http://www.eugenecad.org/pIKELeftCassette_1/annotation_1">
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<bioStart>1</bioStart>
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<bioEnd>54</bioEnd>
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<strand>+</strand>
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<subComponent>
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<DnaComponent ns2:about="http://partsregistry.org/part/BBa_R0040">
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<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000167"/>
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<displayId>BBa_R0040</displayId>
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<name>BBa_R0040</name>
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<description>TetR repressible promoter</description>
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<dnaSequence>
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<DnaSequence ns2:about="http://partsregistry.org/part/BBa_R0040_sequence">
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<nucleotides>tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac</nucleotides>
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</DnaSequence>
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</dnaSequence>
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</DnaComponent>
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</subComponent>
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</SequenceAnnotation>
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</annotation>
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<annotation>
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<SequenceAnnotation ns2:about="http://www.eugenecad.org/pIKELeftCassette_1/annotation_2">
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<bioStart>55</bioStart>
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<bioEnd>1194</bioEnd>
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<strand>+</strand>
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<subComponent>
|
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<DnaComponent ns2:about="http://www.eugenecad.org/device/BBa_J61101_BBa_C0012">
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<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000805"/>
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<displayId>BBa_J61101_BBa_C0012</displayId>
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<description>Repressor2</description>
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<dnaSequence>
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<DnaSequence ns2:about="http://www.eugenecad.org/device/BBa_J61101_BBa_C0012_sequence">
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<nucleotides>aaagacaggaccatggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa</nucleotides>
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</DnaSequence>
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</dnaSequence>
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<annotation>
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<SequenceAnnotation ns2:about="http://www.eugenecad.org/pIKELeftCassette_1/Repressor2/annotation_1">
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<bioStart>1</bioStart>
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<bioEnd>12</bioEnd>
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<strand>+</strand>
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<subComponent>
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<DnaComponent ns2:about="http://partsregistry.org/part/BBa_J61101">
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<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000139"/>
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<displayId>BBa_J61101</displayId>
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<name>BBa_J61101</name>
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<description>Ribosome Binding Site Family Member</description>
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<dnaSequence>
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<DnaSequence ns2:about="http://partsregistry.org/part/BBa_J61101_sequence">
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<nucleotides>aaagacaggacc</nucleotides>
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</DnaSequence>
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</dnaSequence>
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</DnaComponent>
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</subComponent>
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</SequenceAnnotation>
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</annotation>
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<annotation>
|
||||
<SequenceAnnotation ns2:about="http://www.eugenecad.org/pIKELeftCassette_1/Repressor2/annotation_2">
|
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<bioStart>13</bioStart>
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<bioEnd>1140</bioEnd>
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<strand>+</strand>
|
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<subComponent>
|
||||
<DnaComponent ns2:about="http://partsregistry.org/part/BBa_C0012">
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<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000316"/>
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<displayId>BBa_C0012</displayId>
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<name>BBa_C0012</name>
