CMM262-Syllabus-2022.ipynb

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    "# CMM262: Quantitative Methods in Genetics and Genomics\n",
    "**University of California, San Diego (UCSD)** <br> **Winter 2022**\n",
    "\n",
    "[![slack badge](https://img.shields.io/badge/Join%20Slack-blueviolet?style=for-the-badge&logo=slack)](https://join.slack.com/t/cmm2622022/shared_invite/zt-10l5ri1dh-CtB8VrNcjW57rgeMfMh6Kw)\n",
    "[![jupyterhub badge](https://img.shields.io/badge/Login%20to%20JupyterHub-grey?style=for-the-badge&logo=jupyter)](https://datahub.ucsd.edu/hub/login)\n",
    "\n",
    "---\n",
    "\n",
    "## What's this course about?\n",
    "CMM262/BIOM262 is designed to teach experimental and analytical approaches in modern genetics and genomics, from experimental design through data analysis in each of several topic areas. Students will come away with an intuition and basic understanding of the function of many computational tools, including their design limitations.\n",
    "\n",
    "<br>\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "    <p><b>Note:</b> This 4-unit course is a <i>core requirement</i> for students in the UCSD Genetics Training Program (<a href=\"http://genetics.ucsd.edu/\">http://genetics.ucsd.edu/</a>).</p>\n",
    "</div>\n",
    "\n",
    "---\n",
    "\n",
    "## Who are the points of contact for this course?\n",
    "\n",
    "### Teaching Staff\n",
    "* **Instructor:** Dr. Alon Goren (agoren@ucsd.edu)\n",
    "* **Teaching Assistant 1:** Eric Kofman (ekofman@eng.ucsd.edu)\n",
    "* **Teaching Assistant 2:** Pratibha Jagannatha (pjaganna@eng.ucsd.edu)\n",
    "* **Teaching Assistant 3:** Hannah Mummey (hmummey@ucsd.edu)\n",
    "* **Teaching Assistant 4:** Arya Massarat (amassara@ucsd.edu)\n",
    "\n",
    "### Guest Lecturers\n",
    "As each module is taught by a separate guest lecturer, their contact information is provided in the syllabus table at the following Google Sheets link: https://docs.google.com/spreadsheets/d/1b83KzQ_g6koA1GSAy6dpqYCgWmoAJcYYfpKNTcaSxjM/edit?usp=sharing\n",
    "\n",
    "<br>\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "    <p><b>Note:</b> We will be using <b>Slack</b> as our primary method of communication for this course!<br>You can join our group using the Slack button at the top of this page.</p>\n",
    "</div>\n",
    "\n",
    "---\n",
    "\n",
    "## Where can I attend class?\n",
    "In keeping with UCSD policy surrounding the Omicron variant, the first four weeks of class will be offered remotely on Zoom. After that, classes will be held in a hybrid format on **Tuesday and Thursday from 9:00 AM - 12:00 PM PST**. We are actively monitoring the pandemic situation and will provide updates with changes to instruction as UCSD policy provides.\n",
    "\n",
    "**Zoom link**: https://ucsd.zoom.us/j/98590568595\n",
    "\n",
    "Every module of this course will include interactive coding sessions in a lab-style format, so we _strongly_ recommend that you attend class in-person whenever possible.\n",
    "\n",
    "---\n",
    "\n",
    "## Will lectures be recorded?\n",
    "You can find recordings of the Zoom lectures here:\n",
    "https://drive.google.com/drive/folders/1EXaGlmVEbuUEBTk6oUQooDMp0ma2wwjC\n",
    "\n",
    "Slides for each lecture will be attached to a `README.md` file within each module folder.\n",
    "\n",
    "---\n",
    "\n",
    "## When are office hours?\n",
    "Office hours will take place after lecture on **Tuesday from 12:00 PM - 1:00 PM PST**. During the first two weeks of the quarter, office hours will be offered remotely on Zoom via the same link as the class.\n",
    "\n",
    "---\n",
    "\n",
    "## Where can I access assignments?\n",
    "You should be able to find all of the assignments for this course on the UCSD Jupyterhub (Data Science) Platform if you're officially enrolled! The Jupyterhub can be found here: https://datahub.ucsd.edu/hub/login.\n",
    "\n",
    "---\n",
    "\n",
    "## How can I submit assignments? \n",
    "We'll be using Gradescope for submitting the homework assignments, as well as the midterm and final exams. If you have not been added to the course, to sign up for Gradescope, please follow the steps outlined below:\n",
    "\n",
    "1. Navigate to the Gradescope Website at https://www.gradescope.com/\n",
    "2. Select the link in the header to \"Sign Up\", and then select the option to sign up as a \"Student\"\n",
    "3. Enter the following Course Entry Code: **`X3668P`**\n",
    "4. Input your Full Name, UCSD Email, and UCSD Student ID (should be A#######); <br>**Note: If you are auditing the course, please enter <i>AUDITOR</i> as your Student ID**\n",
    "5. Select \"Sign up as Student\" to complete the sign-up process, and then check the email you have provided for the link to set your password and log in information\n",
