tutorials/06_Simulate_a_Golden_Gate_simulation_for_checking_parts.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "Friendzymes #6 - Simulate a Golden Gate simulation for checking parts.ipynb",
      "provenance": [],
      "collapsed_sections": [
        "96PZqanZBAle",
        "cZwRFE9UAGIs",
        "3STJpf80Bl9Z"
      ]
    },
    "kernelspec": {
      "display_name": "Go",
      "name": "gophernotes"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "dW2UGT4s32-x"
      },
      "source": [
        "# **How to: simulate a Golden Gate simulation for checking parts**\n",
        "\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "PZJDiu_W3_FT"
      },
      "source": [
        "# Configurations for this tutorial\n",
        "\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Xqjf_sf0Am-X"
      },
      "source": [
        "\n",
        "First let's run some important settings so you can run this tutorial successfully. \n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "96PZqanZBAle"
      },
      "source": [
        "Colab notebooks use python kernels to run each cell. However, because ***Poly*** is written in **Go language (golang)**, we need to install and configure some things in colab to make feasible run something in go lang here.\n",
        "\n",
        "### **1. In order to start the golang environment, run the line below:**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "caT1iMfshw62",
        "outputId": "1aa484a3-9d7e-43cf-f17d-d1adf3410ea0"
      },
      "source": [
        "# this process may take a few minutes\n",
        "!add-apt-repository ppa:longsleep/golang-backports -y\n",
        "!apt update\n",
        "!apt install golang-go\n",
        "%env GOPATH=/root/go\n",
        "!go get -u github.com/gopherdata/gophernotes\n",
        "!cp ~/go/bin/gophernotes /usr/bin/\n",
        "!npx degit gopherdata/gophernotes/kernel \\\n",
        "     /usr/local/share/jupyter/kernels/gophernotes"
      ],
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
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            "env: GOPATH=/root/go\n",
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            "go: downloading github.com/go-zeromq/goczmq/v4 v4.2.2\n",
            "go: downloading golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9\n",
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            "go: downloading golang.org/x/tools v0.1.7\n",
            "go: downloading github.com/rivo/uniseg v0.1.0\n",
            "go: downloading golang.org/x/sys v0.0.0-20210119212857-b64e53b001e4\n",
            "go: downloading github.com/rivo/uniseg v0.2.0\n",
            "go: downloading golang.org/x/mod v0.3.0\n",
            "go: downloading golang.org/x/mod v0.5.1\n",
            "go: downloading golang.org/x/sys v0.0.0-20211020174200-9d6173849985\n",
            "go get: installing executables with 'go get' in module mode is deprecated.\n",
            "\tUse 'go install pkg@version' instead.\n",
            "\tFor more information, see https://golang.org/doc/go-get-install-deprecation\n",
            "\tor run 'go help get' or 'go help install'.\n",
            "\u001b[K\u001b[?25hnpx: installed 1 in 2.41s\n",
            "\u001b[36m> cloned \u001b[1mgopherdata/gophernotes\u001b[22m#\u001b[1mHEAD\u001b[22m to /usr/local/share/jupyter/kernels/gophernotes\u001b[39m\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "cZwRFE9UAGIs"
      },
      "source": [
        "### **2. Download important data to run this tutorial**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "wHmBJ418_5tX"
      },
      "source": [
        "!rm -rf $GOPATH/pkg/mod/github.com/!open-!science-!global\n",
        "!rm -rf $GOPATH/pkg/mod/cache/download/github.com/!open-!science-!global\n",
        "!go get -u github.com/Open-Science-Global/poly@e3e1c61"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "3STJpf80Bl9Z"
      },
      "source": [
        "### **3. Connect Colab Notebook to your GDrive (not required)**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ftGzhtH5AOZM"
      },
      "source": [
        "The previous code will download the files temporarily. If you want to download them to a folder on your drive and save it for later analysis or if you are already using this notebook to run your own files, you should connect your Google Drive to Colab and you will be able to access, read and save files permanently. \n",
        "So, if you prefer, you can do this with the code line below:\n",
        "\n"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "sh661uGn_8R1",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 527
        },
        "outputId": "9d874164-d5ca-4b63-ac83-aa544d2d0fdd"
      },
      "source": [
        "from google.colab import drive\n",
        "drive.mount('/content/drive')"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "error",
          "ename": "KeyboardInterrupt",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
            "\u001b[0;32m/usr/local/lib/python3.7/dist-packages/ipykernel/kernelbase.py\u001b[0m in \u001b[0;36m_input_request\u001b[0;34m(self, prompt, ident, parent, password)\u001b[0m\n\u001b[1;32m    728\u001b[0m             \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 729\u001b[0;31m                 \u001b[0mident\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreply\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msession\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstdin_socket\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    730\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0mException\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.7/dist-packages/jupyter_client/session.py\u001b[0m in \u001b[0;36mrecv\u001b[0;34m(self, socket, mode, content, copy)\u001b[0m\n\u001b[1;32m    802\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 803\u001b[0;31m             \u001b[0mmsg_list\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msocket\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecv_multipart\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmode\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcopy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    804\u001b[0m         \u001b[0;32mexcept\u001b[0m \u001b[0mzmq\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mZMQError\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.7/dist-packages/zmq/sugar/socket.py\u001b[0m in \u001b[0;36mrecv_multipart\u001b[0;34m(self, flags, copy, track)\u001b[0m\n\u001b[1;32m    624\u001b[0m         \"\"\"\n\u001b[0;32m--> 625\u001b[0;31m         \u001b[0mparts\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflags\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcopy\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtrack\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mtrack\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    626\u001b[0m         \u001b[0;31m# have first part already, only loop while more to receive\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32mzmq/backend/cython/socket.pyx\u001b[0m in \u001b[0;36mzmq.backend.cython.socket.Socket.recv\u001b[0;34m()\u001b[0m\n",
            "\u001b[0;32mzmq/backend/cython/socket.pyx\u001b[0m in \u001b[0;36mzmq.backend.cython.socket.Socket.recv\u001b[0;34m()\u001b[0m\n",
            "\u001b[0;32mzmq/backend/cython/socket.pyx\u001b[0m in \u001b[0;36mzmq.backend.cython.socket._recv_copy\u001b[0;34m()\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.7/dist-packages/zmq/backend/cython/checkrc.pxd\u001b[0m in \u001b[0;36mzmq.backend.cython.checkrc._check_rc\u001b[0;34m()\u001b[0m\n",
            "\u001b[0;31mKeyboardInterrupt\u001b[0m: ",
            "\nDuring handling of the above exception, another exception occurred:\n",
            "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
            "\u001b[0;32m<ipython-input-4-d5df0069828e>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mgoogle\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolab\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mdrive\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mdrive\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmount\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'/content/drive'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
            "\u001b[0;32m/usr/local/lib/python3.7/dist-packages/google/colab/drive.py\u001b[0m in \u001b[0;36mmount\u001b[0;34m(mountpoint, force_remount, timeout_ms, use_metadata_server)\u001b[0m\n\u001b[1;32m    111\u001b[0m       \u001b[0mtimeout_ms\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mtimeout_ms\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    112\u001b[0m       \u001b[0muse_metadata_server\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0muse_metadata_server\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 113\u001b[0;31m       ephemeral=ephemeral)\n\u001b[0m\u001b[1;32m    114\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    115\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.7/dist-packages/google/colab/drive.py\u001b[0m in \u001b[0;36m_mount\u001b[0;34m(mountpoint, force_remount, timeout_ms, use_metadata_server, ephemeral)\u001b[0m\n\u001b[1;32m    290\u001b[0m       \u001b[0;32mwith\u001b[0m \u001b[0m_output\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0muse_tags\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'dfs-auth-dance'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    291\u001b[0m         \u001b[0;32mwith\u001b[0m \u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfifo\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'w'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mfifo_file\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 292\u001b[0;31m           \u001b[0mfifo_file\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwrite\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mget_code\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mauth_prompt\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m'\\n'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    293\u001b[0m       \u001b[0mwrote_to_fifo\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    294\u001b[0m     \u001b[0;32melif\u001b[0m \u001b[0mcase\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m5\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.7/dist-packages/ipykernel/kernelbase.py\u001b[0m in \u001b[0;36mraw_input\u001b[0;34m(self, prompt)\u001b[0m\n\u001b[1;32m    702\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_parent_ident\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    703\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_parent_header\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 704\u001b[0;31m             \u001b[0mpassword\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    705\u001b[0m         )\n\u001b[1;32m    706\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.7/dist-packages/ipykernel/kernelbase.py\u001b[0m in \u001b[0;36m_input_request\u001b[0;34m(self, prompt, ident, parent, password)\u001b[0m\n\u001b[1;32m    732\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0mKeyboardInterrupt\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    733\u001b[0m                 \u001b[0;31m# re-raise KeyboardInterrupt, to truncate traceback\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 734\u001b[0;31m                 \u001b[0;32mraise\u001b[0m \u001b[0mKeyboardInterrupt\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    735\u001b[0m             \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    736\u001b[0m                 \u001b[0;32mbreak\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "GbPLWTJ05uH4"
      },
      "source": [
        "## After running these steps, click on **Runtime** in the menu bar & **Change Runtime Type** to Go, if it hasn't changed yet.\n",
        "\n",
        "This will make Colab starting use a open source go kernel called Gopher Notes.\n",
        "\n",
        "Now we are ready to work."