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<description>lacI repressor from E. coli (+LVA)</description>
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<dnaSequence>
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<DnaSequence ns2:about="http://partsregistry.org/part/BBa_C0012_sequence">
|
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<nucleotides>atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa</nucleotides>
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||||
</DnaSequence>
|
||||
</dnaSequence>
|
||||
</DnaComponent>
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||||
</subComponent>
|
||||
</SequenceAnnotation>
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</annotation>
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||||
</DnaComponent>
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||||
</subComponent>
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</SequenceAnnotation>
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||||
</annotation>
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<annotation>
|
||||
<SequenceAnnotation ns2:about="http://www.eugenecad.org/pIKELeftCassette_1/annotation_3">
|
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<bioStart>1195</bioStart>
|
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<bioEnd>1284</bioEnd>
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<strand>+</strand>
|
||||
<subComponent>
|
||||
<DnaComponent ns2:about="http://www.eugenecad.org/parts/ECK120029600">
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||||
<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000141"/>
|
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<displayId>ECK120029600</displayId>
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||||
<name>ECK120029600</name>
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<description>Terminator</description>
|
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<dnaSequence>
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<DnaSequence ns2:about="http://www.eugenecad.org/parts/ECK120029600_sequence">
|
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<nucleotides>ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa</nucleotides>
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||||
</DnaSequence>
|
||||
</dnaSequence>
|
||||
</DnaComponent>
|
||||
</subComponent>
|
||||
</SequenceAnnotation>
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||||
</annotation>
|
||||
</DnaComponent>
|
||||
</subComponent>
|
||||
</SequenceAnnotation>
|
||||
</annotation>
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<annotation>
|
||||
<SequenceAnnotation ns2:about="http://www.async.ece.utah.edu#anno1_10_2_2014_15_7_48_611_iBioSim">
|
||||
<bioStart>1285</bioStart>
|
||||
<bioEnd>2941</bioEnd>
|
||||
<bioEnd>1657</bioEnd>
|
||||
<strand>+</strand>
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||||
<subComponent>
|
||||
<DnaComponent ns2:about="http://www.eugenecad.org/pIKERightCassette_1">
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@ -2550,6 +2432,124 @@
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</DnaSequence>
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||||
</dnaSequence>
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||||
</DnaComponent>
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||||
</subComponent>
|
||||
</SequenceAnnotation>
|
||||
</annotation>
|
||||
</DnaComponent>
|
||||
</subComponent>
|
||||
</SequenceAnnotation>
|
||||
</annotation>
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||||
<annotation>
|
||||
<SequenceAnnotation ns2:about="http://www.async.ece.utah.edu#anno1_5_4_2015_20_2_22_118_iBioSim">
|
||||
<bioStart>1658</bioStart>
|
||||
<bioEnd>2941</bioEnd>
|
||||
<strand>-</strand>
|
||||
<subComponent>
|
||||
<DnaComponent ns2:about="http://www.eugenecad.org/pIKELeftCassette_1">
|
||||
<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000805"/>
|
||||
<displayId>pIKELeftCassette_1</displayId>
|
||||
<description>pIKELeftCassette_1</description>
|
||||
<dnaSequence>
|
||||
<DnaSequence ns2:about="http://www.eugenecad.org/pIKELeftCassette_1_sequence">
|
||||
<nucleotides>tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcacaaagacaggaccatggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataattcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa</nucleotides>
|
||||
</DnaSequence>
|
||||
</dnaSequence>
|
||||
<annotation>
|
||||
<SequenceAnnotation ns2:about="http://www.eugenecad.org/pIKELeftCassette_1/annotation_1">
|
||||
<bioStart>1</bioStart>
|
||||
<bioEnd>54</bioEnd>
|
||||
<strand>+</strand>
|
||||
<subComponent>
|
||||
<DnaComponent ns2:about="http://partsregistry.org/part/BBa_R0040">
|
||||
<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000167"/>
|
||||
<displayId>BBa_R0040</displayId>
|
||||
<name>BBa_R0040</name>
|
||||
<description>TetR repressible promoter</description>
|
||||
<dnaSequence>
|
||||
<DnaSequence ns2:about="http://partsregistry.org/part/BBa_R0040_sequence">
|
||||
<nucleotides>tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac</nucleotides>
|
||||
</DnaSequence>
|
||||
</dnaSequence>
|
||||
</DnaComponent>
|
||||
</subComponent>
|
||||
</SequenceAnnotation>
|
||||
</annotation>
|
||||
<annotation>
|
||||
<SequenceAnnotation ns2:about="http://www.eugenecad.org/pIKELeftCassette_1/annotation_2">
|
||||
<bioStart>55</bioStart>
|
||||
<bioEnd>1194</bioEnd>
|
||||
<strand>+</strand>
|
||||
<subComponent>
|
||||
<DnaComponent ns2:about="http://www.eugenecad.org/device/BBa_J61101_BBa_C0012">
|
||||
<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000805"/>
|
||||
<displayId>BBa_J61101_BBa_C0012</displayId>
