This is an archived file from the Spring 2022 version of the course.
See the current course website for a more recent version.

Syllabus

This syllabus is a “semi-living document” (i.e., more like a virus than a bacterium) subject to change as we adapt during the semester. The course website is managed through a public github repository, so you can see past versions and changes there.

The version as posted on the first day of class is here.

Overview

Course Description: This course will look at connections between computing and biology, with a focus on DNA. It will include computational methods used in biology focusing on how computing can be used to analyze and design DNA, as well as opportunities to use biological substances and ideas to compute.

Course Objectives: Students who succeed in the course will:

  • Understand at a high (but deep) level how life works, and why certain aspects of known life on Earth seem to have evolved with common, robust mechanisms.

  • Be able to implement and reason about algorithms for analyzing DNA including algorithms for genome assembly, genome alignment, and phylogeny, as well as algorithms used to try and understand genetic factors in diseases.

  • Gain understanding how mRNA vaccines are developed, and what scientists have learned about SARS-CoV-2.

  • Connect theoretical understanding of computing to biological mechanisms, including information theoretic understanding of genomes and immune systems and algorithmic perspectives on evolutionary processes.

  • Learn to think like a computational biologist.

  • Be able to read and understand some research papers in computational biology, and present key ideas in biomedical work in ways that are understandable to computer scientists.

Class Meetings: The full class meetings of the course are scheduled for Mondays and Wednesday, 12:30 – 1:45pm in Olsson Hall 018.

Pandemic Policies. The challenges we are facing with the current pandemic places our community under tremendous stress, and we appreciate that many of our students are dealing with extreme personal challenges this semester. You should prioritize your own physical and mental health, and the well-being of your friends and family, over any class. We want the class to be a low stress, high value experience for everyone.

Following current University policies, classes will be held in person and designed to maximize their value to students able to attend in person. This means we will use some of the class time for small group discussions and sometimes have graded activites in class. We will provide all the course materials (e.g., lecture slides and notes) openly on this website, but will not be routinely recording or live-streaming classes since doing this can diminish the value of the class to attendees (at a minimum, it divides the instructor’s attention, and precludes any activites that expect student participation). Students who are not able to make it to class for medical, family, or personal reasons will not be impacted negatively by not participating in any in-class graded activities.

I will do everything I can to accommodate students varying situations, and to ensure that every student has the best opportunity possible to succeed in the class and have a good experience. Please communicate with me about difficulties you are facing, or anything I can do to make things better for you.

I will expect everyone associated with the class (including the instructor, TAs, and students) to follow University policies regarding health and safety requirements. These regulations may change during the semester. The ones currently in effect as of 16 January 2022 state that “all students who live, learn, or work in person at the University of Virginia during the 2021-2022 academic year must be fully vaccinated” and “masks are required for all people (students, faculty, staff, contractors, and visitors), both vaccinated and unvaccinated, who enter UVA properties.” This applies to all indoor spaces, including our classroom. Following these regulations is both important for your own health and for the safety and comfort for everyone in the community, including many who may have different risk profiles than your own such as living with elderly relatives or children too young to be vaccinated.

Preparation

Official Prerequisites: Students entering this course are expected to have successfully completed cs2150, and at least one of cs3102 or cs4102, or comparable experience.

Expected Background: We expect all students in the class to be living human beings and to have been curious observers of the life that surrounds us, but do not expect an previous formal background in biology.

We expect students to have solid understanding of core ideas in theoretical computer science and be comfortable using asymptotic notation and talking about computational complexity. To check your understanding and refresh your memory, read the post on Computer Science Background.

We expect students to be able to program in Python, and to be able to read and write programs with a few thousand lines of code, and to be able to figure out how to use libraries and APIs from their provided documentation and other resources. We expect students to have experience with software engineering practices, and to be able to write readable programs and test them systematically.

Course Staff

Instructor: The course is taught by David Evans (evans@virginia.edu). Feel free to contact me with any questions about the course, computer science, or anything else you think I can help with (but please read the section below on communications to determine if it would be better to post a message in slack or github discussions instead of by personal email). I have been teaching at UVA for more than 20 years, but this is my first computational biology course. The last formal biology course I took was in high school (long before any of you were born), but I did previously teach a seminar on Biologically-Inspired Computing, have given talks on What Biology Can (and Can’t) Teach Us About Security, and published a few minor papers that connect computing and biology. Most of my research is in security and privacy.

