Table of contents

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

Syllabus

Course Description

This course studies the application of computing techniques to solving problems in the field of bioinformatics and computational molecular biology. 3 lectures, 1 laboratory.

Professor Information

Paul Anderson, PhD

Email: pander14@calpoly.edu

Office: 222 Building 14

Office hours:

• By appointment (email)
• Mondays at 12 - 3 PM PST. Zoom link

Graders

Viet Nguyen

Course Prerequisites

CSC 349

Course Learning Objectives

1. Know the main problems in the field of bioinformatics and computational molecular biology.
2. Understand the key algorithms used to solve computational biology and bioinformatics problems
3. Model computational biology problems
4. Apply algorithmic techniques to solve problems in computational biology and bioinformatics
5. Gain experience working on software projects on multidisciplinary teams.

Textbook and Other Material

I recognize that students are often able to complete a course without buying a book, but this quarter is different. With all of your classes being online, I recommend you buy all of your books. The author has a wonderful website (in comparison to others). They provide a few of the chapters free of charge. Unfortunately, they do not yet have all the chapters. You will struggle in this course during some weeks if you do not have a copy of the textbook. I have tried to pick chapters for the first two weeks that fit our goals and are online.

Phillip Compeau, Pavel Pevzner, Bioinformatics Algorithms: An Active Learning Approach, Active Learning Publishers, 3rd Edition

Grading

All grades are subject to being prorated due to illness. For example, if you are sick for a week, you will not have to make up that week. Your grade will just be computed out of fewer total points.

Labs and assignments: 70% (Due each week)

• The primary form of labs and assignments will be programming exercises that are supported by the textbook which is supplemented by videos.
• Labs and assignments will be submitted to GitHub classroom. A link to each lab and assignment will be on the schedule.

Weekly participation: 15%

• Monday (9-9:50 AM) (8%)
  • Synchronous Zoom interaction between 9-9:50 AM PST
  • Our most important synchronous activity of the week!
  • Students will be divided equally into five groups for smaller breakout Zoom meetings (starting week 2)
  • I (instructor) will spend 10 minutes with each of the five groups from 9 - 9:50 AM (starting week 2)
  • The point of this synchronous interaction is less about content delivery and more about forming a community. Consider it a time for discussion.
  • If you make and participate in all 8 synchronous discussions, you will receive 8/8.
• Monday (10 - 10:50) (2%)
  • If you stay online with your group for the lab to continue the discussions on at least 6 weeks, then you will get 2/2.
  • If you stay online with your group for the lab to continue the discussions on at least 4 weeks, then you will get 1/2.
  • Anything less than 4 weeks of Monday lab activity will result in a 0/2.
• Wednesday and Friday (9-11 AM) (5%)
  • If you are active on Canvas/Slack throughout the week but especially during this time, you will get 5/5.
  • If you are not that active on Canvas/Slack throughout the week, then you will get 2/5.
  • If you are mostly absent from Canvas/Slack, then you will get 0/5.

Important to recap: Labs and assignments are fully asynchronous and individual. Though you may use Slack or Canvas discussions to communicate. Monday is our most important day for synchronous communication. If you complete all labs and assignments fully and you participate in this class as described above, you can achieve 85% in this class (i.e., you get a B). So how do you go for the A?