|
||||
<description>Repressor2</description>
|
||||
<dnaSequence>
|
||||
<DnaSequence ns2:about="http://www.eugenecad.org/device/BBa_J61101_BBa_C0012_sequence">
|
||||
<nucleotides>aaagacaggaccatggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa</nucleotides>
|
||||
</DnaSequence>
|
||||
</dnaSequence>
|
||||
<annotation>
|
||||
<SequenceAnnotation ns2:about="http://www.eugenecad.org/pIKELeftCassette_1/Repressor2/annotation_1">
|
||||
<bioStart>1</bioStart>
|
||||
<bioEnd>12</bioEnd>
|
||||
<strand>+</strand>
|
||||
<subComponent>
|
||||
<DnaComponent ns2:about="http://partsregistry.org/part/BBa_J61101">
|
||||
<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000139"/>
|
||||
<displayId>BBa_J61101</displayId>
|
||||
<name>BBa_J61101</name>
|
||||
<description>Ribosome Binding Site Family Member</description>
|
||||
<dnaSequence>
|
||||
<DnaSequence ns2:about="http://partsregistry.org/part/BBa_J61101_sequence">
|
||||
<nucleotides>aaagacaggacc</nucleotides>
|
||||
</DnaSequence>
|
||||
</dnaSequence>
|
||||
</DnaComponent>
|
||||
</subComponent>
|
||||
</SequenceAnnotation>
|
||||
</annotation>
|
||||
<annotation>
|
||||
<SequenceAnnotation ns2:about="http://www.eugenecad.org/pIKELeftCassette_1/Repressor2/annotation_2">
|
||||
<bioStart>13</bioStart>
|
||||
<bioEnd>1140</bioEnd>
|
||||
<strand>+</strand>
|
||||
<subComponent>
|
||||
<DnaComponent ns2:about="http://partsregistry.org/part/BBa_C0012">
|
||||
<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000316"/>
|
||||
<displayId>BBa_C0012</displayId>
|
||||
<name>BBa_C0012</name>
|
||||
<description>lacI repressor from E. coli (+LVA)</description>
|
||||
<dnaSequence>
|
||||
<DnaSequence ns2:about="http://partsregistry.org/part/BBa_C0012_sequence">
|
||||
<nucleotides>atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa</nucleotides>
|
||||
</DnaSequence>
|
||||
</dnaSequence>
|
||||
</DnaComponent>
|
||||
</subComponent>
|
||||
</SequenceAnnotation>
|
||||
</annotation>
|
||||
</DnaComponent>
|
||||
</subComponent>
|
||||
</SequenceAnnotation>
|
||||
</annotation>
|
||||
<annotation>
|
||||
<SequenceAnnotation ns2:about="http://www.eugenecad.org/pIKELeftCassette_1/annotation_3">
|
||||
<bioStart>1195</bioStart>
|
||||
<bioEnd>1284</bioEnd>
|
||||
<strand>+</strand>
|
||||
<subComponent>
|
||||
<DnaComponent ns2:about="http://www.eugenecad.org/parts/ECK120029600">
|
||||
<ns2:type ns2:resource="http://purl.obolibrary.org/obo/SO_0000141"/>
|
||||
<displayId>ECK120029600</displayId>
|
||||
<name>ECK120029600</name>
|
||||
<description>Terminator</description>
|
||||
<dnaSequence>
|
||||
<DnaSequence ns2:about="http://www.eugenecad.org/parts/ECK120029600_sequence">
|
||||
<nucleotides>ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa</nucleotides>
|
||||
</DnaSequence>
|
||||
</dnaSequence>
|
||||
</DnaComponent>
|
||||
</subComponent>
|
||||
</SequenceAnnotation>
|
||||
</annotation>
|
||||
|
|
|
|||
|
|
@ -4,18 +4,18 @@
|
|||
<comp:externalModelDefinition comp:md5="f1aec8d614b2cf9419a189c03d413468" comp:source="file:LacI_Inverter.xml" comp:id="LacI_Inverter"/>
|
||||
<comp:externalModelDefinition comp:md5="d34b0aad693c9a48a4754bbfabb6189c" comp:source="file:TetR_Inverter.xml" comp:id="TetR_Inverter"/>
|
||||
</comp:listOfExternalModelDefinitions>
|
||||
<model id="GeneticToggle" metaid="iBioSim2">
|
||||
<model id="GeneticToggle" metaid="iBioSim30">
|
||||
<annotation>
|
||||
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
||||
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
||||
<rdf:Description rdf:about="#iBioSim2">
|
||||
<rdf:Description rdf:about="#iBioSim30">
|
||||
<mts:DNAComponents>
|
||||
<rdf:Seq>
|
||||
<rdf:li rdf:resource="http://www.async.ece.utah.edu#comp_10_2_2014_15_7_48_611_iBioSim"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
|
||||
<rdf:li rdf:resource="http://www.async.ece.utah.edu#comp_5_4_2015_20_2_22_118_iBioSim"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
|
||||
</annotation>
|
||||
<comp:listOfSubmodels xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
|
||||
<comp:submodel comp:modelRef="LacI_Inverter" metaid="iBioSim1" comp:id="C1"/>
|
||||
<comp:submodel comp:modelRef="TetR_Inverter" metaid="iBioSim29" comp:id="C2"/>
|
||||
<comp:submodel comp:modelRef="LacI_Inverter" metaid="iBioSim2" comp:id="C1"/>
|
||||
<comp:submodel comp:modelRef="TetR_Inverter" metaid="iBioSim31" comp:id="C2"/>
|
||||
</comp:listOfSubmodels>
|
||||
<layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<layout:layout layout:id="iBioSim">
|
||||
|
|
@ -161,8 +161,8 @@
|
|||
<layout:listOfReactionGlyphs>
|
||||
<layout:reactionGlyph layout:id="Glyph__IPTG__complex__IPTG_LacI">
|
||||
<layout:boundingBox>
|
||||
<layout:position/>
|
||||
<layout:dimensions/>
|
||||
<layout:position layout:x="310" layout:y="375"/>
|
||||
<layout:dimensions layout:width="0" layout:height="0"/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfSpeciesReferenceGlyphs>
|
||||
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__IPTG__complex__IPTG_LacI" layout:role="product" layout:speciesGlyph="Glyph__IPTG_LacI">
|
||||
|
|
@ -179,8 +179,8 @@
|
|||
</layout:reactionGlyph>
|
||||
<layout:reactionGlyph layout:id="Glyph__LacI__complex__IPTG_LacI">
|
||||
<layout:boundingBox>
|
||||
<layout:position/>
|
||||
<layout:dimensions/>
|
||||
<layout:position layout:x="310" layout:y="375"/>
|
||||
<layout:dimensions layout:width="0" layout:height="0"/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfSpeciesReferenceGlyphs>
|
||||
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__LacI__complex__IPTG_LacI" layout:role="product" layout:speciesGlyph="Glyph__IPTG_LacI">
