{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Introduction to Integrase Enumerator\n", "\n", "In BioCRNpyler, `Integrase_Enumerator` is a way to modularly define DNA constructs that can be recombined into other forms using integrases. Integrases in general are proteins that bind to a specific sequence and then cause a recombination event between two such sequences. In the case of `Serine Integrases`, these sequences are called `attP` and `attB`. So one very simple way to express an integrase reaction (where Bxb1 is an integrase) would be like this:\n", "\n", "$attB + 2 Bxb1 \\rightleftharpoons attB:Bxb1$\n", "\n", "$attP + 2 Bxb1 \\rightleftharpoons attP:Bxb1$\n", "\n", "$attB:Bxb1 + attP:Bxb1 \\xrightarrow{k_{int}} attL:Bxb1 + attR:Bxb1$\n", "\n", "(Bxb1 unbinding from attL and attR is not shown)\n", "\n", "With this simple schematic, very complex dna manipulations can be performed.\n", "\n" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "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 # type: ignore[import]\n", " %matplotlib inline\n", " dpl_enabled = True\n", "except (ModuleNotFoundError,ImportError) as e:\n", " dpl_enabled = False\n", "\n", "def plotNetwork(inCRN,use_pretty_print=True,colordict = None,iterations=2000,rseed=30,posscale=1,export=False,layout=\"force\",**keywords):\n", " try:\n", " from bokeh.models import (Plot , Range1d)\n", " from biocrnpyler.utils.plotting import render_network_bokeh\n", " import bokeh.plotting\n", " import bokeh.io\n", " bokeh.io.output_notebook() #this makes the graph appear in line with the notebook\n", " layout_str = \"force\"\n", " plot = render_network_bokeh(inCRN,use_pretty_print=use_pretty_print,\\\n", " colordict=colordict,layout=layout_str,posscale=posscale,\\\n", " iterations=iterations,rseed=rseed,**keywords) #this creates the networkx objects\n", " \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" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "28\n", "42\n" ] }, { "data": { "text/html": [ " \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", " const events = require('base/js/events');\n", " const 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", " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " const NB_LOAD_WARNING = {'data': {'text/html':\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", " \"
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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", " \"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",
" \"from bokeh.resources import INLINE\\n\"+\n",
" \"output_notebook(resources=INLINE)\\n\"+\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 \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"