Project: 15%

• A large part of this class will be devoted to the novel coronavirus (COVID-19), and your project score will reflect this more than anything else.
• While the labs will have connections to the virus, the mission of the project is to analyze and incorporate real data generated by leading scientists and institutions into our class.
• Each student will have a blank webpage created for them and hosted on GitHub pages. I will use your email addresses for the path. This page is yours to customize.
• Every student will have write permissions, but git can obviously handle large teams. Stick to modifying your own files, and I doubt we’ll have many merge conflicts.
• This main page is your landing page. The actual analysis will be made available through Jupyter notebooks that will be public to the world, but unique to each student.
• You can incorporate your links using nbviewer.
• These aren’t like lab assignments that typically have a single (or limited number of) correct answer(s). The data and analysis will evolve.
• Grading for this will be qualitative in a manner that is similar to grading a paper for your english class. I will not be grading this weekly though you must make progress every week to get a good grade. Let’s walk through a few scenarios:
  • A student makes good progress on each week’s assignment. The resulting score for the project may be between 12/15-15/15 depending on quality, accuracy, organization, etc.
  • A student makes intermittent progress and effort for most of the weeks. The resulting score for the project may be between 5-12 depending on quality, accuracy, organization, etc.
  • Anything less than this will result in 0/12.

Late Policy

No late days will be allowed.

Grading Scale

Grading Scale: A: 90-100; B: 80-89; C: 70-79; D: 60-69; F: <60. Plusses and minuses will be used at the discretion of the instructor.

Honor Code

Lying, cheating, attempted cheating, and plagiarism are violations of our Honor Code that, when identified, are investigated. Each instance is examined to determine the degree of deception involved.

Incidents where the professor believes the student’s actions are clearly related more to ignorance, miscommunication, or uncertainty, can be addressed by consultation with the student. We will craft a written resolution designed to help prevent the student from repeating the error in the future. The resolution, submitted by form and signed by both the professor and the student, is forwarded to the Dean of Students and remains on file.

Cases of suspected academic dishonesty will be reported directly to the Dean of Students. A student found responsible for academic dishonesty will receive a XF in the course, indicating failure of the course due to academic dishonesty. This grade will appear on the student’s transcript for two years after which the student may petition for the X to be expunged. The student may also be placed on disciplinary probation, suspended (temporary removal) or expelled (permanent removal) from the College by the Honor Board.

It is important for students to remember that unauthorized collaboration–working together without permission– is a form of cheating. Unless a professor specifies that students can work together on an assignment and/or test, no collaboration is permitted. Other forms of cheating include possessing or using an unauthorized study aid (such as a PDA), copying from another’s exam, fabricating data, and giving unauthorized assistance.

Remember, research conducted and/or papers written for other classes cannot be used in whole or in part for any assignment in this class without obtaining prior permission from the professor.

Diversity Statement (Cal Poly official statement)

At Cal Poly we believe that academic freedom, a cornerstone value, is exercised best when there is understanding and respect for our diversity of experiences, identities, and world views. Consequently, we create learning environments that allow for meaningful development of self-awareness, knowledge, and skills alongside attention to others who may have experiences, worldviews, and values that are different from our own. In so doing, we encourage our students, faculty, and staff to seek out opportunities to engage with others who are both similar and different from them, thereby increasing their capacity for knowledge, empathy, and conscious participation in local and global communities.

In the spirit of educational equity, and in acknowledgement of the significant ways in which a university education can transform the lives of individuals and communities, we strive to increase the diversity at Cal Poly. As an institution that serves the state of California within a global context, we support the recruitment, retention, and success of talented students, faculty, and staff from across all societies, including people who are from historically and societally marginalized and underrepresented groups.

Cal Poly is an inclusive community that embraces differences in people and thoughts. By being open to new ideas and showing respect for diverse points of view, we support a climate that allows all students, faculty, and staff to feel valued, which in turn facilitates the recruitment and retention of a diverse campus population. We are a culturally invested university whose members take personal responsibility for fostering excellence in our own and others’ endeavors. To this end, we support an increased awareness and understanding of how one’s own identity facets (such as race, ethnicity, gender, sexual orientation, religion, age, disability, social class, and nation of origin) and the combinations of these identities and experiences that may accompany them can affect our different worldviews.

Disability Accomodations

Any student who feels he or she may need an accommodation based on the impact of a disability should contact me individually to discuss your specific needs. Also, please contact the Disability Resource Center: https://drc.calpoly.edu/content/drc-services.