{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# DNA_construct Examples\n", "\n", "DNA_construct is a flexible way to indicate a DNA sequence.\n", "\n", "A DNA sequence is composed of a string of nucleotides. The sequence of these nucleotides can allow binding of other biomolecules such as proteins or RNA. We choose to annotate known binding interactions and other features of DNA sequences by considering them to be \"DNA parts\". a \"part\" has a certain function, and the order and orientation of parts on a dna sequence describes the overall function of that DNA sequence.\n", "\n", "For example, a `Promoter` is a part which binds to RNA polymerase and causes everything downstream to be transcribed into RNA. A `Terminator`, then, is a sequence which stops the transcription of DNA into RNA. Therefore, anything between a `Promoter` and a `Terminator` gets turned into RNA.\n", "\n", "Other parts such as a Ribosome Binding Site or `RBS`, binds to the ribosome, but only if it is made of RNA and not DNA. Thus, an `RBS` is _like_ a `Promoter`, but instead of RNA it makes Protein. As always the position and orientation of parts determines what those parts actually do. If your sequence contains a Coding Sequence (`CDS`) _before_ an `RBS`, then the ribosome actually cannot translate that protein. Likewise if your `RBS` is after a `Terminator`, that `RBS` never gets turned into RNA.\n", "\n", "This type of logic is incorporated into `DNA_construct`." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The basic workflow is to first define a list of parts, then string them together into a `DNA_construct`" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "imports done!\n", "enumerating components\n", "\n", "[ptet_0, RNA_construct = UTR1_GFP_t16]\n", "\n", "CRN species\n", "dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "protein[RNAP]\n", "protein[Ribo]\n", "protein[RNAase]\n", "rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "protein[tetr]\n", "ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "protein[Ribosome]\n", "ordered_polymer[complex[part[UTR1]:protein[Ribosome]-forward]:part[GFP-forward]:part[t16-forward]]\n", "protein[GFP]\n", "complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]]\n", "\n", "CRN reactions\n", "dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", " Kf=k_forward * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\n", " Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\n", " k_forward=100\n", " found_key=(mech=None, partid=None, name=kb).\n", " search_key=(mech=transcription_mm, partid=ptet_leak, name=kb).\n", " k_reverse=10\n", " found_key=(mech=None, partid=None, name=ku).\n", " search_key=(mech=transcription_mm, partid=ptet_leak, name=ku).\n", "\n", "ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\n", " Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\n", " k_forward=0.05\n", " found_key=(mech=None, partid=None, name=ktx).\n", " search_key=(mech=transcription_mm, partid=ptet_leak, name=ktx).\n", "\n", "2protein[tetr]+dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", " Kf=k_forward * protein_tetr^2 * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_\n", " Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\n", " k_forward=100\n", " found_key=(mech=None, partid=None, name=kb).\n", " search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=kb).\n", " k_reverse=10\n", " found_key=(mech=None, partid=None, name=ku).\n", " search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=ku).\n", "\n", "ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", " Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\n", " Kr=k_reverse * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\n", " k_forward=100\n", " found_key=(mech=None, partid=None, name=kb).\n", " search_key=(mech=transcription_mm, partid=ptet_tetr, name=kb).\n", " k_reverse=10\n", " found_key=(mech=None, partid=None, name=ku).\n", " search_key=(mech=transcription_mm, partid=ptet_tetr, name=ku).\n", "\n", "ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\n", " Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\n", " k_forward=0.05\n", " found_key=(mech=None, partid=None, name=ktx).\n", " search_key=(mech=transcription_mm, partid=ptet_tetr, name=ktx).\n", "\n", "rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[Ribosome] <--> ordered_polymer[complex[part[UTR1]:protein[Ribosome]-forward]:part[GFP-forward]:part[t16-forward]]\n", " Kf=k_forward * rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_Ribosome\n", " Kr=k_reverse * ordered_polymer_complex_part_UTR1_protein_Ribosome_forward__part_GFP_forward_part_t16_forward_\n", " k_forward=100\n", " found_key=(mech=None, partid=None, name=kb).\n", " search_key=(mech=translation_mm, partid=UTR1, name=kb).\n", " k_reverse=10\n", " found_key=(mech=None, partid=None, name=ku).\n", " search_key=(mech=translation_mm, partid=UTR1, name=ku).\n", "\n", "ordered_polymer[complex[part[UTR1]:protein[Ribosome]-forward]:part[GFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[GFP]+protein[Ribosome]\n", " Kf=k_forward * ordered_polymer_complex_part_UTR1_protein_Ribosome_forward__part_GFP_forward_part_t16_forward_\n", " k_forward=0.2\n", " found_key=(mech=None, partid=None, name=ktl).\n", " search_key=(mech=translation_mm, partid=UTR1, name=ktl).\n", "\n", "rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]]\n", " Kf=k_forward * rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAase\n", " Kr=k_reverse * complex_protein_RNAase_rna_part_UTR1_forward_part_GFP_forward_part_t16_forward__\n", " k_forward=100\n", " found_key=(mech=None, partid=None, name=kb).\n", " search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kb).\n", " k_reverse=10\n", " found_key=(mech=None, partid=None, name=ku).\n", " search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=ku).\n", "\n", "complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]] --> protein[RNAase]\n", " Kf=k_forward * complex_protein_RNAase_rna_part_UTR1_forward_part_GFP_forward_part_t16_forward__\n", " k_forward=2\n", " found_key=(mech=None, partid=None, name=kdeg).\n", " search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kdeg).\n", "\n" ] } ], "source": [ "from biocrnpyler import *\n", "try:\n", " #dnaplotlib is a cool library for plotting DNAs.\n", " #please use my fork located at https://github.com/dr3y/dnaplotlib\n", " #to install it type: pip install git+git://github.com/dr3y/dnaplotlib.git@master\n", " import dnaplotlib as dpl\n", " %matplotlib inline\n", " dpl_enabled = True\n", "except (ModuleNotFoundError,ImportError) as e:\n", " dpl_enabled = False\n", "print(\"imports done!\")\n", "\n", "def plotNetwork(inCRN,use_pretty_print=True,colordict = None,iterations=2000,rseed=30,posscale=1,export=False,colordict_append=None):\n", " try:\n", " from bokeh.models import (Plot , Range1d)\n", "\n", " import bokeh.plotting\n", " import bokeh.io\n", " bokeh.io.output_notebook() #this makes the graph appear in line with the notebook\n", " if(colordict is None):\n", " colordict={\"complex\":\"cyan\",\"protein\":\"green\",\n", " \"GFP\":\"lightgreen\",\n", " \"RFP\":\"red\",\n", " \"ribosome\":\"blue\",\n", " \"dna\":\"white\",\"rna\":\"orange\",\n", " \"ligand\":\"pink\",\"phosphate\":\"yellow\",\"nothing\":\"purple\"}\n", " if(colordict_append is not None):\n", " colordict.update(colordict_append)\n", " #now you draw the network on the plot. Layout \"force\" is \n", " plot = render_network_bokeh(inCRN,use_pretty_print=use_pretty_print,colordict=colordict,layout=\"force\",iterations=iterations,rseed=rseed,posscale=posscale)\n", " bokeh.io.show(plot) #if you don't type this the plot won't show\n", " if(export):\n", " plot.output_backend = \"svg\"\n", " bokeh.io.export_svgs(plot, \"plot_file.svg\")\n", " \n", " except ModuleNotFoundError:\n", " return None\n", "\n", "\n", "\n", "\n", "ptet = RegulatedPromoter(\"ptet\",[\"tetr\"],leak=True) #this is a repressible promoter\n", "pconst = Promoter(\"pconst\") #constitutive promoter\n", "utr1 = RBS(\"UTR1\") #regular RBS\n", "gfp = CDS(\"GFP\",\"GFP\")\n", "rfp = CDS(\"RFP\",\"RFP\")\n", "t16 = Terminator(\"t16\") #a terminator stops transcription\n", "\n", "\n", "#now that the parts are defined, we can put together our construct.\n", "parameters={\"cooperativity\":2,\"kb\":100, \"ku\":10, \"ktx\":.05, \"ktl\":.2, \"kdeg\":2,\"kint\":.05}\n", "\n", "construct_1 = DNA_construct([[ptet,\"forward\"],[utr1,\"forward\"],[gfp,\"forward\"],[t16,\"forward\"]],\\\n", " mechanisms = {\"transcription\":Transcription_MM(Species(\"RNAP\",material_type=\"protein\")),\\\n", " \"translation\":Translation_MM(Species(\"Ribosome\",material_type=\"protein\")),\\\n", " \"binding\":One_Step_Cooperative_Binding()},parameters=parameters) \n", "''\n", "#some very basic parameters are defined\n", "parameters={\"cooperativity\":2,\"kb\":100, \"ku\":10, \"ktx\":.05, \"ktl\":.2, \"kdeg\":2,\"kint\":.05}\n", "\n", "components = [construct_1]\n", "myMixture = TxTlExtract(name = \"txtl\", parameters = parameters, components = components)\n", "myCRN = myMixture.compile_crn()\n", "print(\"enumerating components\")\n", "comps = myMixture.get_component(construct_1).enumerate_components()\n", "\n", "w = construct_1.enumerate_components()\n", "print()\n", "print(w)\n", "\n", "x = myCRN.species\n", "print()\n", "print(\"CRN species\")\n", "print('\\n'.join([a.pretty_print() for a in x]))\n", "\n", "y = myCRN.reactions\n", "print()\n", "print(\"CRN reactions\")\n", "print('\\n'.join([a.pretty_print() for a in y]))\n", "#'''\n" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "scrolled": true, "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "imports done!