Teaching Assistants:
Hyun Jae Cho, PhD student working in biology and machine learning.
Anshuman Suri, PhD student working on privacy risks of machine learning.

Office Hours: A full schedule of office hours will be posted on the course website later. For the first week of the semester, Dave will hold office hours after class Wednesday.

Learning Materials

There is no required textbook to purchase for the course.

We will be using chapters from three open books:

The three books are all excellent and cover much of the same material, but are quite different in style, expected background, and technical depth. We will often assign readings from one or two of the books, and suggest additional optional readings from the others for students who want more depth or prefer a different kind of presentation.

In addition to these main texts, we will be reading papers (distributed as PDFs through this website) and occasionally viewing videos and other available materials.

Communication

We will primarily use the course website for one-to-many communications (posting course materials), use the course slack for “real-time” messages and immediate course announcements, and use github discussions for discussions.

Course Website: We will post all course materials on the course website, https://computingbiology.github.io/, except for ones that we cannot post publicly, which will be shared using collab or other mechanisms.

Slack: We will use a slack workspace for immediate and real-time communications. All students in the course should join the slack workspace: https://computingbiology.github.io/slack/.You should be able to join directly yourself using a @virginia.edu email address (let the course staff know if you have any problems joining). You will also be able to use slack to form channels for teams.

Github Discussions: We will use github discussions for more persistent and structured discussions. You should use the github discussions if you have questions about concepts in the class, assignments, and readings.

Email: Managing email for a large class like this is difficult, and we prefer to use the course slack and github discussions for most communications relevant to the class. Please use direct messages in slack if you have personal, course-related questions for the instructor (e.g., requesting an extension or exemption). You should feel free to use email for messages peripherally related to the course (e.g., emailing an instructor about interest in their research). You should also use email if you post a question on slack or github discussions but don’t receive an adequate response within 24 hours.

Assignments

The main assignments for the course, and where we expect students will do the most learning, is a series of projects where students implement, analyze, and extend computational biology algorithms.

Because this is a new course, we do not want to commit to the specific topics and deadlines in the pre-semester syllabus, but expect there to be four structured projects, approximately two weeks each, and one longer open-end project for the final 5 weeks of the semester.

The rough schedule and planned topics (which are likely to change) are:

Project 1: Assembling Genomes (out Tuesday 25 January, due Tuesday 8 February)

Project 2: Genome Alignment and Analysis (out Wednesday 9 February, due Thursday 24 February)

Project 3: Engineering a Covid Vaccine (out Friday 25 February, due Friday 18 March) (Spring break is March 7-11, we are not expecting students to work over spring break, assuming you do get started on this the week before spring break)

Final Project (final projects due Monday 2 May, last day of class, with several intermediate deliverables and short presentations). The final project will be open-ended, and could involve either explaning a topic or recent result in biology, doing an original research project, or something else of value and relevant to the course.

Quizzes

To see how well students are understanding concepts in the course, and incentivize students to do preparation readings when assigned, we might have occasional, short quizzes. The details on these quizzes, and how they will be scheduled, will depend on how the class is going.

Grading

Since this is an upper-level elective, we hope students are not overly stressed about grading and mostly focused on learning and doing worthwhile things. That said, we understand students are often stressed about grading and understandably want to know where they stand in a class without having to rely just on the judgment of the course instructor. We aim to grade in a way that is useful (provides students with accurate measure of how well they understood what they should), motivating (encourages the behaviors we prefer, including hard but not obsessive work), fair (assigned higher grades to more deserving students), robust (arbitrary small perturbations do not have a material impact on someone’s grade), and low stress (for both students and the course staff). You will get grades for the projects that make it clear how well you have met our expectations, and will get informative grades for any quizzes.

The final grade in the course will be determined based mostly on the grades on your projects throughout the semester. If you do well on all the projects, you’ll get an A in the course. If you do exceptionally well on the final project, this will more than make up for any mediocre grades on the early projects. Performance on quizzes and other contributions to the class may also be used to adjust student’s grades. In general, I don’t have a single, simple, formula that is a function that takes in point values for all assignments and outputs a grade, but instead will analyze all of your performance in the course in several different ways to determine a grade that best reflects your overall learning and contributions to the course.

