{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Exercise 4.7: Making a stand-alone app for exploring parameters\n",
    "\n",
    "<hr>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Recall that in our [lesson on dashboarding](l26_dashboards.ipynb), we built a dashboard investigating how fold change in gene expression varies with repressor copy number $R$ and inducer concentration $c$. The theoretical curve is\n",
    "\n",
    "\\begin{align}\n",
    "\\text{fold change} = \\left[1 + \\frac{\\frac{R}{K}\\left(1 + c/K_\\mathrm{d}^\\mathrm{A}\\right)^2}{\\left(1 + c/K_\\mathrm{d}^\\mathrm{A}\\right)^2 + K_\\mathrm{switch}\\left(1 + c/K_\\mathrm{d}^\\mathrm{I}\\right)^2}\\right]^{-1},\n",
    "\\end{align}\n",
    "\n",
    "with parameters given in the table below.\n",
    "\n",
    "|Parameter|Description|\n",
    "|:--:|:--:|\n",
    "|$K_\\mathrm{d}^\\mathrm{A}$|dissoc. const. for active repressor binding IPTG|\n",
    "|$K_\\mathrm{d}^\\mathrm{I}$|dissoc. const. for inactive repressor binding IPTG|\n",
    "|$K_\\mathrm{switch}$|equil. const. for switching active/inactive|\n",
    "|$K$|dissoc. const. for active repressor binding operator|\n",
    "|$R$|number of repressors in cell|\n",
    "\n",
    "Rebuild that dashboard, but use JavaScript callbacks so you can have full interactivity with a stand-alone HTML file."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<br />"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Solution \n",
    "\n",
    "<hr>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "    <div class=\"bk-root\">\n",
       "        <a href=\"https://bokeh.org\" target=\"_blank\" class=\"bk-logo bk-logo-small bk-logo-notebook\"></a>\n",
       "        <span id=\"1002\">Loading BokehJS ...</span>\n",
       "    </div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": [
       "\n",
       "(function(root) {\n",
       "  function now() {\n",
       "    return new Date();\n",
       "  }\n",
       "\n",
       "  const 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",
       "  const JS_MIME_TYPE = 'application/javascript';\n",
       "  const HTML_MIME_TYPE = 'text/html';\n",
       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
       "\n",
       "  /**\n",
       "   * Render data to the DOM node\n",
       "   */\n",
       "  function render(props, node) {\n",
       "    const 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",
       "    const cell = handle.cell;\n",
       "\n",
       "    const id = cell.output_area._bokeh_element_id;\n",
       "    const 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",
       "      const cmd_clean = \"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_clean, {\n",
       "        iopub: {\n",
       "          output: function(msg) {\n",
       "            const 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",
       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
       "      cell.notebook.kernel.execute(cmd_destroy);\n",
       "    }\n",
       "  }\n",
       "\n",
       "  /**\n",
       "   * Handle when a new output is added\n",
       "   */\n",
       "  function handleAddOutput(event, handle) {\n",
       "    const output_area = handle.output_area;\n",
       "    const output = handle.output;\n",
       "\n",
       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
       "      return\n",
       "    }\n",
       "\n",
       "    const 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",
       "      const bk_div = document.createElement(\"div\");\n",
       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
       "      const script_attrs = bk_div.children[0].attributes;\n",
       "      for (let 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",
       "      const 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",
       "      const 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",
       "    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",
       "\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",
       "     \"<div style='background-color: #fdd'>\\n\"+\n",
       "     \"<p>\\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",
       "     \"</p>\\n\"+\n",
       "     \"<ul>\\n\"+\n",
       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
       "     \"</ul>\\n\"+\n",
       "     \"<code>\\n\"+\n",
       "     \"from bokeh.resources import INLINE\\n\"+\n",
       "     \"output_notebook(resources=INLINE)\\n\"+\n",
       "     \"</code>\\n\"+\n",
       "     \"</div>\"}};\n",
       "\n",
       "  function display_loaded() {\n",
       "    const el = document.getElementById(\"1002\");\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(url) {\n",
       "      console.error(\"failed to load \" + url);\n",
       "    }\n",
       "\n",
       "    for (let i = 0; i < css_urls.length; i++) {\n",
       "      const url = css_urls[i];\n",
       "      const element = document.createElement(\"link\");\n",
       "      element.onload = on_load;\n",
       "      element.onerror = on_error.bind(null, url);\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",
       "    for (let i = 0; i < js_urls.length; i++) {\n",
       "      const url = js_urls[i];\n",
       "      const element = document.createElement('script');\n",
       "      element.onload = on_load;\n",