\n", "0\n", "0\n", "enumerating components\n", "\n", "CRN species\n", "dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]\n", "protein[RNAP]\n", "protein[Ribo]\n", "protein[RNAase]\n", "rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "protein[tetr]\n", "ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]\n", "ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\n", "ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]]\n", "protein[GFP]\n", "ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]]\n", "protein[RFP]\n", "complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]]\n", "complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]]\n", "\n", "CRN reactions\n", "dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\n", "2protein[tetr]+dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\n", "ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\n", "dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\n", "ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\n", "rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]]\n", "ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[GFP]+protein[Ribo]\n", "rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]]\n", "ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RFP]+protein[Ribo]\n", "rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]]\n", "complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]] --> protein[RNAase]\n", "rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]]\n", "complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]] --> protein[RNAase]\n", "d:\\documents\\github\\biocrnpyler\\biocrnpyler\\plotting.py:500: UserWarning: This figure includes Axes that are not compatible with tight_layout, so results might be incorrect.\n", " plt.tight_layout(pad=0.0001)\n" ] }, { "data": { "image/png": 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" ] }, "metadata": { "needs_background": "light" }, "output_type": "display_data" } ], "source": [ "from biocrnpyler import *\n", "try:\n", " #dnaplotlib is a cool library for plotting DNAs.\n", " #please use my fork located at https://github.com/dr3y/dnaplotlib\n", " #to install it type: pip install git+git://github.com/dr3y/dnaplotlib.git@master\n", " import dnaplotlib as dpl\n", " dpl_enabled = True\n", "except (ModuleNotFoundError,ImportError) as e:\n", " dpl_enabled = False\n", "\n", "print(\"imports done!\")\n", "\n", "#part definitions below\n", "\n", "ptet = RegulatedPromoter(\"ptet\",[\"tetr\"],leak=True) #this is a repressible promoter\n", "pconst = Promoter(\"pconst\") #constitutive promoter\n", "pcomb = CombinatorialPromoter(\"pcomb\",[\"arac\",\"laci\"], leak=False,\n", " tx_capable_list = [[\"arac\"], [\"laci\"]]) #the Combinations A and B or just A or just B be transcribed\n", "utr1 = RBS(\"UTR1\") #regular RBS\n", "utr2 = RBS(\"UTR1\") #regular RBS\n", "gfp = CDS(\"GFP\") #a CDS has a name and a protein name. so this one is called GFP and the protein is also called GFP\n", "fusrfp = CDS(\"fusRFP\",\"RFP\",no_stop_codons=[\"forward\"]) #you can say that a protein has no stop codon. This is a little different from a fusion protein, because in this case you are saying that the ribosome reads through two proteins but still produces two distinct proteins, rather than one fused protein. This can happen in the case of the ta peptide which causes a peptide bond not to be formed while making a protein.\n", "rfp = CDS(\"RFP\") #regular RFP\n", "cfp = CDS(\"CFP\") #cfp\n", "t16 = Terminator(\"t16\") #a terminator stops transcription\n", "\n", "\n", "#now that the parts are defined, we can put together our construct.\n", "construct_1 = DNA_construct([[ptet,\"forward\"],[utr1,\"forward\"],[gfp,\"forward\"],[t16,\"forward\"]])\n", "construct_2 = DNA_construct([[t16,\"reverse\"],[rfp,\"reverse\"],[utr1,\"reverse\"],[pconst,\"reverse\"]])\n", "\n", "#now, we are using dnaplotlib to plot the constructs\n", "\n", "\n", "if(dpl_enabled):\n", " cdict = {\"GFP\":\"green\",\"RFP\":\"red\",\"pconst\":\"black\",\"Terminator\":\"black\"}\n", " render_constructs([construct_1,construct_2],color_dictionary=cdict)\n", "#some very basic parameters are defined\n", "parameters={\"cooperativity\":2,\"kb\":100, \"ku\":10, \"ktx\":.05, \"ktl\":.2, \"kdeg\":2,\"kint\":.05}\n", "\n", "components = [construct_1,construct_2]\n", "myMixture = TxTlExtract(name = \"txtl\", parameters = parameters, components = components)\n", "\n", "print(\"enumerating components\")\n", "#comps = myMixture.get_component(construct_1).enumerate_components()\n", "\n", "myCRN = myMixture.compile_crn()\n", "\n", "x = myCRN.species\n", "print()\n", "print(\"CRN species\")\n", "print('\\n'.join([a.pretty_print() for a in x]))\n", "\n", "y = myCRN.reactions\n", "print()\n", "print(\"CRN reactions\")\n", "print('\\n'.join([str(a) for a in y]))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "You can see that for the first construct, your DNA is given an automatic name: `ptet_f_UTR1_f_GFP_f_t16_f`. \n", "\n", "The RNA made from your DNA is also given an automatic name: `UTR1_f_GFP_f_t16_f`\n", "\n", "Likewise for the second construct, which I've made in reverse to make the difference more apparent. Though you'll see that the RNA from the second construct is still produced in the right orientation, so the RNA is shown in the forwards direction.\n", "\n", "This is because DNA and RNA are now represented as an OrderedPolymer. Each member of the OrderedPolymer represents a part. So, in the case of promoters or RBSes, you'll see ribosomes and polymerases bind directly to the part inside the OrderedPolymer." ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "tags": [] }, "outputs": [ { "data": { "text/html": [ "\n", "
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\\n\"+\n", " \"

\\n\"+\n", " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"

\\n\"+\n", " \"
    \\n\"+\n", " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", " \"
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\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded() {\n", " var el = document.getElementById(\"1001\");\n", " if (el != null) {\n", " el.textContent = \"BokehJS is loading...\";\n", " }\n", " if (root.Bokeh !== undefined) {\n", " if (el != null) {\n", " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n", " }\n", " } else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(display_loaded, 100)\n", " }\n", " }\n", "\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) {\n", " if (callback != null)\n", " callback();\n", " });\n", " } finally {\n", " delete root._bokeh_onload_callbacks\n", " }\n", " console.debug(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(css_urls, js_urls, callback) {\n", " if (css_urls == null) css_urls = [];\n", " if (js_urls == null) js_urls = [];\n", "\n", " root._bokeh_onload_callbacks.push(callback);\n", " if (root._bokeh_is_loading > 0) {\n", " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls == null || js_urls.length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", "\n", " function on_load() {\n", " root._bokeh_is_loading--;\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", " run_callbacks()\n", " }\n", " }\n", "\n", " function on_error() {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " for (var i = 0; i < css_urls.length; i++) {\n", " var url = css_urls[i];\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.rel = \"stylesheet\";\n", " element.type = \"text/css\";\n", " element.href = url;\n", " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", " document.body.appendChild(element);\n", " }\n", "\n", " const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\": \"T2yuo9Oe71Cz/I4X9Ac5+gpEa5a8PpJCDlqKYO0CfAuEszu1JrXLl8YugMqYe3sM\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\": \"98GDGJ0kOMCUMUePhksaQ/GYgB3+NH9h996V88sh3aOiUNX3N+fLXAtry6xctSZ6\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\": \"89bArO+nlbP3sgakeHjCo1JYxYR5wufVgA3IbUvDY+K7w4zyxJqssu7wVnfeKCq8\"};\n", "\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " if (url in hashes) {\n", " element.crossOrigin = \"anonymous\";\n", " element.integrity = \"sha384-\" + hashes[url];\n", " }\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " \n", " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\"];\n", " var css_urls = [];\n", " \n", "\n", " var inline_js = [\n", " function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", " function(Bokeh) {\n", " \n", " \n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " \n", " if (root.Bokeh !== undefined || force === true) {\n", " \n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", " if (force === true) {\n", " display_loaded();\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " } else if (force !== true) {\n", " var cell = $(document.getElementById(\"1001\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\n", "\n", " }\n", "\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", " run_inline_js();\n", " } else {\n", " load_libs(css_urls, js_urls, function() {\n", " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", " run_inline_js();\n", " });\n", " }\n", "}(window));" ], "application/vnd.bokehjs_load.v0+json": "\n(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n \n\n \n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n var NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded() {\n var el = document.getElementById(\"1001\");\n if (el != null) {\n el.textContent = \"BokehJS is loading...\";\n }\n if (root.Bokeh !== undefined) {\n if (el != null) {\n el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(display_loaded, 100)\n }\n }\n\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\": \"T2yuo9Oe71Cz/I4X9Ac5+gpEa5a8PpJCDlqKYO0CfAuEszu1JrXLl8YugMqYe3sM\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\": \"98GDGJ0kOMCUMUePhksaQ/GYgB3+NH9h996V88sh3aOiUNX3N+fLXAtry6xctSZ6\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\": \"89bArO+nlbP3sgakeHjCo1JYxYR5wufVgA3IbUvDY+K7w4zyxJqssu7wVnfeKCq8\"};\n\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n if (url in hashes) {\n element.crossOrigin = \"anonymous\";\n element.integrity = \"sha384-\" + hashes[url];\n }\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n \n var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\"];\n var css_urls = [];\n \n\n var inline_js = [\n function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\n function(Bokeh) {\n \n \n }\n ];\n\n function run_inline_js() {\n \n if (root.Bokeh !