Data Science with R for the Life Sciences

Course Introduction

Notes

Welcome

  • Introduce yourself (include your pronouns)
  • Introduce co-instructors/TAs
  • Depending on class size have students introduce themselves

Course goals

  • Data and how to work with it
  • Data entry -> Data storage -> Data manipulation -> Data visualization
  • Not statistics or machine learning

Expected background

  • Assumes no background in R or any of the other things we’ll learn
  • If you’re already good at R it’s worth spending some time with the website (which we’re about to look at) to see if this a good fit for you
  • Information on more advanced options

Teaching methods (normal year)

  • Flipped classroom
    • You don’t learn how ride a bike just by listening to someone talk about it and the same is true for computing
    • So we use a fair bit of class time for working on exercises, asking questions, and getting help
  • Reading or videos before class
  • I do, we do, you do
    • I will demo an idea using live coding
    • We will work on an associated exercise together in class
    • You will work on additional exercises on your own (both in & out of class)
  • Peer instruction
    • Interact with each other during the we do and you do parts
    • You are at least as likely to learn from your peers as from me
    • If you already know some of the material and are getting ahead, see if there’s someone you can help
    • Introduce yourself to one of your neighbors you don’t know

How to do this online (for 2020)

  • But, it’s 2020, and nothing is normal
  • It has been a long, exhausting, year and it will continue to be so for many of us.
  • Most folks have more responsibilities, more limitations, and less energy than usual.
  • My goal is to help you learn as much as you can, while recognizing that most of us aren’t operating at 100%.

  • And that many of us need flexibility in how we’re learning and working right now.

  • The course is being taught online for the first time due to the pandemic.

  • Building the race car as it drives around the track.

  • Videos in place live demos
  • This means they can also replace advanced readings/videos
  • Still short presentations interspersed with exercises
  • Class time will start with time for group Q&A focused on general questions about how things work
  • The rest of class will be reserved for working on exercises and getting help
  • To participate in class
    • Join the appropriate Zoom meeting (there are different Zoom links for Tuesdays and Fridays)
    • Ask questions via chat or by raising your hand during group Q&A
    • After group Q&A Andrew & I will use breakout rooms to meet with individual students or groups of students
  • For peer instruction and getting help from instructors outside of class we’re using: Piazza
    • Piazza is a course specific Q&A that works well with code
    • If you have questions outside of class you can post to Piazza and other students or instructors can help
  • To provide maximum flexibility the course material can be engaged with in two ways:
    1. Synchronous Q&A: Follow each lesson before class (1st half by Tuesday, 2nd half by Friday), watching the videos and doing the exercises you can. Stop if you get confused. Come to class during the class periods. Ask general questions during the opening Q&A period and work 1:1 afterwards for things you still don’t understand or that won’t work.
    2. Asynchronous: Follow the lessons online and ask for help via Piazza. This is less ideal because of the benefits of direct face-to-face student-instructor interaction for working through misunderstandings, but it should still be effective. Opening class Q&A sessions will be recorded and posted to Canvas.
  • If you have decent internet access the course is designed so that you can do it entirely in a browser without any local software installation
  • There are alternative approaches for folks with limited internet access

  • Aid-a-Gator can also be used to help cover the cost of internet access

  • We have flexible deadline policies to support learning under these difficult circumstances. There is an automatic (no request needed) 48 hour extension on all assignments for those who need it and if you need more time just let me know. You never need to disclose personal information to me to get an extension. Just let me know how long you need.
  • That said, I encourage you to keep up with deadlines to the extent possible. Each step of the course builds on the last step and students who get behind often have a hard time catching up.

Course structure

Open website

  • Lessons integrated with weekly assignments
  • Practice is really important for learning skills like this
  • Work through video lessons and exercises before class
  • Class sessions will have both full class Q&A w/live codeing and 1:1 help
  • All exercises are part of the assignments.
  • Work on them until you get stuck and then ask for help, don’t struggle for hours on online help sites
  • Assignments for the first 12 weeks of class and then optional ungraded content though the end of the semester
  • Assignments due end of the day on Monday, but with an automatic 48 hour extension if you need it

Website

Walk through the website showing the following items

  • Schedule
    • Walk through schedule (quickly)
  • Readings
    • Read before relevant class
    • No need to do any challenges or exercises in readings
  • Lessons
    • Alternating short videos (to introduce idea) and exercise (to start using that idea)
    • Whether you are treating the class as synchronous or asynchronous alternating between video and exercise will be most effective for most of you
  • Lectures
    • Lectures notes used in class
    • Not expected to read in advance; may be useful for review
    • May not match lecture precisely
  • Assignments
    • Answers provided

Syllabus

  • Grading
    • Produces the correct answer using the requested approach: 100%
    • Generally uses the right approach, but a minor mistake results in an incorrect answer: 90%
    • Attempts to solve the problem and makes some progress using the core concept: 50%
    • No answer or answer lacking basic understanding of core concept: 0%
  • Give it a read and let me know if you have any questions

Office Hours

  • Tuesday & Wednesday: 2-3 pm
  • Zoom link in Canvas

Canvas

  • Show Canvas
  • Will publish modules as soon as the material is ready to be worked on
  • First thing Monday at the latest, but hopefully much earlier
  • Handle assignment submission, grading, and announcements through Canvas

Inclusive and Accessible Course

  • Learning computing is hard
  • Learning computing in a classroom that doesn’t provide a supportive environment is awful
  • It’s really important to me that this course provide a positive, inclusive, accessible, learning environment for everyone
  • If that is not the experience you are having for any reason, just let me know and I’ll actively work to correct it.

First day demo

  • With the little time we have left I just want to do a quick demo of some of the things you’ll be able to do by the time we’re half way through the class