       "      element.onerror = on_error.bind(null, url);\n",
       "      element.async = false;\n",
       "      element.src = url;\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",
       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-2.4.2.min.js\"];\n",
       "  const css_urls = [];\n",
       "  \n",
       "\n",
       "  const 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 (let 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",
       "      const cell = $(document.getElementById(\"1002\")).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  const 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  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\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     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    const el = document.getElementById(\"1002\");\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(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\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    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\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  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.4.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-2.4.2.min.js\"];\n  const css_urls = [];\n  \n\n  const 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 (let 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      const cell = $(document.getElementById(\"1002\")).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"
    }
   ],
   "source": [
    "import numpy as np\n",
    "\n",
    "import bokeh.io\n",
    "import bokeh.layouts\n",
    "import bokeh.models\n",
    "import bokeh.plotting\n",
    "\n",
    "bokeh.io.output_notebook()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To build our app, we will first code up the functions to compute the fold change in Python so we can make the starting plot."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def bohr_parameter(c, R, K, KdA, KdI, Kswitch):\n",
    "    \"\"\"Compute Bohr parameter based on MWC model.\"\"\"\n",
    "    # Big nasty argument of logarithm\n",
    "    log_arg = (1 + c / KdA) ** 2 / ((1 + c / KdA) ** 2 + Kswitch * (1 + c / KdI) ** 2)\n",
    "\n",
    "    return -np.log(R / K) - np.log(log_arg)\n",
    "\n",
    "\n",
    "def fold_change(c, R, K, KdA, KdI, Kswitch):\n",
    "    \"\"\"Compute theoretical fold change for MWC model.\"\"\"\n",
    "    return 1.0 / (1.0 + np.exp(-bohr_parameter(c, R, K, KdA, KdI, Kswitch)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next, we can make the sliders we want. We will again vary the parameters on a logarithmic scale, but will use a clever trick with the labels to we do not display the base ten logarithm of the parameter value, but rather the value itself. To do this, we use a `bokeh.models.FuncTickFormatter` to give a snippet of JavaScript code to display the value of the slider. We will raise ten to the value of the log slider and then display the resulting value with a precision of 3."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "slider_format = bokeh.models.FuncTickFormatter(\n",
    "    code=\"return Math.pow(10, tick).toPrecision(3)\"\n",
    ")\n",
    "log_R_slider = bokeh.models.Slider(\n",
    "    title=\"R (1/cell)\", start=0, end=3, step=0.1, value=2, format=slider_format,\n",
    ")\n",
    "log_K_slider = bokeh.models.Slider(\n",
    "    title=\"K (1/cell)\", start=-6, end=3, step=0.1, value=0, format=slider_format,\n",
    ")\n",
    "log_KdA_slider = bokeh.models.Slider(\n",
    "    title=\"KdA (1/mM)\", start=-6, end=3, step=0.1, value=-2, format=slider_format,\n",
    ")\n",
    "log_KdI_slider = bokeh.models.Slider(\n",
    "    title=\"KdI (1/mM)\", start=-6, end=3, step=0.1, value=-2, format=slider_format,\n",
    ")\n",
    "log_Kswitch_slider = bokeh.models.Slider(\n",
    "    title=\"Kswitch\", start=-3, end=6, step=0.1, value=1, format=slider_format,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now, let's build out plot, using a `ColumnDataSource` so we can manipulate the values."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "c = np.logspace(-6, 2, 200)\n",
    "fc = fold_change(\n",
    "    c,\n",
    "    10 ** log_R_slider.value,\n",
    "    10 ** log_K_slider.value,\n",
    "    10 ** log_KdA_slider.value,\n",
    "    10 ** log_KdI_slider.value,\n",
    "    10 ** log_Kswitch_slider.value,\n",
    ")\n",
    "\n",
    "cds = bokeh.models.ColumnDataSource(dict(c=c, fc=fc))\n",
    "\n",
    "p = bokeh.plotting.figure(\n",
    "    frame_height=250,\n",
    "    frame_width=350,\n",
    "    x_axis_label=\"[IPTG] (mM)\",\n",
    "    y_axis_label=\"fold change\",\n",
    "    x_range=[1e-6, 1e2],\n",
    "    y_range=[-0.05, 1.05],\n",
    "    x_axis_type=\"log\",\n",
    ")\n",
    "\n",
    "p.line(source=cds, x=\"c\", y=\"fc\", line_width=2);"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next, we code up the JavaScript code to get triggered when the sliders change values. The JS code is pretty straightforward, directly following what we have seen in the lesson."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "jscode = \"\"\"\n",
    "function bohr_parameter(c, R, K, KdA, KdI, Kswitch){\n",
    "    var log_arg = (1 + c / KdA) ** 2 / ((1 + c / KdA) ** 2 + Kswitch * (1 + c / KdI) ** 2);\n",
    "\n",