|
||||
|
|
@ -197,8 +197,8 @@
|
|||
</layout:reactionGlyph>
|
||||
<layout:reactionGlyph layout:id="Glyph__TetR__complex__aTc_TetR">
|
||||
<layout:boundingBox>
|
||||
<layout:position/>
|
||||
<layout:dimensions/>
|
||||
<layout:position layout:x="740" layout:y="55"/>
|
||||
<layout:dimensions layout:width="0" layout:height="0"/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfSpeciesReferenceGlyphs>
|
||||
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__TetR__complex__aTc_TetR" layout:role="product" layout:speciesGlyph="Glyph__aTc_TetR">
|
||||
|
|
@ -215,8 +215,8 @@
|
|||
</layout:reactionGlyph>
|
||||
<layout:reactionGlyph layout:id="Glyph__aTc__complex__aTc_TetR">
|
||||
<layout:boundingBox>
|
||||
<layout:position/>
|
||||
<layout:dimensions/>
|
||||
<layout:position layout:x="740" layout:y="55"/>
|
||||
<layout:dimensions layout:width="0" layout:height="0"/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfSpeciesReferenceGlyphs>
|
||||
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__aTc__complex__aTc_TetR" layout:role="product" layout:speciesGlyph="Glyph__aTc_TetR">
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
#Graph Data
|
||||
#Sat Oct 25 14:35:07 MDT 2014
|
||||
#Mon May 11 08:39:21 MDT 2015
|
||||
species.filled.2=true
|
||||
species.filled.1=true
|
||||
species.filled.0=true
|
||||
|
|
@ -9,12 +9,12 @@ species.connected.2=true
|
|||
species.connected.1=true
|
||||
species.connected.0=true
|
||||
species.xnumber.2=0
|
||||
y.max=107.8
|
||||
y.max=72.94646744011
|
||||
species.xnumber.1=0
|
||||
species.id.2=IPTG (1)
|
||||
species.xnumber.0=0
|
||||
auto.resize=true
|
||||
species.id.1=GFP (1)
|
||||
species.id.1=GFP (\u03C7)
|
||||
species.id.0=aTc (1)
|
||||
species.number.2=5
|
||||
species.number.1=4
|
||||
|
|
@ -31,13 +31,13 @@ species.directory.1=
|
|||
species.directory.0=
|
||||
x.max=10000.0
|
||||
title=GeneticToggle simulation results
|
||||
y.scale=10.0
|
||||
y.scale=5.0
|
||||
x.scale=1000.0
|
||||
y.min=0.0
|
||||
species.shape.2=Circle
|
||||
species.name.2=IPTG (1)
|
||||
species.shape.1=Triangle
|
||||
species.name.1=GFP (1)
|
||||
species.name.1=GFP (\u03C7)
|
||||
species.name.0=aTc (1)
|
||||
species.shape.0=Square
|
||||
x.axis=time
|
||||
|
|
@ -46,7 +46,7 @@ LogX=false
|
|||
plot.range.grid.line.paint=-4144960
|
||||
plot.domain.grid.line.paint=-4144960
|
||||
species.run.number.2=run-1
|
||||
species.run.number.1=run-1
|
||||
species.run.number.1=Average
|
||||
species.run.number.0=run-1
|
||||
visibleLegend=true
|
||||
x.min=100.0
|
||||
x.min=0.0
|
||||
|
|
|
|||
|
|
@ -1,28 +1,27 @@
|
|||
#GeneticToggle Properties
|
||||
#Thu Jan 22 16:58:46 MST 2015
|
||||
monte.carlo.simulation.start.index=1
|
||||
#Sun May 10 17:02:34 MDT 2015
|
||||
reb2sac.operator.max.concentration.threshold=15
|
||||
reb2sac.qssa.condition.1=0.1
|
||||
monte.carlo.simulation.time.step=inf
|
||||
monte.carlo.simulation.print.interval=100.0
|
||||
monte.carlo.simulation.runs=1
|
||||
reb2sac.simulation.method=monteCarlo
|
||||
reb2sac.simulation.method=Browser
|
||||
ode.simulation.time.limit=10000.0
|
||||
simulation.run.termination.decider=constraint
|
||||
reb2sac.generate.statistics=false
|
||||
monte.carlo.simulation.random.seed=314159
|
||||
ode.simulation.time.step=inf
|
||||
ode.simulation.out.dir=.
|
||||
monte.carlo.simulation.time.limit=10000.0
|
||||
simulation.printer.tracking.quantity=amount
|
||||
reb2sac.iSSA.adaptive=true
|
||||
simulation.printer=tsd.printer
|
||||
monte.carlo.simulation.min.time.step=0.0
|
||||
ode.simulation.absolute.error=1.0E-9
|
||||
ode.simulation.print.interval=100.0
|
||||
ode.simulation.min.time.step=0.0
|
||||
reb2sac.abstraction.method=none
|
||||
reb2sac.abstraction.method.3.3=kinetic-law-constants-simplifier
|
||||
reb2sac.abstraction.method.3.2=reversible-to-irreversible-transformer
|
||||
reb2sac.abstraction.method.3.1=distribute-transformer
|
||||
reb2sac.iSSA.number.paths=1
|
||||
reb2sac.rapid.equilibrium.condition.2=0.1
|
||||
reb2sac.diffusion.stoichiometry.amplification.value=1.0
|
||||
reb2sac.rapid.equilibrium.condition.1=0.1
|
||||
monte.carlo.simulation.out.dir=.
|
||||
selected.simulator=SSA-Direct
|
||||
reb2sac.iSSA.type=medianPath
|
||||
selected.simulator=rkf45
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
<body>
|
||||
|
||||
|
||||
<table border="2"><tr><th>Model ID</th><td>GeneticToggle</td></tr><tr><th>Model Name</th><td>Created by iBioSim flatten routine</td></tr></table>
|
||||
<table border="2"><tr><th>Model ID</th><td>GeneticToggle</td></tr><tr><th>Model Name</th><td>Created by libsbml flatten routine</td></tr></table>
|
||||
|
||||
<br/>
|
||||
<br/>
|
||||
|
|
@ -134,16 +134,16 @@
|
|||
<mrow>
|
||||
<mrow>
|
||||
<mo>(</mo>
|
||||
<mrow>
|
||||
<mo>(</mo>
|
||||
<mi>C1__pLac</mi>
|
||||
<mo>*</mo>
|
||||
<mi>C1__ko</mi>
|
||||
<mo>)</mo>
|
||||
</mrow>
|
||||
<mo>*</mo>
|
||||
<mfrac>
|
||||
<mrow>
|
||||
<mrow>
|
||||
<mo>(</mo>
|
||||
<mi>C1__pLac</mi>
|
||||
<mo>*</mo>
|
||||
<mi>C1__ko</mi>
|
||||
<mo>)</mo>
|
||||
</mrow>
|
||||
<mo>*</mo>
|
||||
<mi>C1__ko_f</mi>
|
||||
</mrow>
|
||||
<mrow>
|
||||
|
|
@ -204,7 +204,7 @@
|
|||
<mo>)</mo>
|
||||
</mrow>
|
||||
<mrow>
|
||||
<mi>nc</mi>
|
||||
<mi>C1__nc</mi>
|
||||
</mrow>
|
||||
</msup>
|
||||
</mrow>
|
||||
|
|
@ -229,16 +229,16 @@
|
|||
<mrow>
|
||||
<mrow>
|
||||
<mo>(</mo>
|
||||
<mrow>
|
||||
<mo>(</mo>
|
||||
<mi>C2__P0</mi>
|
||||
<mo>*</mo>
|
||||
<mi>C2__ko</mi>
|
||||
<mo>)</mo>
|
||||
</mrow>
|
||||
<mo>*</mo>
|
||||
<mfrac>
|
||||
<mrow>
|
||||
<mrow>
|
||||
<mo>(</mo>
|
||||
<mi>C2__P0</mi>
|
||||
<mo>*</mo>