== undefined || force === true) {\n \n for (var i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n if (force === true) {\n display_loaded();\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n var cell = $(document.getElementById(\"1001\")).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" }, "metadata": {}, "output_type": "display_data" }, { "name": "stderr", "output_type": "stream", "text": [ "D:\\anaconda3\\lib\\site-packages\\bokeh\\plotting\\graph.py:120: UserWarning: Node keys in 'layout_function' don't match node keys in the graph. These nodes may not be displayed correctly.\n", " warn(\"Node keys in 'layout_function' don't match node keys in the graph. \"\n" ] }, { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function embed_document(root) {\n", " \n", " var docs_json = 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,{\"attributes\":{\"graph_layout\":{\"0\":[106.11760504237719,-262.93328248224265],\"1\":[-68.46529709670848,53.73728821346814],\"10\":[-29.980392814972294,48.06963935625687],\"11\":[24.400694978062056,-84.42383871599905],\"12\":[-39.373585912767524,105.10849109833147],\"13\":[4.710084802746899,-36.376571968971305],\"14\":[139.3437518249315,117.2502273077492],\"15\":[-4.130506436734984,-101.43659787351196],\"16\":[88.25411892857018,134.0087275363648],\"17\":[44.65043390818529,-42.03836430945647],\"18\":[51.796388544104005,-91.30767927463494],\"19\":[-71.46199552383361,65.85780703441189],\"2\":[-50.189281730598616,99.26446780356507],\"20\":[-95.75625998806953,70.48883085360981],\"21\":[-62.56627823328759,45.24057029801405],\"22\":[-41.91618924023558,56.06363893237493],\"23\":[-20.25869593663629,41.36418122031112],\"24\":[-45.88445452275424,95.02125690833952],\"25\":[-33.353408068123635,114.2915017541421],\"26\":[9.764633023521347,-49.67652758273302],\"27\":[1.7989026916298945,-24.903832984457804],\"28\":[7.584978338950689,-85.14260585492438],\"29\":[-12.24181847573118,-114.3336896614136],\"3\":[-52.876917931298955,72.82886377469504],\"30\":[37.335247815421084,-50.600458236899875],\"31\":[49.84456069271992,-36.41342738497793],\"32\":[39.387858115348884,-81.08031470862291],\"33\":[59.382502806750686,-97.9600391861624],\"4\":[5.877005029165913,-67.49651058103053],\"5\":[40.0952999262234,-66.51695044730117],\"6\":[24.532874254872965,-47.86528633541896],\"7\":[-84.34400209766004,68.6623503857395],\"8\":[-65.3257234737653,39.414752136330215],\"9\":[-51.86660617319355,48.53543772070483]}},\"id\":\"1020\",\"type\":\"StaticLayoutProvider\"},{\"attributes\":{\"fill_color\":{\"value\":\"#fdae61\"},\"size\":{\"units\":\"screen\",\"value\":8}},\"id\":\"1084\",\"type\":\"Square\"},{\"attributes\":{\"data_source\":{\"id\":\"1027\"},\"glyph\":{\"id\":\"1026\"},\"hover_glyph\":null,\"muted_glyph\":null,\"view\":{\"id\":\"1029\"}},\"id\":\"1028\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"fill_color\":{\"field\":\"color\"},\"size\":{\"units\":\"screen\",\"value\":12}},\"id\":\"1094\",\"type\":\"Circle\"},{\"attributes\":{},\"id\":\"1160\",\"type\":\"UnionRenderers\"},{\"attributes\":{\"data\":{\"color\":[\"purple\",\"white\",\"white\",\"green\",\"green\",\"green\",\"orange\",\"grey\",\"green\",\"grey\",\"grey\",\"orange\",\"grey\",\"grey\",\"green\",\"grey\",\"red\",\"cyan\",\"cyan\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\"],\"image\":[\"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in default.]\",\"dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse] in default.]\",\"protein[RNAP in default.]\",\"protein[Ribo in default.]\",\"protein[RNAase in default.]\",\"rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"protein[tetr in default.]\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse] in default.]\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"protein[GFP in default.]\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward] in default.]\",\"protein[RFP in default.]\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] in default.]\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]] in default.]\",\"dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ktx).\\n\",\"2protein[tetr]+dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_tetr^2 * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ktx).\\n\",\"dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[GFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kdeg).\\n\",\"rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kdeg).\\n\"],\"type\":[\"nothing\",\"dna\",\"dna\",\"protein\",\"protein\",\"protein\",\"rna\",\"ordered_polymer\",\"protein\",\"ordered_polymer\",\"ordered_polymer\",\"rna\",\"ordered_polymer\",\"ordered_polymer\",\"protein\",\"ordered_polymer\",\"protein\",\"complex\",\"complex\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\"]},\"selected\":{\"id\":\"1163\"},\"selection_policy\":{\"id\":\"1162\"}},\"id\":\"1037\",\"type\":\"ColumnDataSource\"},{\"attributes\":{\"bottom_units\":\"screen\",\"fill_alpha\":0.5,\"fill_color\":\"lightgrey\",\"left_units\":\"screen\",\"level\":\"overlay\",\"line_alpha\":1.0,\"line_color\":\"black\",\"line_dash\":[4,4],\"line_width\":2,\"right_units\":\"screen\",\"top_units\":\"screen\"},\"id\":\"1159\",\"type\":\"BoxAnnotation\"},{\"attributes\":{},\"id\":\"1168\",\"type\":\"UnionRenderers\"},{\"attributes\":{\"data_source\":{\"id\":\"1037\"},\"glyph\":{\"id\":\"1049\"},\"hover_glyph\":null,\"muted_glyph\":null,\"view\":{\"id\":\"1039\"}},\"id\":\"1038\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"source\":{\"id\":\"1013\"}},\"id\":\"1015\",\"type\":\"CDSView\"},{\"attributes\":{\"fill_color\":{\"value\":\"#abdda4\"},\"size\":{\"units\":\"screen\",\"value\":8}},\"id\":\"1089\",\"type\":\"Square\"},{\"attributes\":{},\"id\":\"1162\",\"type\":\"UnionRenderers\"},{\"attributes\":{},\"id\":\"1125\",\"type\":\"EdgesAndLinkedNodes\"},{\"attributes\":{\"data\":{\"color\":[\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\"],\"index\":[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33],\"k\":[\"100\",\"0.05\",\"100\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"0.2\",\"100\",\"0.2\",\"100\",\"2\",\"100\",\"2\"],\"k_r\":[\"10\",\"None\",\"10\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\"],\"species\":[\"dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ktx).\\n\",\"2protein[tetr]+dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_tetr^2 * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ktx).\\n\",\"dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[GFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kdeg).\\n\",\"rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kdeg).\\n\"],\"type\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\"]},\"selected\":{\"id\":\"1167\"},\"selection_policy\":{\"id\":\"1166\"}},\"id\":\"1009\",\"type\":\"ColumnDataSource\"},{\"attributes\":{\"source\":{\"id\":\"1027\"}},\"id\":\"1029\",\"type\":\"CDSView\"},{\"attributes\":{},\"id\":\"1163\",\"type\":\"Selection\"},{\"attributes\":{},\"id\":\"1114\",\"type\":\"PanTool\"},{\"attributes\":{\"data\":{\"end\":[19,21,24,19,22,24,26,28,30,32,26,30,19,20,21,21,22,22,23,28,32,24,25,26,27,28,29,30,31,32,33,1,3,7,1,6,3,8,1,9,9,3,10,9,6,3,2,3,12,2,11,3,6,4,13,6,14,4,11,4,15,11,16,4,6,5,17,5,11,5,18,5],\"start\":[1,1,2,3,3,3,4,4,5,5,6,6,7,7,8,9,9,10,10,11,11,12,12,13,13,15,15,17,17,18,18,19,19,19,20,20,20,21,21,21,22,22,22,23,23,23,24,24,24,25,25,25,26,26,26,27,27,27,28,28,28,29,29,29,30,30,30,31,32,32,32,33],\"weight\":[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],\"xs\":[[-68.46529709670848,-70.62194407198673,-67.99577825040349,-71.46199552383361,-72.84962451787686,-70.62194407198673],[-68.46529709670848,-64.56232576866573,-67.08933907463302,-62.56627823328759,-62.982154171367284,-64.56232576866573],[-50.189281730598616,-48.37710298487928,-50.72328609540383,-45.88445452275424,-47.21332835268893,-48.37710298487928],[-52.876917931298955,-68.18493921703585,-68.28568087989234,-71.46199552383361,-66.52969870686383,-68.18493921703585],[-52.876917931298955,-43.83142135333392,-46.37816419775153,-41.91618924023558,-42.19318475153939,-43.83142135333392],[-52.876917931298955,-46.93627199649979,-44.8013018174659,-45.88445452275424,-49.570180520636924,-46.93627199649979],[5.877005029165913,9.018615723237918,11.284225892104292,9.764633023521347,6.399126058629448,9.018615723237918],[5.877005029165913,7.247787587178931,4.679441814098385,7.584978338950689,9.656184129644378,7.247787587178931],[40.0952999262234,37.933252384225455,40.53832556208798,37.335247815421084,35.611847634936325,37.933252384225455],[40.0952999262234,39.55767671510201,37.10089856934823,39.387858115348884,42.095009722553286,39.55767671510201],[24.532874254872965,13.238603442632778,13.758226201552839,9.764633023521347,14.366887373907492,13.238603442632778],[24.532874254872965,33.912491189786806,32.578358122488495,37.335247815421084,33.62301125472284,33.912491189786806],[-84.34400209766004,-74.88188630172102,-76.22483084972006,-71.46199552383361,-75.16119531742895,-74.88188630172102],[-84.34400209766004,-92.30024230908391,-91.0854612213164,-95.75625998806953,-91.87563273788074,-92.30024230908391],[-65.3257234737653,-64.06451266462811,-62.16049510287939,-62.56627823328759,-66.67923015902556,-64.06451266462811],[-51.86660617319355,-59.22128558749824,-59.16368043033004,-62.56627823328759,-57.69216573131456,-59.22128558749824],[-51.86660617319355,-44.70736047342336,-43.860996358097275,-41.91618924023558,-46.87773982023946,-44.70736047342336],[-29.980392814972294,-39.00815816889105,-36.9272525572555,-41.91618924023558,-39.70961511527612,-39.00815816889105],[-29.980392814972294,-23.139824390696138,-25.242620815530998,-20.25869593663629,-22.403715151404484,-23.139824390696138],[24.400694978062056,11.081785411057991,11.80439319103104,7.584978338950689,12.017917077093216,11.081785411057991],[24.400694978062056,35.97183414761291,35.705974063111256,39.387858115348884,34.61727492188403,35.97183414761291],[-39.373585912767524,-43.98639801724441,-45.63667790779944,-45.88445452275424,-41.43575927602381,-43.98639801724441],[-39.373585912767524,-35.27233009485371,-33.63669416563812,-33.353408068123635,-37.81822260783706,-35.27233009485371],[4.710084802746899,8.521249394529596,5.889418744375368,9.764633023521347,10.56327070450578,8.521249394529596],[4.710084802746899,2.6597385172704646,5.2871151552357984,1.7989026916298945,0.44070649514537874,2.6597385172704646],[-4.130506436734984,5.54177174735188,7.086957486824244,7.584978338950689,3.0273740096360324,5.54177174735188],[-4.130506436734984,-10.378465839888685,-12.052770991842308,-12.24181847573118,-7.820263905767781,-10.378465839888685],[44.65043390818529,39.608759295556986,38.24724438884576,37.335247815421084,42.04873323512,39.608759295556986],[44.65043390818529,47.47011700049691,48.74365153026203,49.84456069271992,45.07024540568968,47.47011700049691],[51.796388544104005,42.088697832877635,44.31934307836641,39.387858115348884,41.139218314988184,42.088697832877635],[51.796388544104005,56.75098029816443,54.478541246626,59.382502806750686,57.775134815257516,56.75098029816443],[-71.46199552383361,-69.30534854855536,-71.9315143701386,-68.46529709670848,-67.07766810266523,-69.30534854855536],[-71.46199552383361,-56.15397423809671,-56.05323257524022,-52.876917931298955,-57.809214748268744,-56.15397423809671],[-71.46199552383361,-80.92411131977262,-79.58116677177358,-84.34400209766004,-80.6448023040647,-80.92411131977262],[-95.75625998806953,-71.44819199886591,-73.46348611685814,-68.46529709670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"D:\\anaconda3\\lib\\importlib\\_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject\n", " return