Introductory Computational Biology

Course code 01:694:390

Course Information and Policies
Semester: Spring 2025 – anticipate 1x/year in Spring
Classroom: In-Person
Location: Computer teaching lab, e.g. Nelson B125
Credits: 3
Meeting Times: Two 80-minute lectures per week, time TBD
Course Management: Canvas
Office Hours: TBD (see Announcements on Canvas)

For office hours or discussion, times are open. Email to set up a time to meet or talk after class.
You can also ask questions through emails. You can expect us to reply to emails within 1
business day, not including weekends or holidays.

Course URL: https://canvas.rutgers.edu

Course Instructors:
Dr. Miguel Zaratiegui Biurrun [email protected]
Dr. Sam Gu [email protected]
Dr. Yang Lyu (Coordinator) [email protected]
Office hours: by appt

Prerequisites: 01:447:380 Genetics or 01:447:384 Genetic Analysis I

Co-requisites: None

Stop Point (enrollment): 27 (limit due to capacity of a life science computer teaching lab)

Course Description:
Introductory Computational Biology is a hands-on, computer-intensive course designed for
students interested in exploring the intersection of biology and data science. It is suitable for
students with a basic understanding of molecular biology who aspire to scientific or biomedical
careers. The curriculum progresses from Unix and Cloud file management to practical
bioinformatics analyses, such as DNA mutation mapping (module I), RNA-seq data analysis
(module II), and ChIP-seq data analysis (module III). Each module is centered around real-world
research questions, with instruction through R/Python coding examples. Assignments and a
final project are designed to solidify students' skills in applying computational programs to
biological inquiries, preparing them for advanced study or career development in this evolving
discipline.

Course Technology Requirements:

Our course utilizes Google CoLab (https://colab.google/), a web-based platform accessible via
PCs in the classroom or your personal laptop. An Internet connection is required to access
course materials and work on assignments, with no software installation necessary. You can
continue your work outside of class from any location.

Learning Goals for Course:

After completing this course, students will be able to :
1. Explain the basic principles and concepts of computational biology research;
2. Appraise the application of computational techniques in current molecular biology;
3. Independently utilize Python and R programming languages to analyze DNA and RNA
sequences.

These goals aim to provide students with both the theoretical framework and practical expertise
necessary for the pursuit of advanced studies or professional opportunities in modern biology.

Course Materials:
No textbook is required as most of the needed material is available during class.

Weekly readings on the applications of omics analyses will be posted at the Canvas course site.

Students are encouraged to study R and Python with the following sources:

R for Data Science by Hadley Wickham and Garrett Grolemund

Focus: Data science techniques using the tidyverse package.
Link: https://r4ds.had.co.nz/index.html

An Introduction to R
Focus: Basics of R, official manual from The R Project.
Link: https://cran.r-project.org/doc/manuals/r-release/R-intro.html

Automate the Boring Stuff with Python by Al Sweigart

Focus: General Python automation and scripting.
Link: https://automatetheboringstuff.com/

Contacting the instructors:

The best way to reach out to us is through email. For questions about the course, contact the
course coordinator, Dr. Yang Lyu. For questions about the course content and grading, reach
out to the specific instructor. You can expect us to reply to emails within 1 business day, not
including weekends or holidays.

Attendance:
Attendance at all lectures is required. If you anticipate frequent absences or missing several
classes consecutively, please inform the instructor in advance. For any missed lectures, report
your absence through the University's self-reporting system (https://sims.rutgers.edu/ssra/).
Recorded lectures may be provided to those who have reported absences. In-class
demonstrations are crucial and tied to homework assignments. Since each class builds on the
previous one, catching up after absences can be difficult, making continuous attendance
important for understanding the course material fully.

Assignments, Due Dates, and Course Announcements

You're responsible for tracking and meeting all assignment deadlines, which are specified for
each task. Late submissions are not accepted. All assignments must be submitted through
Google Colab, allowing for timely online submissions even if you miss a class. If serious illness
prevents homework completion, please inform us before the due date. There are no options for
extra credit or make-up assignments in this course.

Performance Expectations and Evaluation

Performance Expectations and Evaluation in this course are primarily homework-based,
accounting for 85% of your overall grade for the four named Modules. This emphasizes the
importance of regular, consistent engagement with course assignments to master the material.
We have seven assignments in total over the four modules with the grade breakdown being:
10% Introductory Module and 25% each for Modules 1, 2, 3. The final project contributes 15%
to your grade, providing an opportunity to integrate and apply what you've learned in a
comprehensive manner. This structure ensures a balanced assessment, valuing both your
ongoing efforts and your ability to synthesize knowledge in a culminating project.