|
||||
<mi>C2__ko</mi>
|
||||
<mo>)</mo>
|
||||
</mrow>
|
||||
<mo>*</mo>
|
||||
<mi>C2__ko_f</mi>
|
||||
</mrow>
|
||||
<mrow>
|
||||
|
|
@ -299,7 +299,7 @@
|
|||
<mo>)</mo>
|
||||
</mrow>
|
||||
<mrow>
|
||||
<mi>nc</mi>
|
||||
<mi>C2__nc</mi>
|
||||
</mrow>
|
||||
</msup>
|
||||
</mrow>
|
||||
|
|
|
|||
|
|
@ -1,25 +1,143 @@
|
|||
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
||||
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
|
||||
<model id="GeneticToggle" name="Created by iBioSim flatten routine" metaid="iBioSim1">
|
||||
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" arrays:required="true" fbc:required="false" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" comp:required="true" xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1" version="1" layout:required="false">
|
||||
<model id="GeneticToggle" name="Created by libsbml flatten routine" metaid="iBioSim1">
|
||||
<annotation>
|
||||
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
||||
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
||||
<rdf:Description rdf:about="#iBioSim2">
|
||||
<mts:DNAComponents>
|
||||
<rdf:Seq>
|
||||
<rdf:li rdf:resource="http://www.async.ece.utah.edu#comp_10_2_2014_15_7_48_611_iBioSim"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
|
||||
<rdf:li rdf:resource="http://www.async.ece.utah.edu#comp_10_2_2014_15_7_48_611_iBioSim"/>
|
||||
</rdf:Seq>
|
||||
</mts:DNAComponents>
|
||||
<mts:Strand>+</mts:Strand>
|
||||
</rdf:Description>
|
||||
</rdf:RDF>
|
||||
</ModelToSBOL>
|
||||
</annotation>
|
||||
<listOfCompartments>
|
||||
<compartment id="Cell" constant="true" spatialDimensions="3" size="1">
|
||||
</compartment>
|
||||
<layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<layout:layout layout:id="iBioSim">
|
||||
<layout:dimensions layout:width="1070" layout:height="425"/>
|
||||
<layout:listOfCompartmentGlyphs>
|
||||
<layout:compartmentGlyph layout:id="C1__Glyph__Cell" layout:compartment="Cell">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="0" layout:y="0"/>
|
||||
<layout:dimensions layout:width="1070" layout:height="425"/>
|
||||
</layout:boundingBox>
|
||||
</layout:compartmentGlyph>
|
||||
</layout:listOfCompartmentGlyphs>
|
||||
<layout:listOfSpeciesGlyphs>
|
||||
<layout:speciesGlyph layout:id="C1__Glyph__LacI" layout:species="LacI">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="98" layout:y="66"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="C1__Glyph__TetR" layout:species="TetR">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="90" layout:y="290"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="C1__Glyph__GFP" layout:species="GFP">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="290" layout:y="290"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="C1__Glyph__pLac" layout:species="C1__pLac">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="100" layout:y="170"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
</layout:listOfSpeciesGlyphs>
|
||||
<layout:listOfTextGlyphs>
|
||||
<layout:textGlyph layout:graphicalObject="C1__Glyph__Cell" layout:id="C1__TextGlyph__Cell" layout:text="Cell">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="0" layout:y="0"/>
|
||||
<layout:dimensions layout:width="1070" layout:height="425"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="C1__Glyph__LacI" layout:id="C1__TextGlyph__LacI" layout:text="LacI">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="98" layout:y="66"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="C1__Glyph__TetR" layout:id="C1__TextGlyph__TetR" layout:text="TetR">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="90" layout:y="290"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="C1__Glyph__GFP" layout:id="C1__TextGlyph__GFP" layout:text="GFP">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="290" layout:y="290"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="C1__Glyph__pLac" layout:id="C1__TextGlyph__pLac" layout:text="pLac">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="100" layout:y="170"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
</layout:listOfTextGlyphs>
|
||||
</layout:layout>
|
||||
<layout:layout layout:id="C2__iBioSim">
|
||||
<layout:dimensions layout:width="1070" layout:height="425"/>
|
||||
<layout:listOfCompartmentGlyphs>
|
||||
<layout:compartmentGlyph layout:id="C2__Glyph__Cell" layout:compartment="Cell">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="0" layout:y="0"/>
|
||||
<layout:dimensions layout:width="1070" layout:height="425"/>
|
||||
</layout:boundingBox>
|
||||
</layout:compartmentGlyph>
|
||||
</layout:listOfCompartmentGlyphs>
|
||||
<layout:listOfSpeciesGlyphs>
|
||||
<layout:speciesGlyph layout:id="C2__Glyph__TetR" layout:species="TetR">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="123" layout:y="65"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="C2__Glyph__LacI" layout:species="LacI">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="138" layout:y="216"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
</layout:listOfSpeciesGlyphs>
|
||||
<layout:listOfTextGlyphs>
|
||||
<layout:textGlyph layout:graphicalObject="C2__Glyph__Cell" layout:id="C2__TextGlyph__Cell" layout:text="Cell">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="0" layout:y="0"/>
|
||||
<layout:dimensions layout:width="1070" layout:height="425"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="C2__Glyph__TetR" layout:id="C2__TextGlyph__TetR" layout:text="TetR">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="123" layout:y="65"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="C2__Glyph__LacI" layout:id="C2__TextGlyph__LacI" layout:text="LacI">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="138" layout:y="216"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