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "flsk3_roXwdM"
      },
      "source": [
        "# **Simulate a Golden Gate simulation for checking parts**"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "34gduXzXl-Nb"
      },
      "source": [
        "## **Importing packages and pre-requisites**"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "gQVnSh-tmEvz"
      },
      "source": [
        "import (\n",
        "  \"fmt\"\n",
        "\t\"io/ioutil\"\n",
        "\t\"log\"\n",
        "\n",
        "\t\"github.com/Open-Science-Global/poly/clone\"\n",
        "  \"github.com/Open-Science-Global/poly\"\n",
        ")"
      ],
      "execution_count": 19,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "JjOp36MzMUfw"
      },
      "source": [
        "## **1. Preparations for fixing problematic sequences: functions set up**\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "h4csnPYGanNR"
      },
      "source": [
        "Run the cells below to generate the function to annotate problematic sequences, based on the sequences of your choice. \n",
        "For example: binding sites of restriction enzymes are problematic because they cannot be in your sequence. For iGEM teams these can be the enzymes of the Biobrick system.\n",
        "\n",
        "\n",
        "**Important points:**\n",
        "*   We have below ONE main function (SimulateAndCheck). \n",
        "*   Overall, you don't need to change anything to save and use these functions in the second step of this tutorial (2. Running), except if you want to check more things, like if your sequence actually return a plasmid after the reaction a linearized version for example."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "_-yjSHB6au6m"
      },
      "source": [
        "func SimulateAndCheck(fragments []clone.Part, enzyme string) []clone.Part{\n",
        "\t\tclonedFragments, err := clone.GoldenGate(fragments, enzyme)\n",
        "\t\tif err != nil {\n",
        "\t\t\tfmt.Println(err)\n",
        "\t\t}\n",
        "\t\tif len(clonedFragments) != 1 {\n",
        "\t\t\tfmt.Println(\"More than 1 cloned sequence simulated in basic genes\")\n",
        "\t\t}\n",
        "\t\treturn clonedFragments\n",
        "}"
      ],
      "execution_count": 16,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "NLv21BpfrMjF"
      },
      "source": [
        "# **2. Running**\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "v0alIhMUwLdK"
      },
      "source": [
        "This sequences will be treated genetic parts that will be used in the Golden Gate reaction. To simulate you have to pass the parts and the enzyme you will use to cleave your sequence."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "tYzcxSZnhKFy"
      },
      "source": [
