CSC 448 Spring 2020 Schedule

Table of contents

  1. Syllabus
  2. Schedule
  3. Technology
  4. Project
  5. Deadlines
  6. Corrections

I cannot stress enough that consideration is available for any health or extenuating circumstance that you experience this quarter. Please reach out to me at any time for any reason. Consideration includes but is not limited to individually modified due dates. In other words, do not let this course take priority over your health.

Below is our tentative schedule. It is subject to change, but any changes will be reflected here.

Class Zoom Meetings

Recorded Videos

I’m working to organize the recorded (Zoom) videos via Flipgrid. This allows me to post a short audio description of the video.

Weekly Schedule

Week 1 (Staring Monday 9/14)

Monday

  • (2:10-3 PM) Introduction and welcome to Bioinformatics! (Joint with Dr. Jean Davidson’s Bioinformatics Application Course)
  • (3:10-4 PM) Syllabus and other details specific to Bioinformatics Algorithms (videos broken up above)

Wednesday

  • (2:10-3 PM) Continuation of introduction to Bioinformatics! (Joint with Dr. Jean Davidson’s Bioinformatics Application Course)
  • (3:10-4 PM) Introduction to small group discussions

Friday

  • (2:10-4 PM) Lecture, discussion, activities

Material

Introduction to class slides

Chapter 1 - Where in the Genome Does DNA Replication Begin? (Algorithmic Warmup)

Assignments

Introductions on Flipgrid

Collaborative Bioinformatics Group Exercise

  • Due Sunday at midnight

Syllabus Assignment

Lab 1

Week 2 (Staring Monday 9/21)

Monday

Wednesday

  • (2:10-3 PM) Project working group time
  • (3:10-4 PM) Small group discussions (continue dry run)

Friday

  • (2:10-4 PM) Lecture, discussion, activities

Material

Chapter 5 - How do we compare DNA sequences?

Assignments

Complete the group assignment by Sunday at midnight

Project videos are due starting Week 2 and continue until Week 10. We will be using Flipgrid for this.

Lab 2

Week 3 (Staring Monday 9/28)

Monday

  • (2:10-3 PM) TBD - Tutorial on Jupyter Notebooks, JupyterHub, Git, GitHub, Terminals OR Galaxy Assembly Tutorial (tentative)
  • (3:10-4 PM) Small group discussions

Wednesday

  • (2:10-3 PM) Project working group time
  • (3:10-4 PM) Small group discussions

Friday

  • (2:10-4 PM) Lecture, discussion, activities

Material

Chapter 3 - How do we assemble genomes?

Assignments

Project videos are due starting Week 2 and continue until Week 10. We will be using Flipgrid for this.

Lab 3

Week 4 (Staring Monday 10/5)

Monday

  • (2:10-3 PM) Guest speaker Dr. Benjamin Neely NIST (tentative)
  • (3:10-4 PM) Small group discussions

Wednesday

  • (2:10-3 PM) Project working group time
  • (3:10-4 PM) Small group discussions

Friday

  • (2:10-4 PM) Lecture, discussion, activities

Material

Chapter 11 - Was T. Rex just a big chicken?

Assignments

Project videos are due starting Week 2 and continue until Week 10. We will be using Flipgrid for this.

Lab 4

Week 5 (Staring Monday 10/12)

Monday

  • (2:10-3 PM) Guest speaker Director of Genomics at Ancestry.com (tentative)
  • (3:10-4 PM) Small group discussions

Wednesday

  • (2:10-3 PM) Project working group time
  • (3:10-4 PM) Small group discussions

Friday

  • (2:10-4 PM) Lecture, discussion, activities

Material

Chapter 7 - Which animal gave us SARS?

Assignments

Project videos are due starting Week 2 and continue until Week 10. We will be using Flipgrid for this.

Lab 5

Week 6 (Staring Monday 10/19)

Monday

  • (2:10-3 PM) Guest speaker clinical genomics (tentative)
  • (3:10-4 PM) Small group discussions

Wednesday

  • (2:10-3 PM) Project working group time
  • (3:10-4 PM) Small group discussions

Friday

  • (2:10-4 PM) Lecture, discussion, activities

Material

Chapter 9 - How do we locate disease-causing mutations?

Assignments

Project videos are due starting Week 2 and continue until Week 10. We will be using Flipgrid for this.

Lab 6

Week 7 (Staring Monday 10/26)

Monday

  • (2:10-3 PM) Guest speaker NCBI (tentative)
  • (3:10-4 PM) Small group discussions

Wednesday

  • (2:10-3 PM) Project working group time
  • (3:10-4 PM) Small group discussions

Friday

  • (2:10-4 PM) Lecture, discussion, activities

Material

Chapter 6 - Are there fragile regions in the human genome?

Assignments

Project videos are due starting Week 2 and continue until Week 10. We will be using Flipgrid for this.