    "    return -Math.log(R / K) - Math.log(log_arg);\n",
    "}\n",
    "\n",
    "function fold_change(c, R, K, KdA, KdI, Kswitch) {\n",
    "    return 1 / (1 + Math.exp(-bohr_parameter(c, R, K, KdA, KdI, Kswitch)));\n",
    "}\n",
    "\n",
    "// For convenience, get views into the ColumnDataSource data\n",
    "var c = cds.data['c'];\n",
    "var fc = cds.data['fc'];\n",
    "\n",
    "// Pull the values off of the sliders\n",
    "var R = 10 ** log_R_slider.value;\n",
    "var K = 10 ** log_K_slider.value;\n",
    "var KdA = 10 ** log_KdA_slider.value;\n",
    "var KdI = 10 ** log_KdI_slider.value;\n",
    "var Kswitch = 10 ** log_Kswitch_slider.value;\n",
    "\n",
    "// Loop through and update\n",
    "var cLen = c.length;\n",
    "for (var i = 0; i < cLen; i++) {\n",
    "    fc[i] = fold_change(c[i], R, K, KdA, KdI, Kswitch);\n",
    "}\n",
    "\n",
    "cds.change.emit();\n",
    "\"\"\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Finally, we link the code to the sliders as a `bokeh.models.CustomJS` instance, making sure to specify the arguments that the JS code needs."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "args = dict(\n",
    "    cds=cds,\n",
    "    log_R_slider=log_R_slider,\n",
    "    log_K_slider=log_K_slider,\n",
    "    log_KdA_slider=log_KdA_slider,\n",
    "    log_KdI_slider=log_KdI_slider,\n",
    "    log_Kswitch_slider=log_Kswitch_slider,\n",
    ")\n",
    "code = bokeh.models.CustomJS(code=jscode, args=args)\n",
    "log_R_slider.js_on_change(\"value\", code)\n",
    "log_K_slider.js_on_change(\"value\", code)\n",
    "log_KdA_slider.js_on_change(\"value\", code)\n",
    "log_KdI_slider.js_on_change(\"value\", code)\n",
    "log_Kswitch_slider.js_on_change(\"value\", code)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Great! Now, let's lay out our app and take a look!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "  <div class=\"bk-root\" id=\"89532359-2841-483b-a579-0ab4e5d195f8\" data-root-id=\"1050\"></div>\n"
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     "metadata": {},
     "output_type": "display_data"
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Kswitch);\\n}\\n\\ncds.change.emit();\\n\"},\"id\":\"1047\",\"type\":\"CustomJS\"},{\"attributes\":{\"children\":[{\"id\":\"1004\"},{\"id\":\"1005\"},{\"id\":\"1006\"},{\"id\":\"1007\"},{\"id\":\"1008\"}],\"width\":200},\"id\":\"1049\",\"type\":\"Column\"},{\"attributes\":{},\"id\":\"1028\",\"type\":\"WheelZoomTool\"},{\"attributes\":{\"line_alpha\":0.1,\"line_color\":\"#1f77b4\",\"line_width\":2,\"x\":{\"field\":\"c\"},\"y\":{\"field\":\"fc\"}},\"id\":\"1043\",\"type\":\"Line\"},{\"attributes\":{\"coordinates\":null,\"group\":null},\"id\":\"1051\",\"type\":\"Title\"},{\"attributes\":{\"axis\":{\"id\":\"1023\"},\"coordinates\":null,\"dimension\":1,\"group\":null,\"ticker\":null},\"id\":\"1026\",\"type\":\"Grid\"},{\"attributes\":{\"axis_label\":\"[IPTG] (mM)\",\"coordinates\":null,\"formatter\":{\"id\":\"1057\"},\"group\":null,\"major_label_policy\":{\"id\":\"1058\"},\"ticker\":{\"id\":\"1020\"}},\"id\":\"1019\",\"type\":\"LogAxis\"},{\"attributes\":{\"axis_label\":\"fold 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Application\",\"version\":\"2.4.2\"}};\n",
       "  const render_items = [{\"docid\":\"04a28c7d-4811-4e39-aabe-f1c4c21dca39\",\"root_ids\":[\"1050\"],\"roots\":{\"1050\":\"89532359-2841-483b-a579-0ab4e5d195f8\"}}];\n",
       "  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
       "\n",
       "  }\n",
       "  if (root.Bokeh !== undefined) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    let attempts = 0;\n",
       "    const timer = setInterval(function(root) {\n",
       "      if (root.Bokeh !== undefined) {\n",
       "        clearInterval(timer);\n",
       "        embed_document(root);\n",
       "      } else {\n",
       "        attempts++;\n",
       "        if (attempts > 100) {\n",
       "          clearInterval(timer);\n",
       "          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n",
       "        }\n",
       "      }\n",
       "    }, 10, root)\n",
       "  }\n",
       "})(window);"
      ],
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "1050"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "layout = bokeh.layouts.row(\n",
    "    p,\n",
    "    bokeh.layouts.Spacer(width=15),\n",
    "    bokeh.layouts.column(\n",
    "        log_R_slider,\n",
    "        log_K_slider,\n",
    "        log_KdA_slider,\n",
    "        log_KdI_slider,\n",
    "        log_Kswitch_slider,\n",
    "        width=200,\n",
    "    ),\n",
    ")\n",
    "\n",
    "bokeh.io.show(layout)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Computing environment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "tags": [
     "hide-input"
    ]
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Python implementation: CPython\n",
      "Python version       : 3.9.12\n",
      "IPython version      : 8.3.0\n",
      "\n",
      "numpy     : 1.21.5\n",
      "bokeh     : 2.4.2\n",
      "jupyterlab: 3.3.2\n",
      "\n"
     ]
    }
   ],
   "source": [
    "%load_ext watermark\n",
    "%watermark -v -p numpy,bokeh,jupyterlab"
   ]
  }
 ],
 "metadata": {
  "anaconda-cloud": {},
  "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": "3.9.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}