f(*args, **kwds)\n" ] }, { "data": { "image/png": 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UlKo6eS6vi12mi7H+1+oAaXYpQymPpNVHSlVOJtbwiJVmrP7w40XkZrB6whSRPlUZnFKXSpOCUpVgrP7019sDvT9/EW8xGZgpIiU90DoyFKxS5dEmqUoppUppSUEppVQpTQpKKaVKaVJQSilVSpOCUkqpUpoUlFJKldKkoJRSqpQmBaWUUqX+H4y/jkq5rFSbAAAAAElFTkSuQmCC\n", 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" ] }, "metadata": { "needs_background": "light" }, "output_type": "display_data" } ], "source": [ "#here we are plotting the network diagram and simulating the system with some basic parameters\n", "\n", "plotNetwork(myCRN,colordict_append={\"GFP\":\"green\",\"RFP\":\"red\"})\n", "try:\n", " import numpy as np\n", " import matplotlib.pyplot as plt\n", " timepoints = np.linspace(0, 200, 1000)\n", " x0 = {construct_1.get_species():5.0,\n", " construct_2.get_species():2.0, \"protein_RNAP\":10., \"protein_Ribo\":50.}\n", " Re1 = myCRN.simulate_with_bioscrape_via_sbml(timepoints, initial_condition_dict = x0)\n", " if(Re1 is not None):\n", " plt.plot(timepoints,Re1[\"protein_GFP\"], label = \"protein_GFP\")\n", " plt.plot(timepoints,Re1[\"protein_RFP\"], label = \"protein_RFP\")\n", " plt.title(\"Time trace of two DNA system\")\n", " plt.xlabel(\"time\")\n", " plt.ylabel(\"protein\")\n", " plt.legend()\n", "except ModuleNotFoundError:\n", " print('please install the plotting libraries: pip install biocrnpyler[all]')\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "That seems pretty straightforward but now let's see what happens if we put both on the same piece of DNA:" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "tags": [] }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "d:\\documents\\github\\biocrnpyler\\biocrnpyler\\plotting.py:500: UserWarning: This figure includes Axes that are not compatible with tight_layout, so results might be incorrect.\n", " plt.tight_layout(pad=0.0001)\n", "0\n", "0\n", "d:\\documents\\github\\biocrnpyler\\biocrnpyler\\chemical_reaction_network.py:364: UserWarning: Trying to set species that is not in model: protein_arac\n", " m.set_species(processed)\n" ] }, { "data": { "image/png": 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" ] }, "metadata": { "needs_background": "light" }, "output_type": "display_data" } ], "source": [ "construct_3 = DNA_construct([[ptet,\"forward\"],[utr1,\"forward\"],[gfp,\"forward\"],[t16,\"forward\"],[t16,\"reverse\"],[rfp,\"reverse\"],[utr1,\"reverse\"],[pconst,\"reverse\"]])\n", "#now, we are using dnaplotlib to plot the constructs\n", "\n", "if(dpl_enabled):\n", " render_constructs([construct_3])\n", "\n", "#some very basic parameters are defined\n", "parameters={\"cooperativity\":2,\"kb\":100, \"ku\":10, \"ktx\":.05, \"ktl\":.2, \"kdeg\":2,\"kint\":.05}\n", "\n", "components = [construct_3]\n", "myMixture = TxTlExtract(name = \"txtl\", parameters = parameters, components = components)\n", "myCRN = myMixture.compile_crn()\n", "''\n", "try:\n", " import numpy as np\n", " import matplotlib.pyplot as plt\n", " timepoints = np.linspace(0, 200, 1000)\n", " x0 = {construct_3.get_species():5.0, \"protein_GFP\":20,\"protein_RNAP\":10., \"protein_Ribo\":50.,\"protein_arac\":20}\n", " #I started the GFP at a slightly elevated value so you can see the two lines on top of each other in the graph\n", " Re1 = myCRN.simulate_with_bioscrape_via_sbml(timepoints, initial_condition_dict = x0)\n", " if(Re1 is not None):\n", " plt.figure()\n", " plt.plot(timepoints,Re1[\"protein_GFP\"], label = \"protein_GFP\")\n", " plt.plot(timepoints,Re1[\"protein_RFP\"], label = \"protein_RFP\")\n", " #plt.plot(timepoints,Re1[\"rna_mydna\"], label = \"rna_mydna\")\n", " #plt.gca().set_yscale(\"log\")\n", " plt.title(\"Time trace of single DNA system\")\n", " plt.xlabel(\"time\")\n", " plt.ylabel(\"protein\")\n", " plt.legend()\n", " \n", "except ModuleNotFoundError:\n", " print('please install the plotting libraries: pip install biocrnpyler[all]')\n", "#'''" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The same RNAs and proteins are made, but the network diagram should be a bit more complicated, owing to the combinatorial binding to the DNA molecule" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "tags": [] }, "outputs": [ { "data": { "text/html": [ "\n", "
\n", " \n", " Loading BokehJS ...\n", "
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*/\n", " safe: true,\n", " /* Index of renderer in `output_area.display_order` */\n", " index: 0\n", " });\n", " }\n", "\n", " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", " if (root.Jupyter !== undefined) {\n", " var events = require('base/js/events');\n", " var OutputArea = require('notebook/js/outputarea').OutputArea;\n", "\n", " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", " register_renderer(events, OutputArea);\n", " }\n", " }\n", "\n", " \n", " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " var NB_LOAD_WARNING = {'data': {'text/html':\n", " \"
\\n\"+\n", " \"

\\n\"+\n", " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"

\\n\"+\n", " \"
    \\n\"+\n", " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", " \"
\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded() {\n", " var el = document.getElementById(\"1441\");\n", " if (el != null) {\n", " el.textContent = \"BokehJS is loading...\";\n", " }\n", " if (root.Bokeh !== undefined) {\n", " if (el != null) {\n", " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n", " }\n", " } else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(display_loaded, 100)\n", " }\n", " }\n", "\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) {\n", " if (callback != null)\n", " callback();\n", " });\n", " } finally {\n", " delete root._bokeh_onload_callbacks\n", " }\n", " console.debug(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(css_urls, js_urls, callback) {\n", " if (css_urls == null) css_urls = [];\n", " if (js_urls == null) js_urls = [];\n", "\n", " root._bokeh_onload_callbacks.push(callback);\n", " if (root._bokeh_is_loading > 0) {\n", " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls == null || js_urls.length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", "\n", " function on_load() {\n", " root._bokeh_is_loading--;\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", " run_callbacks()\n", " }\n", " }\n", "\n", " function on_error() {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " for (var i = 0; i < css_urls.length; i++) {\n", " var url = css_urls[i];\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.rel = \"stylesheet\";\n", " element.type = \"text/css\";\n", " element.href = url;\n", " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", " document.body.appendChild(element);\n", " }\n", "\n", " const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\": \"T2yuo9Oe71Cz/I4X9Ac5+gpEa5a8PpJCDlqKYO0CfAuEszu1JrXLl8YugMqYe3sM\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\": \"98GDGJ0kOMCUMUePhksaQ/GYgB3+NH9h996V88sh3aOiUNX3N+fLXAtry6xctSZ6\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\": \"89bArO+nlbP3sgakeHjCo1JYxYR5wufVgA3IbUvDY+K7w4zyxJqssu7wVnfeKCq8\"};\n", "\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " if (url in hashes) {\n", " element.crossOrigin = \"anonymous\";\n", " element.integrity = \"sha384-\" + hashes[url];\n", " }\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " \n", " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\"];\n", " var css_urls = [];\n", " \n", "\n", " var inline_js = [\n", " function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", " function(Bokeh) {\n", " \n", " \n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " \n", " if (root.Bokeh !== undefined || force === true) {\n", " \n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", " if (force === true) {\n", " display_loaded();\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " } else if (force !== true) {\n", " var cell = $(document.getElementById(\"1441\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\n", "\n", " }\n", "\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", " run_inline_js();\n", " } else {\n", " load_libs(css_urls, js_urls, function() {\n", " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", " run_inline_js();\n", " });\n", " }\n", "}(window));" ], "application/vnd.bokehjs_load.v0+json": "\n(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n \n\n \n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n var NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