        "var popen = clone.Part{\"TAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGGCCTACTATTAGCAACAACGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACCTGCACCAGTCAGTAAAACGACGGCCAGTAGTCAAAAGCCTCCGACCGGAGGCTTTTGACTTGGTTCAGGTGGAGTGGGAGTAgtcttcGCcatcgCtACTAAAagccagataacagtatgcgtatttgcgcgctgatttttgcggtataagaatatatactgatatgtatacccgaagtatgtcaaaaagaggtatgctatgaagcagcgtattacagtgacagttgacagcgacagctatcagttgctcaaggcatatatgatgtcaatatctccggtctggtaagcacaaccatgcagaatgaagcccgtcgtctgcgtgccgaacgctggaaagcggaaaatcaggaagggatggctgaggtcgcccggtttattgaaatgaacggctcttttgctgacgagaacagggGCTGGTGAAATGCAGTTTAAGGTTTACACCTATAAAAGAGAGAGCCGTTATCGTCTGTTTGTGGATGTACAGAGTGATATTATTGACACGCCCGGGCGACGGATGGTGATCCCCCTGGCCAGTGCACGTCTGCTGTCAGATAAAGTCTCCCGTGAACTTTACCCGGTGGTGCATATCGGGGATGAAAGCTGGCGCATGATGACCACCGATATGGCCAGTGTGCCGGTCTCCGTTATCGGGGAAGAAGTGGCTGATCTCAGCCACCGCGAAAATGACATCAAAAACGCCATTAACCTGATGTTCTGGGGAATATAAATGTCAGGCTCCCTTATACACAGgcgatgttgaagaccaCGCTGAGGTGTCAATCGTCGGAGCCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCATGGTCATAGCTGTTTCCTGAGAGCTTGGCAGGTGATGACACACATTAACAAATTTCGTGAGGAGTCTCCAGAAGAATGCCATTAATTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGG\", true} // true means it's circular\n",
        "fragment1 := clone.Part{\"GAAGTGCCATTCCGCCTGACCTGAAGACCAGGAGAAACACGTGGCAAACATTCCGGTCTCAAATGGAAAAGAGCAACGAAACCAACGGCTACCTTGACAGCGCTCAAGCCGGCCCTGCAGCTGGCCCGGGCGCTCCGGGTACCGCCGCGGGTCGTGCACGTCGTTGCGCGGGCTTCCTGCGGCGCCAAGCGCTGGTGCTGCTCACGGTGTCTGGTGTTCTGGCAGGCGCCGGTTTGGGCGCGGCACTGCGTGGGCTCAGCCTGAGCCGCACCCAGGTCACCTACCTGGCCTTCCCCGGCGAGATGCTGCTCCGCATGCTGCGCATGATCATCCTGCCGCTGGTGGTCTGCAGCCTGGTGTCGGGCGCCGCCTCCCTCGATGCCAGCTGCCTCGGGCGTCTGGGCGGTATCGCTGTCGCCTACTTTGGCCTCACCACACTGAGTGCCTCGGCGCTCGCCGTGGCCTTGGCGTTCATCATCAAGCCAGGATCCGGTGCGCAGACCCTTCAGTCCAGCGACCTGGGGCTGGAGGACTCGGGGCCTCCTCCTGTCCCCAAAGAAACGGTGGACTCTTTCCTCGACCTGGCCAGAAACCTGTTTCCCTCCAATCTTGTGGTTGCAGCTTTCCGTACGTATGCAACCGATTATAAAGTCGTGACCCAGAACAGCAGCTCTGGAAATGTAACCCATGAAAAGATCCCCATAGGCACTGAGATAGAAGGGATGAACATTTTAGGATTGGTCCTGTTTGCTCTGGTGTTAGGAGTGGCCTTAAAGAAACTAGGCTCCGAAGGAGAGGACCTCATCCGTTTCTTCAATTCCCTCAACGAGGCGACGATGGTGCTGGTGTCCTGGATTATGTGGTACGCGTCTTCAGGCTAGGTGGAGGCTCAGTG\", false}\n",
        "fragment2 := clone.Part{\"GAAGTGCCATTCCGCCTGACCTGAAGACCAGTACGTACCTGTGGGCATCATGTTCCTTGTTGGAAGCAAGATCGTGGAAATGAAAGACATCATCGTGCTGGTGACCAGCCTGGGGAAATACATCTTCGCATCTATATTGGGCCACGTCATTCATGGTGGTATCGTCCTGCCGCTGATTTATTTTGTTTTCACACGAAAAAACCCATTCAGATTCCTCCTGGGCCTCCTCGCCCCATTTGCGACAGCATTTGCTACGTGCTCCAGCTCAGCGACCCTTCCCTCTATGATGAAGTGCATTGAAGAGAACAATGGTGTGGACAAGAGGATCTCCAGGTTTATTCTCCCCATCGGGGCCACCGTGAACATGGACGGAGCAGCCATCTTCCAGTGTGTGGCCGCGGTGTTCATTGCGCAACTCAACAACGTAGAGCTCAACGCAGGACAGATTTTCACCATTCTAGTGACTGCCACAGCGTCCAGTGTTGGAGCAGCAGGCGTGCCAGCTGGAGGGGTCCTCACCATTGCCATTATCCTGGAGGCCATTGGGCTGCCTACTCATGATCTGCCTCTGATCCTGGCTGTGGACTGGATTGTGGACCGGACCACCACGGTGGTGAATGTGGAAGGGGATGCCCTGGGTGCAGGCATTCTCCACCACCTGAATCAGAAGGCAACAAAGAAAGGCGAGCAGGAACTTGCTGAGGTGAAAGTGGAAGCCATCCCCAACTGCAAGTCTGAGGAGGAAACCTCGCCCCTGGTGACACACCAGAACCCCGCTGGCCCCGTGGCCAGTGCCCCAGAACTGGAATCCAAGGAGTCGGTTCTGTGAAGAGCTTAGAGACCGACGACTGCCTAAGGACATTCGCTGCGTCTTCAGGCTAGGTGGAGGCTCAGTG\", false}\n",
