BIOEN 488/588
Computational Protein Design
Winter Quarter 2024

Class Time and Place

Lectures: Thursday and Friday, 10:00 - 11:20 pm
Labs: Fridays 11:30-2:30 pm
Location: N140 Foege

Instructor

Professor Valerie Daggett

Office Hours: Thursdays after class 11:20-12:00 pm
Email: daggett@uw.edu

Teaching Assistant

Sarah Nick
Email: snick36@uw.edu

Labs

Weeks 1-5 will be spent working on 5, 1-week labs, each of that will help familiarize you with computational biology tools. Each lab will be due at the beginning of lab the following week. Weeks 6-10 will be spent working on a project which will depend on which class the student is enrolled in. Week 10 will be presentations.

Project

488 Students: The final 5 weeks of lab will be a design lab that incorporates the tools from the first set of labs but is more self directed. You will have 5 weeks to complete the project and prepare a final paper in journal format. There will be no presentation, but you are expected to attend your classmates' presentations.

588 Students: The final 5 weeks of lab will be spent working on a project of your design. You come up with the topic, research it and make sure it is feasible. The topic needs to be approved by the instructor. You will have 5 weeks to work on the project and prepare a final paper in journal format and presentation describing your project and the results. During the final week of class you will presenting your findings to your classmates.

Grading

Assignments
4 Lab Progress Reports plus one Final Report
1 Project (488: Paper; 588: Paper and Presentation)
1 Literature Review Paper Presentation

Distribution
Lab Reports: 30%
Project: 50%
Participation: 10%
Literature Review: 10%

Other

Plagiarism
Using the words of others without quotation marks and proper attribution is plagiarism and inconsistent with academic integrity. In my experience most plagiarism is not intentional, it is due to cutting and pasting. Don't do it and make sure to allow time to thoroughly edit your writeups before turning them in. The University of Washington’s policy can be found at: https://depts.washington.edu/pswrite/plag.html

Religious Accommodations
Washington state law requires that UW develop a policy for accommodation of student absences or significant hardship due to reasons of faith or conscience, or for organized religious activities. The UW’s policy, including more information about how to request an accommodation, is available at Religious Accommodations Policy (https://registrar.washington.edu/staffandfaculty/religious-accommodations-policy/). Accommodations must be requested within the first two weeks of this course using the Religious Accommodations Request form (https://registrar.washington.edu/students/religious-accommodations-request/).

Accommodations and Access
"If you have already established accommodations with Disability Resources for Students (DRS), please communicate your approved accommodations to me at your earliest convenience so we can discuss your needs in this course. If you have not yet established services through DRS, but have a temporary health condition or permanent disability that requires accommodations (conditions include but not limited to; mental health, attention-related, learning, vision, hearing, physical or health impacts), you are welcome to contact DRS at 206-543-8924 or uwdrs@uw.edu or disability.uw.edu. DRS offers resources and coordinates reasonable accommodations for students with disabilities and/or temporary health conditions. Reasonable accommodations are established through an interactive process between the student, instructor, and DRS. It is the policy and practice of the University of Washington to create inclusive and accessible learning environments consistent with federal and state law.”

Academic Integrity
“Engineering is a profession demanding a high level of personal honesty, integrity and responsibility. Therefore, it is essential that engineering students, in fulfillment of their academic requirements and in preparation to enter the engineering profession, adhere to the College of Engineering Statement of Principles. Any student in this course suspected of academic misconduct (e.g., cheating, plagiarism, or falsification) will be reported to the College of Engineering Dean’s Office and the University’s Office of Community Standards and Student Conduct to initiate the student conduct process. Any student found to have committed academic misconduct may receive a zero for their grade on the impacted academic work (e.g., assignments, project, or exams), and academic consequences, with the possibility of expulsion.” “For any assignment, quiz, or exam that is suspected of academic misconduct, you will be given an “X” grade until after Prof. Y has received notification by the Dean’s office that the conduct process is complete. If a student is found responsible for academic misconduct, the student will receive a grade of zero on the assignment, quiz, or exam. If a student is found not responsible, the student will receive a grade based on the standard grading criteria for that assignment, quiz, or exam.”

Title IX
“UW, through numerous policies, prohibits sex- and gender-based violence and harassment, and we expect students, faculty, and staff to act professionally and respectfully in all work, learning, and research environments. For support, resources, and reporting options related to sex- and gender-based violence or harassment, visit UW Title IX’s webpage (https://www.washington.edu/titleix/), specifically the Know Your Rights & Resources guide (https://www.washington.edu/titleix/2022/10/21/title-ix-rights-and-resources-for-uw-students/). If you choose to disclose information to me about sex- or gender-based violence or harassment, I will connect you (or the person who experienced the conduct) with resources and individuals who can best provide support and options. You can also access those resources directly: • Confidential: Confidential advocates (https://www.washington.edu/sexualassault/support/advocacy/) will not share information with others unless given express permission by the person who has experienced the harm or when required by law. • Private and/or anonymous: SafeCampus (https://www.washington.edu/safecampus/) provides consultation and support and can connect you with additional resources if you want them. You can contact SafeCampus anonymously or share limited information when you call. Please note that some senior leaders and other specified employees have been identified as “Officials Required to Report.” (https://www.washington.edu/titleix/title-ix-officials-required-to-report/) If an Official Required to Report learns of possible sex- or gender-based violence or harassment, they are required to call SafeCampus and report all the details they have in order to ensure that the person who experienced harm is offered support and reporting options (https://www.washington.edu/titleix/resources/).”

Note: The last 4 sections above provided by COE