Lab 7

Week 8 (Staring Monday 11/2)

Monday

  • (2:10-3 PM) Guest speaker TBD (tentative)
  • (3:10-4 PM) Small group discussions

Wednesday

  • (2:10-3 PM) Project working group time
  • (3:10-4 PM) Small group discussions

Friday

  • (2:10-4 PM) Lecture, discussion, activities

Material

Chapter 8 - How Did Yeast Become a Wine Maker? (Expression Data Clustering)

Assignments

Project videos are due starting Week 2 and continue until Week 10. We will be using Flipgrid for this.

Lab 8

Week 9 (Staring Monday 11/9)

Monday

  • (2:10-3 PM) Deep learning bioinformatics notebook tutorial (Breast cancer subtyping)
  • (3:10-4 PM) Small group discussions

Wednesday

  • (2:10-3 PM) Project working group time
  • (3:10-4 PM) Small group discussions

Friday

  • (2:10-4 PM) Lecture, discussion, activities

Material

Chapter 10 - Why have biologists still not developed an a HIV vaccine?

Assignments

Project videos are due starting Week 2 and continue until Week 10. We will be using Flipgrid for this.

Lab 9

Week 10 (Staring Monday 11/16)

Monday

  • (2:10-3 PM) Guest speaker TBD (tentative)
  • (3:10-4 PM) Small group discussions

Wednesday

  • (2:10-3 PM) Project working group time
  • (3:10-4 PM) Small group discussions

Friday

  • (2:10-4 PM) TBA

Material

No new material is scheduled a priori. We reserve this time to reinforce/refine topics from the quarter.

Assignments

Project videos are due starting Week 2 and continue until Week 10. We will be using Flipgrid for this.

TBD

General

We will be using a hybrid asynchronous/synchronous model this semester. We have as much as possible designed each week to be consistent and structured the same. Here are specific take home details:

2:10 - 3 PM on Monday: Tutorials and Guest Speakers

  • Tutorials and guest speakers will be shared event with Bioinformatics Applications (taught by Dr. Jean Davidson)
  • The focus of each week will shift back and forth between more CS+Bioinf to Bio+Bioinf with guest speakers when available.
  • Each tutorial/presentation will have some form of deliverable

2:10 - 3 PM on Wednesday: Synchronous Group Time

  • We recognize the difficulties in scheduling times across all your schedules.
  • We are reserving this time for interaction in your productivity working groups that are organized around a project theme
  • You are free to structure this time in a manner that makes sense to your group.
  • For example, you may schedule a recurring Zoom meeting and invite your group as co-hosts.
  • For example, you may opt for ad hoc Zooming with most of the conversation taking place over Slack
  • As an example of what you shouldn’t do, use this time to catch up on other classes.
  • You must notify us of your planned activity structure for the quarter, and of course, we should be invited to all things :)

3 - 3:10 PM on Monday, Wednesday, and Friday: Get up and stretch. Move around. Get coffee, etc.

3:10 - 4 PM on Monday, Wednesday: Small Groups - Oxford style tutorial system

  • I will be scheduling small group of 3 students (Tutorial System)
  • 10 minutes long, so please be prepared to hit the ground running in a discussion
  • You are only to attend your scheduled time
  • “Student tutorials are generally more academically challenging and rigorous than standard lecture and test format courses, because during each session students are expected to orally communicate, defend, analyse, and critique the ideas of others as well as their own in conversations with the tutor and fellow students” - Tutorial System.
  • I am in the tutorial to facilitate and not to lead.
  • Groups will maintain consistent membership Week 2 and beyond.
  • Each week will have a student discussion lead (rotating)
  • Each group will have a private slack channel created by me (Dr. A)
  • Discussion lead will post the question of the week 24 hours prior to scheduled meeting. This question must be related to recent material covered in class (i.e., it can’t look ahead).
  • Discussion lead is responsible for starting the discussion at the beginning of the session and must ensure that everyone gets the opportunity to speak.
  • All students other than lead are required to take meeting minutes. These minutes must be typed up in addition to a personal reflection no later than 24 hours after the meeting. They must be posted to Slack and commented on by the lead.
  • The goal is not only to work on a topic related to class, but it is to improve your mastery in communication, discussion, and debate.
  • We will be grading these in the same manner as many things in class - with an eye toward mastery. You will get two preliminary grades that are not binding. They are to help you grow into a better communicator.

2:10 - 3 + break + 3:10 - 4 PM on Friday: Our most traditional structure

  • Specific portions will be recorded, but encourage those who want a synchronous class structure to attend.
  • The reason to record smaller portions instead of the entire session is that research basically shows that smaller recordings are more educational.
  • Our general structure is (topic 1 + discussion 1) + (topic 2 + discussion 2) + … + (topic n + discussion n). Once this pattern is completed for the day, then we will have open discussion until the end of our official time.
  • The lecture portion may vary from week to week, but I do not expect to lecture for near two hours straight

If we support one another during this time, I honestly believe we can grow our humanity during this challenging time. Throughout the quarter you’ll definitely get a glimpse of my day-to-day world. Scheduling chaos will enter my world as I know it will enter into your world as well. We must first treat each other as people first and student/instructor second.