✅ Put your name here
" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Day 17 Pre-Class Assignment: Agent Based Modeling of Superbugs" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Goals for today's pre-class assignment\n", "\n", "\n", "\n", "1. Learn a bit about Digital Evolution (MSU BEACON Lab)\n", "1. Learn about bacterial \"Superbugs\"\n", "\n", "\n", "## Assignment instructions\n", "**This assignment is due by 11:59 p.m. the day before class** and should be uploaded into the appropriate \"Pre-class assignments\" submission folder in the Desire2Learn website.\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "----\n", "# 1. Digital Evolution\n", "Watch this quick video about Digital Evolution being done here at MSU and complete the tasks and questions below. " ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "from IPython.display import YouTubeVideo\n", "YouTubeVideo(\"FLaBghtu_os\",width=640,height=360)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**Question 1:** What are the \"genes\" that mutate and change in the digital organism described in this video?" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "✎ Do This - Erase the contents of this cell and replace it with your answer to the above question! (double-click on this text to edit this cell, and hit shift+enter to save the text)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**Question 2:** Briefly describe two evolution experiments described in this video." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "✎ Do This - Erase the contents of this cell and replace it with your answer to the above question! (double-click on this text to edit this cell, and hit shift+enter to save the text)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**Question 3:** What other experiments could you imagine using digital evolution?" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "✎ Do This - Erase the contents of this cell and replace it with your answer to the above question! (double-click on this text to edit this cell, and hit shift+enter to save the text)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "----\n", "# 2. Superbugs\n", "\n", "In the next couple of classes we are going to build an agent based model to simulate the evolution of bacteria to become resistant to antibiotics. Please watch the following video. If you find the video terrifying, you're not alone, this is quite worrisome.\n", "\n", "Our goal is to build a simulation that reconstructs this real world experiment. \n", "\n", "Here's an article that discusses the video: http://www.the-scientist.com/?articles.view/articleNo/46993/title/Giant-Petri-Dish-Displays-Evolution-in-Space-and-Time/" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "from IPython.display import YouTubeVideo\n", "YouTubeVideo(\"yybsSqcB7mE\",width=640,height=360)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**Question :** Think about how you will solve this problem. What datastructures would you need to simulate the world? What classes and functions would you need? Spend about 10-15 minutes outlining the code or writing stub functions. " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "✎ Do This - Erase the contents of this cell and replace it with your answer to the above question! (double-click on this text to edit this cell, and hit shift+enter to save the text)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# Put any useful/necessary stub functions here\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "----\n", "# Assignment wrap-up\n", "\n", "Please fill out the form that appears when you run the code below. **You must completely fill this out in order to receive credit for the assignment!**" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "from IPython.display import HTML\n", "HTML(\n", "\"\"\"\n", "\n", "\"\"\"\n", ")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "---------\n", "### Congratulations, you're done with your pre-class assignment!\n", "\n", "Now, you just need to submit this assignment by uploading it to the course Desire2Learn web page for today's submission folder (Don't forget to add your name in the first cell)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "© Copyright Michigan State University Board of Trustees" ] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python 3", "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": "3.7.6" } }, "nbformat": 4, "nbformat_minor": 4 }