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},{\"attributes\":{\"attachment\":\"right\",\"callback\":null,\"renderers\":[{\"id\":\"1447\"}],\"tooltips\":[[\"reaction\",\"@species\"],[\"type\",\"@type\"],[\"k_f\",\"@k\"],[\"k_r\",\"@k_r\"]]},\"id\":\"1551\",\"type\":\"HoverTool\"},{\"attributes\":{},\"id\":\"1615\",\"type\":\"LinearScale\"},{\"attributes\":{\"callback\":null},\"id\":\"1552\",\"type\":\"TapTool\"},{\"attributes\":{\"source\":{\"id\":\"1463\"}},\"id\":\"1465\",\"type\":\"CDSView\"},{\"attributes\":{},\"id\":\"1655\",\"type\":\"UnionRenderers\"},{\"attributes\":{\"edge_renderer\":{\"id\":\"1454\"},\"inspection_policy\":{\"id\":\"1633\"},\"layout_provider\":{\"id\":\"1460\"},\"node_renderer\":{\"id\":\"1450\"},\"selection_policy\":{\"id\":\"1628\"}},\"id\":\"1447\",\"type\":\"GraphRenderer\"},{\"attributes\":{},\"id\":\"1643\",\"type\":\"NodesOnly\"},{\"attributes\":{},\"id\":\"1554\",\"type\":\"PanTool\"},{\"attributes\":{},\"id\":\"1555\",\"type\":\"WheelZoomTool\"},{\"attributes\":{\"fill_color\":{\"value\":\"#fdae61\"},\"size\":{\"units\":\"screen\",\"value\":8}},\"id\":\"1524\",\"type\":\"Square\"},{\"attributes\":{},\"id\":\"1563\",\"type\":\"NodesAndLinkedEdges\"},{\"attributes\":{\"source\":{\"id\":\"1481\"}},\"id\":\"1483\",\"type\":\"CDSView\"},{\"attributes\":{\"source\":{\"id\":\"1467\"}},\"id\":\"1469\",\"type\":\"CDSView\"},{\"attributes\":{},\"id\":\"1565\",\"type\":\"EdgesAndLinkedNodes\"},{\"attributes\":{\"data_source\":{\"id\":\"1449\"},\"glyph\":{\"id\":\"1519\"},\"hover_glyph\":{\"id\":\"1529\"},\"muted_glyph\":null,\"selection_glyph\":{\"id\":\"1524\"},\"view\":{\"id\":\"1451\"}},\"id\":\"1450\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"active_drag\":\"auto\",\"active_inspect\":\"auto\",\"active_multi\":null,\"active_scroll\":\"auto\",\"active_tap\":\"auto\",\"tools\":[{\"id\":\"1549\"},{\"id\":\"1550\"},{\"id\":\"1551\"},{\"id\":\"1552\"},{\"id\":\"1553\"},{\"id\":\"1554\"},{\"id\":\"1555\"}]},\"id\":\"1556\",\"type\":\"Toolbar\"},{\"attributes\":{\"data_source\":{\"id\":\"1481\"},\"glyph\":{\"id\":\"1494\"},\"hover_glyph\":{\"id\":\"1504\"},\"muted_glyph\":null,\"selection_glyph\":{\"id\":\"1499\"},\"view\":{\"id\":\"1483\"}},\"id\":\"1482\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"data\":{\"color\":[\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\"],\"index\":[21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46],\"k\":[\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"0.2\",\"100\",\"0.2\",\"100\",\"2\",\"100\",\"2\"],\"k_r\":[\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"10\",\"None\",\"10\",\"None\",\"10\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\"],\"species\":[\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * ordered_polymer_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ktx).\\n\",\"2protein[tetr]+ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] <--> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * protein_tetr^2 * ordered_polymer_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]+protein[RNAP] <--> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ktx).\\n\",\"dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]\\n Kf=k_forward * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]] --> dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ktx).\\n\",\"2protein[tetr]+dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]] <--> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]\\n Kf=k_forward * protein_tetr^2 * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]] --> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ktx).\\n\",\"dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[GFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kdeg).\\n\",\"rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kdeg).\\n\"],\"type\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\"]},\"selected\":{\"id\":\"1652\"},\"selection_policy\":{\"id\":\"1651\"}},\"id\":\"1449\",\"type\":\"ColumnDataSource\"},{\"attributes\":{},\"id\":\"1638\",\"type\":\"NodesOnly\"},{\"attributes\":{\"data_source\":{\"id\":\"1477\"},\"glyph\":{\"id\":\"1489\"},\"hover_glyph\":null,\"muted_glyph\":null,\"view\":{\"id\":\"1479\"}},\"id\":\"1478\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"data\":{\"end\":[],\"start\":[]},\"selected\":{\"id\":\"1654\"},\"selection_policy\":{\"id\":\"1653\"}},\"id\":\"1467\",\"type\":\"ColumnDataSource\"},{\"attributes\":{\"end\":204.6414626606991,\"start\":-425.80565038018926},\"id\":\"1517\",\"type\":\"Range1d\"},{\"attributes\":{\"data\":{\"color\":[\"purple\",\"white\",\"green\",\"green\",\"green\",\"grey\",\"orange\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"orange\",\"green\",\"grey\",\"lightgreen\",\"grey\",\"red\",\"cyan\",\"cyan\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\"],\"image\":[\"iVBORw0KGgoAAAANSUhEUgAAADcAAABACAYAAAC+/O8/AAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAAlwSFlzAAAOxAAADsQBlSsOGwAAAAZiS0dEAP8A/wD/oL2nkwAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAxOS0wNi0yOVQxMjo0Mjo1MyswODowMLVKQ5EAAAAldEVYdGRhdGU6bW9kaWZ5ADIwMTYtMDQtMjNUMDA6NDA6MjErMDg6MDD8dsOAAAAAVHRFWHRzdmc6YmFzZS11cmkAZmlsZTovLy9ob21lL2RiL3N2Z19pbmZvL3N2Zy85My8xNy85MzE3YzE3MDc3MWRkYjhkMjA1ZGI0ZDQyMDBkZTA5MS5zdmcgfPYlAAAJH0lEQVRoQ92bV2gVzxfHJ5ZEY6zR2LEm1mhiLCSiokLsqGB50DwIPojlxUIUjQjBrsResSIW7BVEUESCsUWwEhuxxxZ7L/Ob7+TsvXd3z957k7v5Q/4fOGZ298yce3Z3zs6cGcOkQvwfMHHiRBETEyPmzZtHZxRwrqyzZcsWPCAtffv2lc+ePdPny7xzFy5ckFFRUR7nIG3btpUfPnyQZfq1fPXqlWjatKn48eMHnfGSmJgoyqxzX79+1X3s27dvdMaMenKl49z79+/Fw4cPxa9fv8T9+/dFQUGBNvbz509RqVIlUb16dVG/fn0RFxcnKlSoIGJjY/W54pCcnCxycnLoyEvlypXFkSNHRGpqqnpBXWT37t1yzpw5ulOjH4SFhXn6ASe4XrVqVdmvXz+ZkZEhDx48SC35Z/bs2Wx7EFwzCNm5wsJCuXLlStmhQwcZHh7OGgxW1F2X8fHxctu2bVI9dbJgZtWqVWxdCG6qLyV2TnViuWPHDqleM9ZQqBIdHS2PHz8u//79SxalPHDgAKsLUYGFtLyUyLkTJ07oO8wZcVu6d+8ur127Jm/fvs1eh1SrVk3m5+fTr/NSbOfWrFnDGnASFTB0v0IfhKAcGRkZsD/6Cuo1btyYvYZXedeuXfTrzAQdLRHpVGcVy5cvpzPONGrUSHTq1EkkJCSIlJQUUatWLfHv3z99TTmFGyqePHkibty4oeXKlSvi5cuX+npxWbRokUhPT6cjC3AuEOpbIgcNGmS7a1Zp37693Ldvn3z+/LlUzlBt/0BPOSr37Nkj27Rpw7brJDNmzKBWeAI69/v3bzlgwAC2cUMw3EHnd4PDhw/r9jg7vpKWlkY1nAno3OTJk9nGDcH3qTRo2bIla8+QadOmkaYzfp3buHEj2zBEjTDkzp07SdNdEB2tg2FOtm7dSjV4HJ07e/asDrFco4h2Dx48IE13UYFFNmnShLVrlTp16kgVjKimHdY5FRn1kIhrsGLFiqTlPggsLVq0YO06yYgRI6i2HdY5pyEOvk25ubmk5S4Y8QwePJi1C0FkVINr9tqGDRuoFTM25969e+fYmTGGLC2mTJnC2oTAaaC+aex1jJa+f/+udXyxObd582a2gWHDhsk/f/6QlrusW7eOtQnp3bu3/PTpk9Z7+/at7NatG6uHVIMVm3MYHlkr4nU4f/48abgLPvpWe4Z07txZO+QLxrUIaFZdDM+smJxDCLZWgowaNYo03CU7O1vWrFmTtYmb7BSRBw4cyNYxEkMGJucQebhKd+7cIQ33wA/3N7NQs2nStIObwtUZO3YsaRRhco4Lw7169aKr7tK1a1ebLUOWLl1KWs7ExcXZ6uGcLx7nTp06JatUqWKrgAmp2zi9VpBghlVg2bJltrpq9iEvX75MGj7OOeUl1JSENNwBP56zAxk/fjxpBSYnJ4dtY+7cuaTh49ykSZNsipjCuMmmTZtkuXLlbHYgycnJsqCggDQD8/HjR9mwYUNbO1OnTiUNKcupEzoH+PTpUxRNREdHUyl0rl69KtQowzNp9QXpvUOHDom6devSmcCoca9o0KABHXlREVOoaZoua+fUR1Jnb62oeRWVQqdLly5C3W06MnPp0iVRr149OgoeNXCmkpfCwkLx5csXXdbOIYmqhl36hC/FuZP+QGrBCTxRpCRKQqtWrajkBc7hTQTaOWSGuXw7ssOhoIZrYujQoXRkJzMzUyQlJdFR8VEfeip5wWsPu0A7p/qeFivly5enUsnAWtmxY8foyMzo0aPFzJkz6cg98JaooKXL+t/w8HARERGhT/hivLslAa/b/Pnz6cgMAsjevXv131DgFkHgh5pz6rJ2rkaNGmxkRKApCVigQADhwJ01olmo5OXlUckL/IiKitJl7RxWWLhodevWLSoFD0IxVmA4YLgkbTrx5s0bKnnBKo/pycFTJFKtcJX9AceGDx9OR2bQf7Oyslz7vCAiYmnMivqwewJhUc9TqKkHlbyo2YBQo3c6CgwCBPoaR0ZGhkhLS6Oj0Ll7967Iz8+nIy+mdT49TlFgbYxbsVEjB9LwD4Y91rqGjBw5krTcY+3atTY7Knbo6ZCBxznQrFkzWwWM4AOxYMECWz1DSmvKlJCQYLMVGxtLV4swOde/f39bBQhSbk74WzNTEVM+fvyYNN0DuUrOnvp2kkYRJudOnz7NVnLKy9+8edNx8TEmJkZev36dNN0FySrOpuqHpFGEyTnAVapdu7Yts4vMcGJiIqsPCbavFhc8AC7VjpVYKzbn1q9fb6sIGTNmDGkUzaX69OnD6kGw8F8aIHHrtOKElKQVm3N4Ik6rmEbKwSnVDklPT9c6pQFyK5xNJJGx8cCKzTmwcOFCthGsm/kL+ejQvgv0bnLmzBnWJmTFihWkZYZ1DvumevTowTbkJAjDWFEtLTibkNTUVP26crDOAaxwYrGea9AqeC0+f/5MNd0FiWKn34FsHZ6oE47OATVlYRv1FayRuZ0hM8DiIqIgZxeCnRX+8OsccPqwG5KSkkKa7oJtVpw9Q8aNG0eazgR0LphdDEjLufX08JohpcjZMQQbb5z6mS9+nZs+fTrbuJMgCOHjDcPBRk1s1UAY379/v17V4dr1FYxVEfCCwXGTzeLFi0uc4+jYsaNo3bq16Nmzp4iPj9fzK5jBnE45rWfjmI/l5uaKixcv6o029+7do9rOTJgwQSxZsoRNDLHAOSsYYWDbES5bJZhdBr6CsSeWo7B5AMtVKEMiIiJYfSdZvXo1/brgsTmHbxUWFDgDEITmkydPsqns0hAMHI4ePUq/rnjYnMPWPs4IBNMbA7z3WCMv7hMIVvDEt2/frrdmlRSTc/7GjFlZWaRlBmNR1Tdd26KISImFfWw8CBWPc5mZmawxyKxZs0jLP5hRYEsFHA12dAO9pKQkvYSGVSA30dHy3LlzYsiQIZ4cuy/YUpidnU1HwYHEDTJTyJ4hCr548UKovqwjJdJuyLRhhQYbt5HuwzGXfQuVMMzNnHaGR0ZGitevXws1hqMzoaHuo99FEbcpp772VDSDb9OjR49ccwz8Lx3TYNjUvHlzUz/Atwz/jaSsowNKXl6ebNeuncc5bspeFjENv5AKx5qBinp0piwjxH8G5Zz6mESqhwAAAABJRU5ErkJggg==\",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],\"index\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46],\"k\":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"0.2\",\"100\",\"0.2\",\"100\",\"2\",\"100\",\"2\"],\"k_r\":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"10\",\"None\",\"10\",\"None\",\"10\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\"],\"species\":[\"nothing\",\"dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse] in default.]\",\"protein[RNAP in default.]\",\"protein[Ribo in default.]\",\"protein[RNAase in default.]\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse] in default.]\",\"rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse] in default.]\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse] in default.]\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse] in default.]\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse] in default.]\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse] in default.]\",\"ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse] in default.]\",\"rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"protein[tetr in default.]\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"protein[GFP in default.]\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward] in default.]\",\"protein[RFP in default.]\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]] in default.]\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] in default.]\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * ordered_polymer_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ktx).\\n\",\"2protein[tetr]+ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] <--> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * protein_tetr^2 * ordered_polymer_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]+protein[RNAP] <--> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ktx).