</layout:listOfTextGlyphs>
|
||||
</layout:layout>
|
||||
</layout:listOfLayouts>
|
||||
<listOfCompartments>
|
||||
<compartment id="Cell" constant="true" spatialDimensions="3" size="1"/>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species id="GFP" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim11" boundaryCondition="false" compartment="Cell">
|
||||
</species>
|
||||
<species id="LacI" constant="false" initialAmount="60" hasOnlySubstanceUnits="true" metaid="iBioSim12" boundaryCondition="false" compartment="Cell">
|
||||
</species>
|
||||
<species id="TetR" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim13" boundaryCondition="false" compartment="Cell">
|
||||
</species>
|
||||
<species id="GFP" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim11" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="LacI" constant="false" initialAmount="60" hasOnlySubstanceUnits="true" metaid="iBioSim12" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="TetR" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim13" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="IPTG" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim14" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="aTc" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim15" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="IPTG_LacI" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim16" boundaryCondition="false" compartment="Cell"/>
|
||||
|
|
@ -138,14 +256,11 @@
|
|||
<minus/>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kc_f </ci>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kc_f </ci>
|
||||
<apply>
|
||||
<power/>
|
||||
<ci> IPTG </ci>
|
||||
<ci> nc_IPTG </ci>
|
||||
</apply>
|
||||
<power/>
|
||||
<ci> IPTG </ci>
|
||||
<ci> nc_IPTG </ci>
|
||||
</apply>
|
||||
<apply>
|
||||
<power/>
|
||||
|
|
@ -180,14 +295,11 @@
|
|||
<minus/>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kc_f </ci>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kc_f </ci>
|
||||
<apply>
|
||||
<power/>
|
||||
<ci> TetR </ci>
|
||||
<ci> nc_TetR </ci>
|
||||
</apply>
|
||||
<power/>
|
||||
<ci> TetR </ci>
|
||||
<ci> nc_TetR </ci>
|
||||
</apply>
|
||||
<apply>
|
||||
<power/>
|
||||
|
|
@ -237,35 +349,26 @@
|
|||
<divide/>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> C1__pLac </ci>
|
||||
<ci> C1__ko </ci>
|
||||
<apply>
|
||||
<divide/>
|
||||
<apply>
|
||||
<times/>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> C1__pLac </ci>
|
||||
<ci> C1__ko </ci>
|
||||
</apply>
|
||||
<ci> C1__ko_f </ci>
|
||||
</apply>
|
||||
<ci> C1__ko_f </ci>
|
||||
<ci> C1__ko_r </ci>
|
||||
</apply>
|
||||
<ci> C1__nr </ci>
|
||||
</apply>
|
||||
<apply>
|
||||
<plus/>
|
||||
<cn type="integer"> 1 </cn>
|
||||
<apply>
|
||||
<plus/>
|
||||
<cn type="integer"> 1 </cn>
|
||||
<times/>
|
||||
<apply>
|
||||
<times/>
|
||||
<apply>
|
||||
<divide/>
|
||||
<ci> C1__ko_f </ci>
|
||||
<ci> C1__ko_r </ci>
|
||||
</apply>
|
||||
<ci> C1__nr </ci>
|
||||
<divide/>
|
||||
<ci> C1__ko_f </ci>
|
||||
<ci> C1__ko_r </ci>
|
||||
</apply>
|
||||
<ci> C1__nr </ci>
|
||||
</apply>
|
||||
<apply>
|
||||
<power/>
|
||||
|
|
@ -278,7 +381,7 @@
|
|||
</apply>
|
||||
<ci> LacI </ci>
|
||||
</apply>
|
||||
<ci> nc </ci>
|
||||
<ci> C1__nc </ci>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
|
|
@ -299,35 +402,26 @@
|
|||
<divide/>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> C2__P0 </ci>
|
||||
<ci> C2__ko </ci>
|
||||
<apply>
|
||||
<divide/>
|
||||
<apply>
|
||||
<times/>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> C2__P0 </ci>
|
||||
<ci> C2__ko </ci>
|
||||
</apply>
|
||||
<ci> C2__ko_f </ci>
|
||||
</apply>
|
||||
<ci> C2__ko_f </ci>
|
||||
<ci> C2__ko_r </ci>
|
||||
</apply>
|
||||
<ci> C2__nr </ci>
|
||||
</apply>
|
||||
<apply>
|
||||
<plus/>
|
||||
<cn type="integer"> 1 </cn>
|
||||
<apply>
|
||||
<plus/>
|
||||
<cn type="integer"> 1 </cn>
|
||||
<times/>
|
||||
<apply>
|
||||
<times/>
|
||||
<apply>
|
||||
<divide/>
|
||||
<ci> C2__ko_f </ci>
|
||||
<ci> C2__ko_r </ci>
|
||||
</apply>
|
||||
<ci> C2__nr </ci>
|
||||
<divide/>
|
||||
<ci> C2__ko_f </ci>
|
||||
<ci> C2__ko_r </ci>
|
||||
</apply>
|
||||
<ci> C2__nr </ci>
|
||||
</apply>
|
||||
<apply>
|
||||
<power/>
|
||||
|
|
@ -340,7 +434,7 @@
|
|||
</apply>
|
||||
<ci> TetR </ci>
|
||||
</apply>
|
||||
<ci> nc </ci>
|
||||
<ci> C2__nc </ci>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,9 @@
|
|||
Executing:
|
||||
reb2sac.mac64 --target.encoding=xhtml --out=GeneticToggle.xhtml /Users/myers/research/nobackup/workspace/BioSim/docs//SynBioTutorial/GeneticToggle/GeneticToggle.xml
|
||||
|
||||
Total Simulation Time: 0.072144 seconds for GeneticToggle
|
||||
|
||||
|
||||
Executing:
|
||||
open /Users/myers/research/nobackup/workspace/BioSim/docs//SynBioTutorial/GeneticToggle/GeneticToggle.xhtml
|
||||
|
||||
1
docs/SynBioTutorial/GeneticToggle/mean.tsd
Normal file
1
docs/SynBioTutorial/GeneticToggle/mean.tsd
Normal file
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
1
docs/SynBioTutorial/GeneticToggle/standard_deviation.tsd
Normal file
1
docs/SynBioTutorial/GeneticToggle/standard_deviation.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","GFP","LacI","TetR","IPTG","aTc","IPTG_LacI","aTc_TetR","C1__pLac","C2__P0"),(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(10000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0))
|
||||
|
|
@ -62,9 +62,7 @@ Initial Reaction Rate Array:
|
|||
0.000000
|
||||
0.000000
|
||||
0.000000
|
||||
0.450000
|
||||
0.000110
|
||||
0.049749
|
||||
0.000000
|
||||
0.000000
|
||||
0.000000
|
||||
|
||||
|
|
@ -73,13 +71,11 @@ kd * GFP
|
|||
kd * TetR
|
||||
kd * IPTG_LacI
|
||||
kd * aTc_TetR
|
||||
kc_f * IPTG ^ Complex_IPTG_LacI_nc_IPTG * LacI ^ Complex_IPTG_LacI_nc_LacI
|
||||
kc_f * TetR ^ Complex_aTc_TetR_nc_TetR * aTc ^ Complex_aTc_TetR_nc_aTc
|
||||
kc_f * IPTG ^ Complex_IPTG_LacI_nc_IPTG * LacI ^ Complex_IPTG_LacI_nc_LacI - kc_r * IPTG_LacI
|
||||
kc_f * TetR ^ Complex_aTc_TetR_nc_TetR * aTc ^ Complex_aTc_TetR_nc_aTc - kc_r * aTc_TetR
|
||||
kd * LacI
|
||||
C1__pLac * C1__ko * C1__ko_f / C1__ko_r * C1__nr / ( 1 + C1__ko_f / C1__ko_r * C1__nr + ( C1__kr_f / C1__kr_r * LacI ) ^ nc )
|
||||
C2__P0 * C2__ko * C2__ko_f / C2__ko_r * C2__nr / ( 1 + C2__ko_f / C2__ko_r * C2__nr + ( C2__kr_f / C2__kr_r * TetR ) ^ nc )
|
||||
kc_r * IPTG_LacI
|
||||
kc_r * aTc_TetR
|
||||
C1__pLac * C1__ko * C1__ko_f / C1__ko_r * C1__nr / ( 1 + C1__ko_f / C1__ko_r * C1__nr + ( C1__kr_f / C1__kr_r * LacI ) ^ C1__nc )
|
||||
C2__P0 * C2__ko * C2__ko_f / C2__ko_r * C2__nr / ( 1 + C2__ko_f / C2__ko_r * C2__nr + ( C2__kr_f / C2__kr_r * TetR ) ^ C2__nc )
|
||||
|
||||
Reactant Matrix:
|
||||
1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
||||
|
|
@ -91,8 +87,6 @@ Reactant Matrix:
|
|||
0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
||||
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
||||
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
||||
0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000
|
||||
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000
|
||||
|
||||
Delta Matrix:
|
||||
-1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
||||
|
|
@ -104,5 +98,3 @@ Delta Matrix:
|
|||
0.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
||||
10.000000 0.000000 10.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
||||
0.000000 10.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
||||
0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000
|
||||
0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000
|
||||
|
|
|
|||
1
docs/SynBioTutorial/GeneticToggle/variance.tsd
Normal file
1
docs/SynBioTutorial/GeneticToggle/variance.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","GFP","LacI","TetR","IPTG","aTc","IPTG_LacI","aTc_TetR","C1__pLac","C2__P0"),(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(1900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(2900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(3900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(4900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(5900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(6900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(7900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(8900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9400.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9500.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9600.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9700.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9800.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(9900.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0),(10000.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0))
|
||||
|
|
@ -39,9 +39,11 @@
|
|||
<a href="#tth_sEc6"
|
||||
>6 Reaction-based Abstraction</a><br />
|
||||
<a href="#tth_sEc7"
|
||||
>7 Learn Tool</a><br />
|
||||
>7 State-based Abstraction</a><br />
|
||||
<a href="#tth_sEc8"
|
||||
>8 Advanced Modeling</a><br />
|
||||
>8 Learn Tool</a><br />
|
||||
<a href="#tth_sEc9"
|
||||
>9 Advanced Modeling</a><br />
|
||||
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
|
@ -453,7 +455,7 @@ Once you have made your selections, you can now play back the simulation. You c
|
|||
6</a> Reaction-based Abstraction</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
The efficiency of simulation can be improved by employing various automatic abstraction techniques. Go back to the Schematic tab and change the degradation rate of CI back to the default value. Also, go to the SBML elements tab and uncheck the rule for CI_total. To activate abstraction, click on the Simulation Options tab, select Abstraction and change the simulation ID to <tt>abs</tt>. Press the Save and Run icon and note that the simulation time is substantially faster. Plot both the SSA results for CI_total and CII with the abstraction results for CI (note this is now equivalent to CI_total after abstraction) and CII.
|
||||
The efficiency of simulation can be improved by employing various automatic abstraction techniques. Go back to the Schematic tab and click on the Total_CI rule to exclude it from the analysis. To activate abstraction, click on the Simulation Options tab, select Reaction-based Abstraction and change the simulation ID to <tt>abs</tt>. Press the Save and Run icon and note that the simulation time is substantially faster. Plot both the SSA results for CI_total and CII with the abstraction results for CI (note this is now equivalent to CI_total after abstraction) and CII.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
|
|
@ -461,13 +463,17 @@ The efficiency of simulation can be improved by employing various automatic abst
|
|||
</center>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
One way to understand why abstraction is so much faster is by looking at the complexity of the reaction-based model before and after abstraction. The reaction-based model after abstraction is shown below which is clearly much simpler than the full model shown earlier.