Accommodations: It is the University’s long-standing policy and practice to reasonably accommodate students so that they do not experience an adverse academic consequence when sincerely held religious beliefs or observances conflict with academic requirements. Although University policy only recognizes religious accomodations, the course instructor believes they are many other valid reasons for accomdations that are at least as justifiable as ones for religious observance and consider family obligations, personal crises, and extraordinary opportunities to all be potentially valid reasons for accomodations.

In general, I don’t think I should make value judgements about this - what matters is that it is something important to you, that you have little scheduling control over, and that you make the request as early as you should be able to know an accomodation is necessary and are flexible in working with me to find an alternative.

Honor Expectations

We believe strongly in the value of a community of trust, and expect all of the students in this class to contribute to strengthening and enhancing that community.

The course will be better for everyone if everyone can assume everyone is trustworthy. The course staff starts with the assumption that all students at the university deserve to be trusted.

To ensure that expectations are clear to everyone, all students are required to read, understand, and sign (virtually on your registration survey) the course pledge.

Collaboration Policy: Many of the assignments in this course will require or allow you to work with others; some may require you to work on your own. The collaboration policy will be described on each assignment document. The main expectation is that you do not misrepresent others work as your own, or do things that obviously violate the intent of the stated collaboration policy. We aim to make the language describing the policy as clear and unambiguous as possible, but if anything is ever unclear about the stated policy for an assignment, please clarify with the course staff. The penalty for policy violations will be considered on a case-by-case basis, with a penalty commensurate the severity of the offense.

Additional Information

This is generic information that is probably included in most of your course syllabi.

Special Circumstances: The University of Virginia strives to provide accessibility to all students. If you require an accommodation to fully access this course, please contact the Student Disability Access Center (SDAC) at (434) 243-5180 or sdac@virginia.edu. If you are unsure if you require an accommodation, or to learn more about their services, you may contact the SDAC at the number above or by visiting their website https://studenthealth.virginia.edu/sdac

Safe Environment: The University of Virginia is dedicated to providing a safe and equitable learning environment for all students. To that end, it is vital that you know two values that we and the University hold as critically important:

  1. Power-based personal violence will not be tolerated.
  2. Everyone has a responsibility to do their part to maintain a safe community on grounds (including in virtual environments).

If you or someone you know has been affected by power-based personal violence, more information can be found on the UVA Sexual Violence website that describes reporting options and resources available: https://www.virginia.edu/sexualviolence.

As your professor and as a human, know that I care about you and your well-being and stand ready to provide support and resources as I can. As a faculty member, I am a responsible employee, which means that I am required by University policy and federal law to report what you tell me to the University’s Title IX Coordinator. The Title IX Coordinator’s job is to ensure that the reporting student receives the resources and support that they need, while also reviewing the information presented to determine whether further action is necessary to ensure survivor safety and the safety of the University community. If you would rather keep this information confidential, there are Confidential Employees you can talk to on Grounds (see https://eocr.virginia.edu/chart-confidential-resources ). The worst possible situation would be for you or your friend to remain silent when there are so many here willing and able to help.

Student Support Team: You have many resources available to you when you experience academic or personal stresses. In addition to your professor, the School of Engineering and Applied Science has three staff members located in Thornton Hall who you can contact to help manage academic or personal challenges (students in the College or other schools may have additional resources available to you through your enrolled school, but since this course is offered through SEAS, these resources are available to any student in this class). Please do not wait until the end of the semester to ask for help!

Lisa Lampe, Director of Undergraduate Education (academic), ll4uu@virginia.edu
Blake Calhoun, Director of Undergraduate Success (academic), bic4sc@virginia.edu
Alex Hall, Assistant Dean of Students (non-academic issues), aec5d@virginia.edu

In addition to having an Assistant Dean of Students embedded in Engineering, we are also fortunate to have two CAPS counsellors embedded in SEAS. You may schedule time with Elizabeth Ramirez-Weaver or Katie Fowler through Student Health (https://www.studenthealth.virginia.edu/getting-started-caps). You are also urged to use TimelyCare for either scheduled or on-demand 24/7 mental health care.

Finally, the Center for Diversity in Engineering facilitates free tutoring during the academic year, helps students locate internships and research opportunities, and connects students with the many organizations on Grounds that provide information and support. The center also engages with student organizations, particularly those serving students who are traditionally underrepresented in engineering.