\\n\",\"dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]\\n Kf=k_forward * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]] --> dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_leak, name=ktx).\\n\",\"2protein[tetr]+dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]] <--> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]\\n Kf=k_forward * protein_tetr^2 * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n Kr=k_reverse * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]\\n Kf=k_forward * ordered_polymer_complex_part_ptet_protein_tetr_2x_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ku).\\n\",\"ordered_polymer[complex[complex[part[ptet]:2x_protein[tetr]]:protein[RNAP]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]] --> ordered_polymer[complex[part[ptet]:2x_protein[tetr]-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_complex_complex_part_ptet_protein_tetr_2x__protein_RNAP_forward__part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=ptet_tetr, name=ktx).\\n\",\"dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+protein[RNAP] <--> ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]]\\n Kf=k_forward * dna_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_pconst_reverse_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[pconst]:protein[RNAP]-reverse]] --> dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse]]+rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_ptet_forward_part_UTR1_forward_part_GFP_forward_part_t16_forward_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_pconst_protein_RNAP_reverse__\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[GFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]] --> rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kdeg).\\n\",\"rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kdeg).\\n\"],\"type\":[\"nothing\",\"dna\",\"protein\",\"protein\",\"protein\",\"ordered_polymer\",\"rna\",\"ordered_polymer\",\"ordered_polymer\",\"ordered_polymer\",\"ordered_polymer\",\"ordered_polymer\",\"ordered_polymer\",\"rna\",\"protein\",\"ordered_polymer\",\"protein\",\"ordered_polymer\",\"protein\",\"complex\",\"complex\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\"]},\"selected\":{\"id\":\"1648\"},\"selection_policy\":{\"id\":\"1647\"}},\"id\":\"1477\",\"type\":\"ColumnDataSource\"},{\"attributes\":{\"data\":{\"color\":[\"purple\",\"white\",\"green\",\"green\",\"green\",\"grey\",\"orange\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"orange\",\"green\",\"grey\",\"lightgreen\",\"grey\",\"red\",\"cyan\",\"cyan\"],\"image\":[\"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\",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],\"index\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],\"species\":[\"nothing\",\"dna[part[ptet-forward]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]:part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[pconst-reverse] 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"markdown", "metadata": {}, "source": [ "Now you can see that many more arrows lead to each RNA. But there is still only one promoter per RNA, how can it be? Well, now that both promoters and transcripts are on the same DNA, we must take into account the fact that you can have both promoters with RNA polymerase bound, so for example Promoter1 can lead to RNA1 whether or not Promoter2 is bound by RNAP.\n", "\n", "We can even make a more complicated DNA construct, such as what happens before and after a promoter is \"flipped\" by integrase activity" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0\n", "0\n", "done\n", "d:\\documents\\github\\biocrnpyler\\biocrnpyler\\plotting.py:500: UserWarning: This figure includes Axes that are not compatible with tight_layout, so results might be incorrect.\n", " plt.tight_layout(pad=0.0001)\n" ] }, { "data": { "image/png": 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\n", 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" ] }, "metadata": { "needs_background": "light" }, "output_type": "display_data" } ], "source": [ "attB = IntegraseSite(\"attB\",\"attB\",integrase=\"Bxb1\")\n", "attP = IntegraseSite(\"attP\",\"attP\",integrase=\"Bxb1\")\n", "\n", "diffatt = IntegraseSite(\"attL\",\"attL\",integrase=\"phic31\")\n", "\n", "construct_1 = DNA_construct([[t16,\"reverse\"],[rfp,\"reverse\"],[utr1,\"reverse\"],[attP,\"forward\"],[pconst,\"forward\"],[attB,\"reverse\"],[utr1,\"forward\"],[gfp,\"forward\"],[t16,\"forward\"]])\n", "\n", "components = [construct_1]\n", "bxb1 = Integrase_Enumerator(\"Bxb1\", int_mechanisms={\"Bxb1\":IntegraseRule(\"Bxb1\")})\n", "\n", "myMixture = TxTlExtract(name = \"txtl\", parameters = parameters, components = components,global_component_enumerators=[bxb1])\n", "\n", "\n", "#now, we are using dnaplotlib to plot the constructs\n", "enumerated_constructs = myMixture.global_component_enumeration(recursion_depth=4)\n", "myCRN = myMixture.compile_crn()\n", "if(dpl_enabled):\n", " conlist = []\n", " for con in enumerated_constructs:\n", " if(isinstance(con,DNA_construct)):\n", " conlist += [con]\n", " render_constructs(conlist)\n", "#some very basic parameters are defined\n", "parameters={\"cooperativity\":2,\"kb\":100, \"ku\":10, \"ktx\":.05, \"ktl\":.2, \"kdeg\":2,\"kint\":.05}\n", "\n", "\n", "print(\"done\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "And we can see that this construct 'knows' that a forward facing promoter will not produce RNAs that face the reverse direction." ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "tags": [] }, "outputs": [ { "data": { "text/html": [ "\n", "
\n", " \n", " Loading BokehJS ...\n", "
" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var force = true;\n", "\n", " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", " root._bokeh_onload_callbacks = [];\n", " root._bokeh_is_loading = undefined;\n", " }\n", "\n", " var JS_MIME_TYPE = 'application/javascript';\n", " var HTML_MIME_TYPE = 'text/html';\n", " var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", " var CLASS_NAME = 'output_bokeh rendered_html';\n", "\n", " /**\n", " * Render data to the DOM node\n", " */\n", " function render(props, node) {\n", " var script = document.createElement(\"script\");\n", " node.appendChild(script);\n", " }\n", "\n", " /**\n", " * Handle when an output is cleared or removed\n", " */\n", " function handleClearOutput(event, handle) {\n", " var cell = handle.cell;\n", "\n", " var id = cell.output_area._bokeh_element_id;\n", " var server_id = cell.output_area._bokeh_server_id;\n", " // Clean up Bokeh references\n", " if (id != null && id in Bokeh.index) {\n", " Bokeh.index[id].model.document.clear();\n", " delete Bokeh.index[id];\n", " }\n", "\n", " if (server_id !== undefined) {\n", " // Clean up Bokeh references\n", " var cmd = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", " cell.notebook.kernel.execute(cmd, {\n", " iopub: {\n", " output: function(msg) {\n", " var id = msg.content.text.trim();\n", " if (id in Bokeh.index) {\n", " Bokeh.index[id].model.document.clear();\n", " delete Bokeh.index[id];\n", " }\n", " }\n", " }\n", " });\n", " // Destroy server and session\n", " var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", " cell.notebook.kernel.execute(cmd);\n", " }\n", " }\n", "\n", " /**\n", " * Handle when a new output is added\n", " */\n", " function handleAddOutput(event, handle) {\n", " var output_area = handle.output_area;\n", " var output = handle.output;\n", "\n", " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", " if ((output.output_type != \"display_data\") || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n", " return\n", " }\n", "\n", " var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", "\n", " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", " // store reference to embed id on output_area\n", " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", " }\n", " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", " var bk_div = document.createElement(\"div\");\n", " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", " var script_attrs = bk_div.children[0].attributes;\n", " for (var i = 0; i < script_attrs.length; i++) {\n", " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", " }\n", " // store reference to server id on output_area\n", " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", " }\n", " }\n", "\n", " function register_renderer(events, OutputArea) {\n", "\n", " function append_mime(data, metadata, element) {\n", " // create a DOM node to render to\n", " var toinsert = this.create_output_subarea(\n", " metadata,\n", " CLASS_NAME,\n", " EXEC_MIME_TYPE\n", " );\n", " this.keyboard_manager.register_events(toinsert);\n", " // Render to node\n", " var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", " render(props, toinsert[toinsert.length - 1]);\n", " element.append(toinsert);\n", " return toinsert\n", " }\n", "\n", " /* Handle when an output is cleared or removed */\n", " events.on('clear_output.CodeCell', handleClearOutput);\n", " events.on('delete.Cell', handleClearOutput);\n", "\n", " /* Handle when a new output is added */\n", " events.on('output_added.OutputArea', handleAddOutput);\n", "\n", " /**\n", " * Register the mime type and append_mime function with output_area\n", " */\n", " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", " /* Is output safe? */\n", " safe: true,\n", " /* Index of renderer in `output_area.display_order` */\n", " index: 0\n", " });\n", " }\n", "\n", " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", " if (root.Jupyter !== undefined) {\n", " var events = require('base/js/events');\n", " var OutputArea = require('notebook/js/outputarea').OutputArea;\n", "\n", " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", " register_renderer(events, OutputArea);\n", " }\n", " }\n", "\n", " \n", " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " var NB_LOAD_WARNING = {'data': {'text/html':\n", " \"
\\n\"+\n", " \"

\\n\"+\n", " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"

\\n\"+\n", " \"
    \\n\"+\n", " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", " \"