|
||||
One way to understand why abstraction is so much faster is by looking at the complexity of the reaction-based model before and after abstraction. To see the difference, select the Network option, then generate the graph for None, Expand Reactions, and Reaction-based Abstraction options. The reaction-based model after abstraction is shown below which is clearly much simpler than the full model shown earlier.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<center><img src="screenshots/viewNetworkAbs.png" alt="screenshots/viewNetworkAbs.png" />
|
||||
</center>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h2><a name="tth_sEc7">
|
||||
7</a> State-based Abstraction</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
Next, let's try checking some properties. To do this, go to the SBML Elements tab and check the boxes next to the constraints. Recall that these constraints terminate simulation whenever CI goes above 20 molecules or CII goes above 50 molecules. Go back to the Simulation Options tab and change abstraction back to none, the Simulation Type to Monte Carlo, and Simulation ID to prob, then press the Save and Run icon. Now, let's plot the results on a histogram by clicking on the Histogram tab and then double-clicking on the graph to bring up the histogram graph editor shown below. Open the prob folder, select the sim-rep file, and check the Use check box to get all fields.
|
||||
|
||||
|
|
@ -493,8 +499,8 @@ These results can also be visualized using the TSD graph tool. Click on the TSD
|
|||
</center>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h2><a name="tth_sEc7">
|
||||
7</a> Learn Tool</h2>
|
||||
<h2><a name="tth_sEc8">
|
||||
8</a> Learn Tool</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
This section describes how a model can be learned from time series data using <tt>iBioSim</tt>'s Learn Tool. To demonstrate the Learn Tool, first create a simple model, <tt>learnModel</tt>, which just includes the two species CI and CII as shown below. This model represents any background knowledge you have about the model that you wish to learn. Any influences that you add between species will be assumed as part of the final learned model. You can also indicate definite knowledge about there not being any influence between two species by selecting the No Influence icon
|
||||
|
|
@ -530,8 +536,8 @@ Now, click on the Learn tab. Here you can edit the various learning options. F
|
|||
</center>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h2><a name="tth_sEc8">
|
||||
8</a> Advanced Modeling</h2>
|
||||
<h2><a name="tth_sEc9">
|
||||
9</a> Advanced Modeling</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
This section is less detailed than the others but it gives some intuition about modeling using reactions, components, and grids.
|
||||
|
|
@ -642,5 +648,5 @@ is available in the <tt>docs</tt> directory that comes with the distribution.
|
|||
T<sub><font size="-1">E</font></sub>X
|
||||
by <a href="http://hutchinson.belmont.ma.us/tth/">
|
||||
T<sub><font size="-1">T</font></sub>H</a>,
|
||||
version 3.81.<br />On 26 Feb 2015, 21:48.</small>
|
||||
version 3.81.<br />On 27 Mar 2015, 14:47.</small>
|
||||
</html>
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -307,18 +307,20 @@ Once you have made your selections, you can now play back the simulation. You c
|
|||
|
||||
\section{Reaction-based Abstraction}
|
||||
|
||||
The efficiency of simulation can be improved by employing various automatic abstraction techniques. Go back to the Schematic tab and change the degradation rate of CI back to the default value. Also, go to the SBML elements tab and uncheck the rule for CI\_total. To activate abstraction, click on the Simulation Options tab, select Abstraction and change the simulation ID to {\tt abs}. Press the Save and Run icon and note that the simulation time is substantially faster. Plot both the SSA results for CI\_total and CII with the abstraction results for CI (note this is now equivalent to CI\_total after abstraction) and CII.
|
||||
The efficiency of simulation can be improved by employing various automatic abstraction techniques. Go back to the Schematic tab and click on the Total\_CI rule to exclude it from the analysis. To activate abstraction, click on the Simulation Options tab, select Reaction-based Abstraction and change the simulation ID to {\tt abs}. Press the Save and Run icon and note that the simulation time is substantially faster. Plot both the SSA results for CI\_total and CII with the abstraction results for CI (note this is now equivalent to CI\_total after abstraction) and CII.
|
||||
|
||||
\begin{center}
|
||||
\includegraphics[width=160mm]{screenshots/absResults}
|
||||
\end{center}
|
||||
|
||||
One way to understand why abstraction is so much faster is by looking at the complexity of the reaction-based model before and after abstraction. The reaction-based model after abstraction is shown below which is clearly much simpler than the full model shown earlier.
|
||||
One way to understand why abstraction is so much faster is by looking at the complexity of the reaction-based model before and after abstraction. To see the difference, select the Network option, then generate the graph for None, Expand Reactions, and Reaction-based Abstraction options. The reaction-based model after abstraction is shown below which is clearly much simpler than the full model shown earlier.
|
||||
|
||||
\begin{center}
|
||||
\includegraphics[width=100mm]{screenshots/viewNetworkAbs}
|
||||
\end{center}
|
||||
|
||||
\section{State-based Abstraction}
|
||||
|
||||
Next, let's try checking some properties. To do this, go to the SBML Elements tab and check the boxes next to the constraints. Recall that these constraints terminate simulation whenever CI goes above 20 molecules or CII goes above 50 molecules. Go back to the Simulation Options tab and change abstraction back to none, the Simulation Type to Monte Carlo, and Simulation ID to prob, then press the Save and Run icon. Now, let's plot the results on a histogram by clicking on the Histogram tab and then double-clicking on the graph to bring up the histogram graph editor shown below. Open the prob folder, select the sim-rep file, and check the Use check box to get all fields.
|
||||
|
||||
\begin{center}
|
||||
|
|
|
|||
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Before Width: | Height: | Size: 117 KiB After Width: | Height: | Size: 130 KiB |
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Add table
Add a link
Reference in a new issue