        "\n",
        "result := SimulateAndCheck([]clone.Part{fragment1, fragment2, popen}, \"BbsI\")"
      ],
      "execution_count": 17,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "OhbF8wWluxAf"
      },
      "source": [
        "You could also see if the result is only one final plasmid, for example, or if this actually lead to a different result from what you expected. "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "88VLPqbevEYH",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "e94471b6-145d-40b8-d06c-eda2dc790b46"
      },
      "source": [
        "result"
      ],
      "execution_count": 18,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "[{GTACGTACCTGTGGGCATCATGTTCCTTGTTGGAAGCAAGATCGTGGAAATGAAAGACATCATCGTGCTGGTGACCAGCCTGGGGAAATACATCTTCGCATCTATATTGGGCCACGTCATTCATGGTGGTATCGTCCTGCCGCTGATTTATTTTGTTTTCACACGAAAAAACCCATTCAGATTCCTCCTGGGCCTCCTCGCCCCATTTGCGACAGCATTTGCTACGTGCTCCAGCTCAGCGACCCTTCCCTCTATGATGAAGTGCATTGAAGAGAACAATGGTGTGGACAAGAGGATCTCCAGGTTTATTCTCCCCATCGGGGCCACCGTGAACATGGACGGAGCAGCCATCTTCCAGTGTGTGGCCGCGGTGTTCATTGCGCAACTCAACAACGTAGAGCTCAACGCAGGACAGATTTTCACCATTCTAGTGACTGCCACAGCGTCCAGTGTTGGAGCAGCAGGCGTGCCAGCTGGAGGGGTCCTCACCATTGCCATTATCCTGGAGGCCATTGGGCTGCCTACTCATGATCTGCCTCTGATCCTGGCTGTGGACTGGATTGTGGACCGGACCACCACGGTGGTGAATGTGGAAGGGGATGCCCTGGGTGCAGGCATTCTCCACCACCTGAATCAGAAGGCAACAAAGAAAGGCGAGCAGGAACTTGCTGAGGTGAAAGTGGAAGCCATCCCCAACTGCAAGTCTGAGGAGGAAACCTCGCCCCTGGTGACACACCAGAACCCCGCTGGCCCCGTGGCCAGTGCCCCAGAACTGGAATCCAAGGAGTCGGTTCTGTGAAGAGCTTAGAGACCGACGACTGCCTAAGGACATTCGCTGAGGTGTCAATCGTCGGAGCCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCATGGTCATAGCTGTTTCCTGAGAGCTTGGCAGGTGATGACACACATTAACAAATTTCGTGAGGAGTCTCCAGAAGAATGCCATTAATTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGGCCTACTATTAGCAACAACGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACCTGCACCAGTCAGTAAAACGACGGCCAGTAGTCAAAAGCCTCCGACCGGAGGCTTTTGACTTGGTTCAGGTGGAGTGGGAGAAACACGTGGCAAACATTCCGGTCTCAAATGGAAAAGAGCAACGAAACCAACGGCTACCTTGACAGCGCTCAAGCCGGCCCTGCAGCTGGCCCGGGCGCTCCGGGTACCGCCGCGGGTCGTGCACGTCGTTGCGCGGGCTTCCTGCGGCGCCAAGCGCTGGTGCTGCTCACGGTGTCTGGTGTTCTGGCAGGCGCCGGTTTGGGCGCGGCACTGCGTGGGCTCAGCCTGAGCCGCACCCAGGTCACCTACCTGGCCTTCCCCGGCGAGATGCTGCTCCGCATGCTGCGCATGATCATCCTGCCGCTGGTGGTCTGCAGCCTGGTGTCGGGCGCCGCCTCCCTCGATGCCAGCTGCCTCGGGCGTCTGGGCGGTATCGCTGTCGCCTACTTTGGCCTCACCACACTGAGTGCCTCGGCGCTCGCCGTGGCCTTGGCGTTCATCATCAAGCCAGGATCCGGTGCGCAGACCCTTCAGTCCAGCGACCTGGGGCTGGAGGACTCGGGGCCTCCTCCTGTCCCCAAAGAAACGGTGGACTCTTTCCTCGACCTGGCCAGAAACCTGTTTCCCTCCAATCTTGTGGTTGCAGCTTTCCGTACGTATGCAACCGATTATAAAGTCGTGACCCAGAACAGCAGCTCTGGAAATGTAACCCATGAAAAGATCCCCATAGGCACTGAGATAGAAGGGATGAACATTTTAGGATTGGTCCTGTTTGCTCTGGTGTTAGGAGTGGCCTTAAAGAAACTAGGCTCCGAAGGAGAGGACCTCATCCGTTTCTTCAATTCCCTCAACGAGGCGACGATGGTGCTGGTGTCCTGGATTATGTG true}]"
            ]
          },
          "metadata": {},
          "execution_count": 18
        }
      ]
    }
  ]
}