\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded() {\n", " var el = document.getElementById(\"1926\");\n", " if (el != null) {\n", " el.textContent = \"BokehJS is loading...\";\n", " }\n", " if (root.Bokeh !== undefined) {\n", " if (el != null) {\n", " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n", " }\n", " } else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(display_loaded, 100)\n", " }\n", " }\n", "\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) {\n", " if (callback != null)\n", " callback();\n", " });\n", " } finally {\n", " delete root._bokeh_onload_callbacks\n", " }\n", " console.debug(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(css_urls, js_urls, callback) {\n", " if (css_urls == null) css_urls = [];\n", " if (js_urls == null) js_urls = [];\n", "\n", " root._bokeh_onload_callbacks.push(callback);\n", " if (root._bokeh_is_loading > 0) {\n", " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls == null || js_urls.length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", "\n", " function on_load() {\n", " root._bokeh_is_loading--;\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", " run_callbacks()\n", " }\n", " }\n", "\n", " function on_error() {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " for (var i = 0; i < css_urls.length; i++) {\n", " var url = css_urls[i];\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.rel = \"stylesheet\";\n", " element.type = \"text/css\";\n", " element.href = url;\n", " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", " document.body.appendChild(element);\n", " }\n", "\n", " const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\": \"T2yuo9Oe71Cz/I4X9Ac5+gpEa5a8PpJCDlqKYO0CfAuEszu1JrXLl8YugMqYe3sM\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\": \"98GDGJ0kOMCUMUePhksaQ/GYgB3+NH9h996V88sh3aOiUNX3N+fLXAtry6xctSZ6\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\": \"89bArO+nlbP3sgakeHjCo1JYxYR5wufVgA3IbUvDY+K7w4zyxJqssu7wVnfeKCq8\"};\n", "\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " if (url in hashes) {\n", " element.crossOrigin = \"anonymous\";\n", " element.integrity = \"sha384-\" + hashes[url];\n", " }\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " \n", " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\"];\n", " var css_urls = [];\n", " \n", "\n", " var inline_js = [\n", " function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", " function(Bokeh) {\n", " \n", " \n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " \n", " if (root.Bokeh !== undefined || force === true) {\n", " \n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", " if (force === true) {\n", " display_loaded();\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " } else if (force !== true) {\n", " var cell = $(document.getElementById(\"1926\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\n", "\n", " }\n", "\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", " run_inline_js();\n", " } else {\n", " load_libs(css_urls, js_urls, function() {\n", " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", " run_inline_js();\n", " });\n", " }\n", "}(window));" ], "application/vnd.bokehjs_load.v0+json": "\n(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n \n\n \n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n var NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
  • use INLINE resources instead, as so:
    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded() {\n var el = document.getElementById(\"1926\");\n if (el != null) {\n el.textContent = \"BokehJS is loading...\";\n }\n if (root.Bokeh !== undefined) {\n if (el != null) {\n el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(display_loaded, 100)\n }\n }\n\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\": \"T2yuo9Oe71Cz/I4X9Ac5+gpEa5a8PpJCDlqKYO0CfAuEszu1JrXLl8YugMqYe3sM\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\": \"98GDGJ0kOMCUMUePhksaQ/GYgB3+NH9h996V88sh3aOiUNX3N+fLXAtry6xctSZ6\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\": \"89bArO+nlbP3sgakeHjCo1JYxYR5wufVgA3IbUvDY+K7w4zyxJqssu7wVnfeKCq8\"};\n\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n if (url in hashes) {\n element.crossOrigin = \"anonymous\";\n element.integrity = \"sha384-\" + hashes[url];\n }\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n \n var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js\"];\n var css_urls = [];\n \n\n var inline_js = [\n function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\n function(Bokeh) {\n \n \n }\n ];\n\n function run_inline_js() {\n \n if (root.Bokeh !== undefined || force === true) {\n \n for (var i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n if (force === true) {\n display_loaded();\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n var cell = $(document.getElementById(\"1926\")).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" }, "metadata": {}, "output_type": "display_data" }, { "name": "stderr", "output_type": "stream", "text": [ "D:\\anaconda3\\lib\\site-packages\\bokeh\\plotting\\graph.py:120: UserWarning: Node keys in 'layout_function' don't match node keys in the graph. These nodes may not be displayed correctly.\n", " warn(\"Node keys in 'layout_function' don't match node keys in the graph. \"\n" ] }, { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function embed_document(root) {\n", " \n", " var docs_json = {\"34e0bd13-73dd-49b1-986c-15fdbf488d92\":{\"roots\":{\"references\":[{\"attributes\":{\"plot_height\":500,\"plot_width\":500,\"renderers\":[{\"id\":\"1960\"},{\"id\":\"1932\"},{\"id\":\"1946\"}],\"title\":{\"id\":\"2144\"},\"toolbar\":{\"id\":\"2041\"},\"x_range\":{\"id\":\"2002\"},\"x_scale\":{\"id\":\"2142\"},\"y_range\":{\"id\":\"2003\"},\"y_scale\":{\"id\":\"2145\"}},\"id\":\"1929\",\"type\":\"Plot\"},{\"attributes\":{\"data\":{\"color\":[\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"yellow\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"yellow\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\",\"cornflowerblue\"],\"index\":[29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70],\"k\":[\"100\",\"0.05\",\"100\",\"100\",\"100\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"100\",\"0.05\",\"100\",\"0.05\",\"100\",\"100\",\"0.05\",\"100\",\"100\",\"0.05\",\"100\",\"100\",\"100\",\"100\",\"100\",\"0.05\",\"100\",\"100\",\"0.05\",\"100\",\"100\",\"100\",\"0.05\",\"100\",\"100\",\"0.2\",\"100\",\"0.2\",\"100\",\"2\",\"100\",\"2\"],\"k_r\":[\"10\",\"None\",\"10\",\"10\",\"10\",\"10\",\"None\",\"10\",\"None\",\"10\",\"10\",\"None\",\"10\",\"None\",\"10\",\"10\",\"None\",\"10\",\"10\",\"None\",\"10\",\"10\",\"10\",\"10\",\"10\",\"None\",\"10\",\"10\",\"None\",\"10\",\"10\",\"10\",\"None\",\"10\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\",\"10\",\"None\"],\"species\":[\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=kint).\\n search_key=(mech=Bxb1, partid=Bxb1, name=kint).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=kint).\\n search_key=(mech=Bxb1, partid=Bxb1, name=kint).\\n\",\"2protein[Bxb1]+dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=ku).\\n\",\"dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=ku).\\n\",\"2protein[Bxb1]+dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=ku).\\n\",\"dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=ku).\\n\",\"rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[part[attB-reverse]:complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_part_attB_reverse_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[part[attB-reverse]:complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]] --> rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[GFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_part_attB_reverse_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[part[attR-reverse]:complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_part_attR_reverse_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[part[attR-reverse]:complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]] --> rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_part_attR_reverse_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kdeg).\\n\",\"rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kdeg).\\n\"],\"type\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\"]},\"selected\":{\"id\":\"2182\"},\"selection_policy\":{\"id\":\"2181\"}},\"id\":\"1934\",\"type\":\"ColumnDataSource\"},{\"attributes\":{\"source\":{\"id\":\"1948\"}},\"id\":\"1950\",\"type\":\"CDSView\"},{\"attributes\":{},\"id\":\"2181\",\"type\":\"UnionRenderers\"},{\"attributes\":{},\"id\":\"1951\",\"type\":\"MultiLine\"},{\"attributes\":{\"data\":{\"color\":[\"purple\",\"white\",\"green\",\"green\",\"green\",\"white\",\"grey\",\"orange\",\"grey\",\"yellow\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"orange\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"lightgreen\",\"grey\",\"red\",\"cyan\",\"cyan\"],\"image\":[\"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\",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],\"index\":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28],\"species\":[\"nothing\",\"dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] 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in default.]\",\"protein[RNAP in default.]\",\"protein[Ribo in default.]\",\"protein[RNAase in default.]\",\"dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"protein[Bxb1 in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"ordered_polymer[part[attB-reverse]:complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward] in default.]\",\"protein[GFP in default.]\",\"ordered_polymer[part[attR-reverse]:complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward] in default.]\",\"protein[RFP in default.]\",\"complex[protein[RNAase]:rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] in default.]\",\"complex[protein[RNAase]:rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]] in default.]\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=kint).\\n search_key=(mech=Bxb1, partid=Bxb1, name=kint).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_forward__complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=kint).