    "\n",
    "### How will homework be assigned?\n",
    "Homework will be assigned on Thursdays and due on the following Thursday throughout the quarter. There will *not* be an assignment every week. Assignments will be announced in the week they are assigned. Submission of homework will be conducted through GradeScope and will be due by **9:00 AM PST on Thursday mornings**. \n",
    "\n",
    "### When's the midterm and final? \n",
    "* **Midterm Examination**: \n",
    "    * Released on February 10th, 2022 (Week 6) \n",
    "    * Submission via GradeScope on February 17th, 2022 (Week 7) by 9:00 AM PST\n",
    "* **Final Examination**: \n",
    "    * Released on March 8th, 2022 (Week 10)\n",
    "    * Submission via GradeScope on March 15th, 2022 (Finals Week) by 11:59 PM PST\n",
    "\n",
    "### What's the policy on late submissions?\n",
    "If for whatever reason you cannot deliver an assignment by its associated due date, you should report it at least a day before the due date. \n",
    "\n",
    "* **First Late Submission**: 10% of the maximal number of points is deducted for every day or part of a day that an assignment is handed in late\n",
    "* **Subsequent Late Submissions**: 20% of the maximal number of points is deducted for every day or part of a day that an assignment is handed in late\n",
    "\n",
    "<br>\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "    <p><b>Note:</b> We know that things happen!<br>If you're experiencing a health or family emergency, please let the course instructors and teaching assistants know and we can work something out!</p>\n",
    "</div>\n",
    "\n",
    "### What's the grading breakdown?\n",
    "\n",
    "| Percentage | Category     |\n",
    "|------------|--------------|\n",
    "| 55%        | Homework     |\n",
    "| 20%        | Midterm      |\n",
    "| 20%        | Final        |\n",
    "|  5%        | Participation|\n",
    "\n",
    "---\n",
    "\n",
    "## Participation\n",
    "Participation grades will be given based off of attendance, class participation, and number of weekly surveys completed.\n",
    "\n",
    "### Class participation\n",
    "This course is designed to be highly interactive, so we greatly appreciate your participation and engagement with the material and class sessions. Specifically on zoom we encourage you to **have your camera on and ask questions** at any time by raising your hand or using the chat. We would like to show respect for all instructors, especially those volunteering their time to be guest lecturers, by engaging with their content.\n",
    "\n",
    "### Surveys\n",
    "Please fill out our survey at the end of each week. We really value your feedback! It helps us improve the modules each year.\n",
    "\n",
    "**Survey link:** https://docs.google.com/forms/d/e/1FAIpQLSfJVxGBYh5PBT1sf2Am5yWDIEXTggngRuicaTmbX2IHiCKrPw/viewform\n",
    "\n",
    "---\n",
    "\n",
    "## What's the policy on collaboration and plagiarism?\n",
    "Plagiarism will not be tolerated. Do not copy and paste answers from the internet, and make sure all answers on homework and exams are completely in your own words.\n",
    "\n",
    "Questions may be discussed with classmates but all work must be done individually.\n",
    "\n",
    "---\n",
    "\n",
    "## What's the policy on emailing the course instructors and TAs?\n",
    "Please use office hours for questions regarding the homework assignments or take-home exams. It can be difficult, especially with code and software, to troubleshoot your problems via email. If you must email regarding a question, please do not expect an response to your email unless it is within working hours (Monday-Friday, 7:00 AM - 8:00 PM PST), otherwise, there is no guarantee you will receive a response. \n",
    "\n",
    "---\n",
    "\n",
    "## What's the course schedule?\n",
    "You can find the schedule of what we'll be covering day-by-day at the following Google Sheets link:\n",
    "https://docs.google.com/spreadsheets/d/1b83KzQ_g6koA1GSAy6dpqYCgWmoAJcYYfpKNTcaSxjM/edit?usp=sharing\n",
    "\n",
    "---\n",
    "## What if I can't log into DataHub?\n",
    "Try the suggestions in this doc and see if they help:\n",
    "\n",
    "https://docs.google.com/document/d/1GJpt8vLCDAzCVMrEfm8c-vFst2B8wR3Mj-m3058q8Mw\n",
    "\n",
    "---\n",
    "## Will I lose access to DataHub after the course is over?\n",
    "You will lose access to DataHub at the end of the spring quarter of this year, but you can download all of your materials before that happens! Follow [these instructions](https://docs.google.com/document/d/1kquyVU-8bKfQFfwDykjb_b1YIFMSfc01PcOwyW_uh-A) to retain access to all of your work.\n",
    "\n",
    "Alternatively, you can request an extension to your access [here](https://go.ucsd.edu/2wc5gH0%29)."
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