Syllabus

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 materials 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.

• 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 Tuesdays and Thursdays, 12:30pm – 1:45pm in Olsson Hall 120.

Preparation

Official Prerequisites: Students entering this course are expected to have successfully completed cs2130, and at least one of cs3100 or cs3120, 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 the github discussions instead of by personal email).

Teaching Assistants:
Ashley Gao, PhD student studying affective computing and transfer learning.
Jack Heavey, PhD student studying computational epidemiology.

See the Schedule for updated information on staff office hours.

Learning Materials

There is no required textbook to purchase for the course.

We will be using chapters from three open books:

• Bert Hubert’s The Technology of Life: A DNA-centric tour of biology. This is a new book currently under development. The author has graciously agreed to share an early version of the book with us. You will need a password to access this, which will be distributed through the collab mailing list.

• Phillip Compeau and Pavel Pevzner’s Bioinformatics Algorithms. Several chapters of the book are freely available, and we will only assign these chapters for reading. The full book is available as a printed book ($90), but is not necessary to purchase for the course. (There is also an on-line course ($90) connected to this book, which you may find useful and interesting.)

• Manolis Kellis' Computational Biology - Genomes, Networks, and Evolution. (Transcriptions of lectures from MIT 6.047 course. Various versions of this course, and recorded videos of the lectures, are available on-line, and we will use some of these materials.)

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.

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

Assignments

The course will include two structured project assignments, and a large open-ended final project.

The schedule for the two projects is:

Project 1: Assembling Genomes (due Monday, 5 September, 8:59pm)

Project 2: Genome Alignment and Phylogeny (due Wednesday, 21 September, 8:59pm)

Final Project: 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. There will be a series of separate deliverables and deadlines for the final project, leading up to project paper submissions on 7 November. You will get a preliminary grade on your project and feedback on these submissions, and an opportunity to revise them, to submit a final project paper the last day of class (6 December).

Quizzes

To see how well students are understanding concepts in the course, and incentivize students to do preparation readings when assigned, we will have a few short quizzes.

These are tentatively scheduled for:

Quiz 1: Tuesday, 11 October
Quiz 2: Thursday, 27 October
Quiz 3: Tuesday, 15 November

(Depending on how things are going and other scheduling issues, there might be a Quiz 4 on 1 December.)

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).

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.

You can ensure an “A” grade in the course by doing any one of these:

• Doing a great job on the final project, and demonstrating an acceptable level of effort on the structured projects and quizzes.

• Doing reasonably well on the final project, and doing at or above expectations on both of the structured projects, and doing well on at least two of the quizzes.

• Putting a reasonable effort into a project but ultimately not succeeding in producing a satisfactory project, but doing above expectations on both of the structured projects and well on all of the quizzes.

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 agree to the course pledge. If you are not willing to agree to any of the expectations there, please let Prof. Evans know. On your course registration survey, you will be expected to virtually sign acceptance of the course pledge.

Additional Information

This is standard 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.