Grade Breakdown and Course Content

10% Introductory Module: 2 classes: basic Unix/file management (1 assignment)
25% Module 1: 8 classes: DNA Mutation Analysis (2 assignments)
25% Module 2: 8 classes: RNA-seq Analysis (2 assignments)
25% Module 3: 8 classes: Chip-seq Analysis (2 assignments)
15% Final project at the end-of-term equating to 2 classes

The grade is based on the seven Assignments listed above and the Final project.
There will be no final exam. We do not have reading assignments for the course.

Grading Scale
Letter Grade Range *
A 90 to 100%
B+ 85 to 89%
B 80 to 84%
C+ 75 to 79%
 C 70 to 74%
D 65 to 69%
C 0 to 64%

* ≥0.5 % rounds up to the higher integer and <0.5% rounds down to the lower integer.
The instructors reserve the right to lower the grade cut-offs depending on Assignment
outcomes.

AI Utilization in Introductory Computational Biology Coursework

Our computational biology course supports the judicious use of Artificial Intelligence (AI) as an
educational tool. However, it is important for students to develop their own coding and analytical
skills. To this end, assignments must be the student’s original work, and any use of AI must be
as a supplementary aid, not as a substitute for problem-solving. Students are expected to
understand and explain their submissions and cite any AI assistance, adhering strictly to our
academic integrity standards.

Guidelines for AI Use:

Learning Aid Only: AI should be used as a learning aid, not as a means to complete
assignments. It can be used to understand complex concepts or to provide examples of how
certain problems can be approached, but not to generate complete solutions.

Original Work: All submitted assignments must be the original work of the student. While AI can
be consulted for understanding, all final code and analysis should be conceived and executed
by the student.

Code Understanding: Students must be able to explain their code and the reasoning behind
their chosen methods. This ensures that even if AI tools are used in the learning process, the
student has a deep understanding of the material.

Ethical Use: Students are expected to adhere to academic integrity policies when using AI. This
includes not using AI to generate work that is to be presented as solely the student’s own.

Citation Requirement: If AI is used to inform any part of a student's work, it must be clearly cited,
explaining what role AI played in the learning or developmental process.

We recognize the potential of AI to transform education and research, but it must be leveraged
in a way that enhances learning and supports the academic growth of our students. We
encourage our students to approach these tools with curiosity and integrity, ensuring that their
academic journey in computational biology is both enriched and honorable.

Academic Integrity:
Students are expected to be familiar with Rutgers’ Code of Academic Integrity and the possible
penalties (including suspension and expulsion) for violating the policy. Academic dishonesty
includes (but is not limited to):
● Cheating
● Plagiarism
● Aiding others in committing a violation or allowing others to use your work
● Failure to cite sources correctly, including artificial intelligence-based tools
● Fabrication
● Using another person’s ideas or words without attribution, including re-using a previous
assignment
● Unauthorized collaboration
● Sabotaging another student’s work
We have a zero-tolerance policy for cheating, and all violations will result in substantial
penalties. If you have any doubts or questions about what constitutes academic misconduct,
please do not hesitate to contact Dr. Lyu.

Student Support and Mental Wellness

• Student Success Essentials: https://success.rutgers.edu

• Student Support Services: https://www.rutgers.edu/academics/student-support
• The Learning Centers: https://rlc.rutgers.edu
• Rutgers Libraries: https://www.libraries.rutgers.edu
• Bias Incident Reporting: https://studentaffairs.rutgers.edu/bias-incident-reporting
• Dean of Students – Student Support Office:
https://success.rutgers.edu/resource/deanstudents-student-support-office
• Office of Veteran and Military Programs and Services: https://veterans.rutgers.edu
• Student Health Services: http://health.rutgers.edu
• Counseling, Alcohol and Other Drug Assistance Program & Psychiatric Services (CAPS):
http://health.rutgers.edu/medical-counseling-services/counseling
• UWill: free immediate access to teletherapy; you can choose a therapist based on your
preferences including issue, gender, language, ethnicity: http://health.rutgers.edu/uwill
• Office for Violence Prevention and Victim Assistance: www.vpva.rutgers.edu
• Office of Disability Services: https://ods.rutgers.edu
• Basic Needs Assistance (food, housing, and other
essentials): https://ruoffcampus.rutgers.edu/basic-needs
• Rutgers Student Food Pantry: https://ruoffcampus.rutgers.edu/food-pantry

Disability Services

(848) 445-6800 / Lucy Stone Hall, Suite A145, Livingston Campus, 54 Joyce Kilmer Avenue,
Piscataway, NJ 08854 / https://ods.rutgers.edu/

The Office of Disability Services works with students with a documented disability to determine
the eligibility of reasonable accommodations, facilitates and coordinates those accommodations
when applicable, and lastly engages with the Rutgers community at large to provide and
connect students to appropriate resources.