\\n search_key=(mech=Bxb1, partid=Bxb1, name=kint).\\n\",\"2protein[Bxb1]+dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attP]:2x_protein[Bxb1]-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attP_protein_Bxb1_2x_forward__part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attP, name=ku).\\n\",\"dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:complex[part[pconst]:protein[RNAP]-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_complex_part_pconst_protein_RNAP_forward__part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attP-forward]:part[pconst-forward]:complex[part[attB]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attP_forward_part_pconst_forward_complex_part_attB_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attB, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=ku).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:complex[part[pconst]:protein[RNAP]-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__complex_part_pconst_protein_RNAP_reverse__complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=ku).\\n\",\"2protein[Bxb1]+dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:complex[part[attR]:2x_protein[Bxb1]-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_complex_part_attR_protein_Bxb1_2x_forward__part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attR, name=ku).\\n\",\"dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAP] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAP\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=transcription_mm, partid=pconst, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=transcription_mm, partid=pconst, name=ku).\\n\",\"ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:complex[part[pconst]:protein[RNAP]-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] --> dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAP]\\n Kf=k_forward * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_complex_part_pconst_protein_RNAP_reverse__part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=0.05\\n found_key=(mech=None, partid=None, name=ktx).\\n search_key=(mech=transcription_mm, partid=pconst, name=ktx).\\n\",\"2protein[Bxb1]+dna[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:part[attL-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]] <--> ordered_polymer[part[t16-reverse]:part[RFP-reverse]:part[UTR1-reverse]:part[attR-forward]:part[pconst-reverse]:complex[part[attL]:2x_protein[Bxb1]-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * protein_Bxb1^2 * dna_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_part_attL_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n Kr=k_reverse * ordered_polymer_part_t16_reverse_part_RFP_reverse_part_UTR1_reverse_part_attR_forward_part_pconst_reverse_complex_part_attL_protein_Bxb1_2x_reverse__part_UTR1_forward_part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=one_step_cooperative_binding, partid=attL, name=ku).\\n\",\"rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[part[attB-reverse]:complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_part_attB_reverse_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[part[attB-reverse]:complex[part[UTR1]:protein[Ribo]-forward]:part[GFP-forward]:part[t16-forward]] --> rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[GFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_part_attB_reverse_complex_part_UTR1_protein_Ribo_forward__part_GFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[Ribo] <--> ordered_polymer[part[attR-reverse]:complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]]\\n Kf=k_forward * rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_Ribo\\n Kr=k_reverse * ordered_polymer_part_attR_reverse_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=translation_mm, partid=UTR1, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=translation_mm, partid=UTR1, name=ku).\\n\",\"ordered_polymer[part[attR-reverse]:complex[part[UTR1]:protein[Ribo]-forward]:part[RFP-forward]:part[t16-forward]] --> rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RFP]+protein[Ribo]\\n Kf=k_forward * ordered_polymer_part_attR_reverse_complex_part_UTR1_protein_Ribo_forward__part_RFP_forward_part_t16_forward_\\n k_forward=0.2\\n found_key=(mech=None, partid=None, name=ktl).\\n search_key=(mech=translation_mm, partid=UTR1, name=ktl).\\n\",\"rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[attB-reverse]:part[UTR1-forward]:part[GFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attB_reverse_part_UTR1_forward_part_GFP_forward_part_t16_forward_, name=kdeg).\\n\",\"rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]+protein[RNAase] <--> complex[protein[RNAase]:rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]]\\n Kf=k_forward * rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward_ * protein_RNAase\\n Kr=k_reverse * complex_protein_RNAase_rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=100\\n found_key=(mech=None, partid=None, name=kb).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=kb).\\n k_reverse=10\\n found_key=(mech=None, partid=None, name=ku).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward_, name=ku).\\n\",\"complex[protein[RNAase]:rna[part[attR-reverse]:part[UTR1-forward]:part[RFP-forward]:part[t16-forward]]] --> protein[RNAase]\\n Kf=k_forward * complex_protein_RNAase_rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward__\\n k_forward=2\\n found_key=(mech=None, partid=None, name=kdeg).\\n search_key=(mech=rna_degredation_mm, partid=rna_part_attR_reverse_part_UTR1_forward_part_RFP_forward_part_t16_forward_, 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"plotNetwork(myCRN,colordict={\"complex\":\"cyan\",\"protein\":\"green\",\n", " \"GFP\":\"lightgreen\",\n", " \"RFP\":\"red\",\n", " \"ribosome\":\"blue\",\n", " \"dna\":\"white\",\"rna\":\"orange\",\n", " \"ligand\":\"pink\",\"phosphate\":\"yellow\",\"nothing\":\"purple\", \"Bxb1\":\"yellow\"})" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Overview for developers\n", "Several key additions had to be made to biocrnpyler to make this possible. \n", "\n", "1. `Complex()` is a new function that you should use every time you want to make a ComplexSpecies. It should do exactly the same thing as the ComplexSpecies constructor, unless one of the species that you gave it is an OrderedComplexSpecies that has a 'bindloc' attribute, then instead of making a ComplexSpecies the function will make an OrderedComplexSpecies that is correctly formed.\n", "\n", "2. `OrderedPolymer` `OrderedMonomer` and `OrderedPolymerSpecies` are new data members that represent sequences of parts. A piece of DNA with many binding sites is represented as an OrderedPolymerSpecies. Because mechanisms and Components are agnostic of binding location; that is to say, they usually have code that looks like this: `make_complex([dna,protein])`, we must give them some way of knowing _where_ on that `dna` the `protein` should end up. To do this, you must pass an `OrderedMonomer` into a `Component` which belongs to an `OrderedPolymer`. Through the use of the `Complex()` function, the proper complex will be made, to the correct member of the `OrderedPolymer` which the `OrderedMonomer` belongs to.\n", "\n", "3. `DNA_part` inherits from `Component`, and every dna part such as `Promoter` now inherits from `DNA_part` instead of `Component`. This allows the storage of things like position, direction, and parent construct inside anything that used to be a `Component`\n", "\n", "4. `CDS` is a `DNA_part` which gives rise to a `Species`. It felt weird to put `Protein` objects into a DNA sequence so I created this. It only makes the protein if it is read in the 'forward' direction.\n", "\n", "4. `DNA_construct` contains a list of `DNA_part`s together with their directions. `DNA_construct` also has `update_species()` and `update_reactions()` so that it can generate the necessary species and reactions if it will be part of a CRN. Likewise, `RNA_construct` does the same thing for RNA. A `DNA_construct` can give rise to many `RNA_construct`s when it compiles. This is done through the action of `explore_txtl()`\n", "\n", "5. `explore_txtl()` is a function of `DNA_construct` which figures out the RNA and Proteins that a DNA produces. It works basically by going along a DNA part by part, remembering which parts came before, and taking into account the directions of parts. In general it will traverse a `DNA_construct` in the \"forward\" and \"reverse\" directions. It is hard coded to know that `RBS` parts make proteins and `Promoter` parts make RNAs, but only when their orientation is \"forward\" relative to the direction it's currently looking at. Other things are taken account too, for example, an `RBS` can only make a `Protein` if it is part of an RNA. Most of this logic is encapsulated in an object called `TxTl_explorer`.\n", "\n", "6. `update_components()` is a function of `DNA_construct` which creates many copies of the `DNA_part`s which make up the `DNA_construct`. This is necessary for making all combinatorial complexes. First, every `DNA_part` is fed in an `OrderedComplexSpecies` corresponding to the unbound DNA, which has the appropriate \"bindloc_\". Then, the `Species` produced by `update_species()` each have complexes in only one location. All possible combinations of bound species are then generated from this set of `OrderedComplexSpecies`. Then, these combinatorial complexes are fed _back_ into the `DNA_part`s, generating a new `DNA_part` that is responsible for generating species and reactions that include that combinatorial complex. For example, if you have `DNA_construct` containing a `Promoter` and an `AttachmentSite`, then `update_components()` should generate two `Promoter` parts, one that has the unbound `OrderedComplexSpecies` and one that has an `OrderedComplexSpecies` that has integrases bound to it. Then, these new `Component`s can be used to make species and reactions using their respective `update_species()` and `update_reactions()`\n" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.12.4" } }, "nbformat": 4, "nbformat_minor": 4 }