1-positive-feedback.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "040ae377-699a-471a-bbdf-c469ecfea4d5",
   "metadata": {},
   "outputs": [],
   "source": [
    "import dinkum\n",
    "from dinkum.vfg import Gene, Receptor\n",
    "from dinkum.vfn import Tissue"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1e9b35b7-c230-4a41-9a1a-cb2cf34bb68b",
   "metadata": {},
   "source": [
    "Change the below code to implement a positive feedback subcircuit:\n",
    "\n",
    "![positive feedback](images/positive-feedback-loop.png)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "989780fe-2f7a-4ac2-ae47-d9ee1bd967ee",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initializing: dinkum v0.3.1\n",
      "start=1 stop=10\n"
     ]
    },
    {
     "data": {
      "image/jpeg": 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",
      "image/png": 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",
      "text/plain": [
       "<PIL.Image.Image image mode=RGB size=160x380>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dinkum.reset()\n",
    "\n",
    "x = Gene(name='X')\n",
    "y = Gene(name='Y')\n",
    "m = Tissue(name='M')\n",
    "\n",
    "x.is_present(where=m, start=1)\n",
    "\n",
    "# now define a regulatory relationship!\n",
    "y.activated_by(source=x, delay=2)\n",
    "\n",
    "# run for 5 ticks (1 to 10)\n",
    "dinkum.run_and_display(stop=10)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c80a7dd5-5511-4543-837b-e28558c23f08",
   "metadata": {},
   "source": [
    "and indeed, we see that these genes are now completely locked on."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2a926379-f81b-410b-adbe-7be0bcea95ac",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "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": "3.11.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}