Today’s objectives

• What is Comp Bio?
• Course overview
• Exercise 1
  • Starting to setup ASC account

GTAs

• Sean Onileowo (sao0027)
• Alex Systun (ats0100)
• Kyndall Skelton (kps0016)

Instructor

Dr. Jamie Oaks

phyletica.org | GitHub: joaks1

Phyletica Lab Research

Computational biology

• The study of life using computational techniques, theoretical models, and data
• Conceptual

Comp Bio is as broad as biology

• All fields of biology can now generate enormous quantities of data that require computational approaches
• For this class, we will focus on:
  • Evolutionary biology
  • Molecular evolution & phylogenetics
  • Genomics
• Modeling and computational skills generalize to other fields

Algos & models used in comp bio

A model is a parametric explanation of biological observations

Probabilistic models

• Maximum likelihood
• Bayesian inference
• Machine learning
• Markov chain models

Used across biology

Algorithms

• String algos
  • sort, search, etc
• Optimization algos
  • Dynamic programming
  • Linear programming
  • Greedy algos, heuristic methods
  • Expectation-maximization

Used across biology

Science is based on models

All science is based on models, and every scientific model comprises three distinct stages: statement of well-defined hypotheses; deduction of all the consequences of these hypotheses, and nothing but these consequences; confrontation of these consequences with observed data. - Maurice Allais

Course format

• This course will be in-person
• We will do a mix of
  • Lecture
  • “Follow-along” demos
  • Exercises
• I will record classes as Panopto webcasts and post them to Canvas
  • BUT, this will not replace exercises

Course objectives

Enable you to:

• Apply basic Linux/Unix command-line utilities
• Use basic programming for data processing
• Use version-control tools for reproducibility
• Understand probabilistic models for biological questions
• Encode and apply computational algorithms to biological data

Course materials

• You will need a computer you can bring to class with you
  • Laptop/tablet running Linux, macOS, or Windows is ideal
  • Up-to-date browser
• A free GitHub account
• A free Marimo molab account

Course content

Found on the course

• Website
  • Slides & documentation
  • Exercises
• Canvas page
  • Syllabus
  • Announcements
  • Some exercises
  • Assignment submission

Textbook

• There is no required textbook
• Practical Computing for Biologists, by Haddock and Dunn, is a good resource
• I might distribute readings throughout the semester

Office hours

• GTAs and I will setup booking pages in Outlook
  • Here’s mine
• Use these to book 30-minute appointments with us
  • 1-on-1 meetings are ideal for computational topics

Where’s Dr. Oaks?

My philosophy for high-level courses

• I assume you’re here for the right reasons
• If so, I think you’ll have fun and learn a lot
• At your stage, you should be motivated to acquire knowledge and skills
  • Not by grades
• Can you get a good grade without learning much?
  • Quite possibly

Lab exercises

• Low-stake opportunities to apply what you’re learning
• Mostly completed in class
• Work together, but submit your own work
• Graded for effort
• We will do a number of these and your 2 lowest scores will be dropped

Capstone projects

• Similar in format to exercises, but more challenging
• Do not work together
• Graded for correctness
• Mostly done out of class, but you will have opportunities to work on them in class
• Start early and use office hours

Late exercises and projects

• 20% deduction per day late

Course grading

Your final percentage will be calculated as:

Final percent = ( lab exercises % \(\times\) 0.6 )

\(+\) ( capstone projects % \(\times\) 0.4 )

Grading scale

AI policy

• I will not teach it, but you are encouraged to try out generative AI tools
• Use them to help (not hinder) your learning
• When used, you need to disclose

Class courtesy

• It’s our shared responsibility to create a positive learning environment for everyone
• Please use the “Anonymous Feedback” module in Canvas to report any issues

Make sure your VPN is setup and working

Setting up ASC account

• You should have received a Canvas message with your username and password for the ASC
  • Please let me know if you didn’t
• Go to the “Exercise-01” Module on Canvas and use the “Setting-up-DUO-for-ASC-account.pdf” PDF to:
  • Set up 2-factor authentication for your ASC account
  • Access the ASC user documentation
  • From “Getting started” page, read:
    • About this website
    • Rules of behavior
    • Getting help
• Then, answer the questions for the “Exercise 1” quiz
• Due before class next Monday

Wednesday

• Intro to command-line shell environment
• Access Linux Thinlinc environment
  • COSAM IT will be on-hand to help troubleshoot