BIFX 547: AI and Web-Based Bioinformatics

Spring 2026

Author
Affiliation

Dr Randy Johnson

Hood College

Published

April 23, 2026

BIFX 547: AI and Web-Based Bioinformatics

Faculty Contact Information

Course Description

Prerequisites: Prerequisites: A minimum grade of “B-” in BIFX 502 or CSIT 512; or permission of the instructor.

The goal of this course is to provide the students with a more in-depth knowledge of web-based bioinformatics tools and other freely available tools. The course will emphasize a hands-on approach using available web-based tools and public domain data. Secondly the class will cover the foundation for developing novel web-resources using HTML, CSS, Javascript and web frameworks such as Shiny and Streamlit.

Class Meeting Time:

Thursdays at 5:30 - 8:15 PM

Location:

Hodson Technology, 315

Course Outline

This tentative outline of course topics and assignments may be modified at the discretion of faculty at any point during the semester AND it is the student’s responsibility to remain abreast of updates. The syllabus on Blackboard and the course website will be updated in the event of changes to this schedule.

Date Topics Projects Preparation & Quizes
Jan 22 Agentic Programming Your First Streamlit App
Jan 29 Collaborative Programming and Project Management Quiz
Feb 5 Reactive Programming Gene Expression Explorer
Feb 12 Code Review
Feb 19 Advanced Shiny
Feb 26 Cloud Hosting
Mar 5 Interactive Reporting Quiz
Mar 12 Spring Break
Mar 19 Database Design VCF Metadata
Mar 26 API integration
Apr 2 Prompt Engineering Lecacy code refactorization
Apr 9 Streamlit DNA Analyzer Quiz
Apr 16 Package Maintenance & Automation App dockerization
Apr 23 Working session GitHub Actions
Apr 30 Local LLMs & Review Quiz
May 7 Final Exam (Async)

Modality

Bimodal: This course will be held simultaneously on-campus in the assigned room and virtually as indicated on Blackboard. Both in-person and virtual participants will be expected to participate in class discussions and activities.

Course Materials, Required Textbooks, Technology

There are no required books for purchase, but we will be using the following open source texts and online resources (additional readings will be shared via Blackboard):

You will need regular and dependable access to a computer and the internet. All registered students may use the on-campus computers and printers for this course if necessary. We will use Blackboard for activities, announcements, email, and assignments.

Classes will be recorded and posted on Blackboard each week for review.

Course Grading Components

The Blackboard Gradebook will be updated throughout the course and will give students a current snapshot of their grade throughout the class. Graded components include:

  • Class participation: Full credit will be given for students who attend and participate in class. In the event of an excused absence, a makeup assignment will be provided.
  • Homework will consist of both formative and summative assignments.
    • Formative assignments: Most homework will fall in this category. Formative homework will be clearly identified in Blackboard, and full credit will be given as long as students make a good faith effort and turn in all required work (i.e. all assignments will require code and output, and most assignments will require pushing code to GitHub).
    • Summative assignments: Summative homework will be accompanied by a grading rubric to increase clarity and understanding for the assignment.
  • Projects: Two projects will be completed. Both can be done either individually or as a small group.
  • Quizes: A quiz will be given at the end of each major section of the class. These consist of short answer questions and will be administered on Blackboard.
  • Final exam: The final exam will consist of a take-home programming challenge that will implement programming principles discussed in the class and an oral interview discussing your code.

Each graded component will be weighted for calculation of the final grade as follows:

Component Grade
Class participation 15%
Homework 25%
Projects 10%
Quizes 25%
Final Exam 25%

Late Policy

THERE IS NO EXCUSE FOR LATE ASSIGNMENTS. You will have ONE week to work on all the assignments for that week. All assignments are due at the beginning of class on the date listed in Blackboard. Late assignments are generally not accepted, but if you have a special circumstance and will not be able to meet the deadline, let me know before the assignment is due. Only medical excuses, recognized religious holidays, Hood College approved activities, or written work obligations will make a student eligible to hand in an assignment late without penalty.

  • Assignments that are turned in after the scheduled due date but before one week past this date will have their assignment grade reduced by one letter grade.
  • Homework assignments received more than one week late will be reduced by 50% (i.e. will start with a grade of “F”) prior to being graded. Assignments that are more than two weeks late will not be accepted.

Hood College Approved Grading Scale

Grade Weighted %
A [100-93]
A- [90-93)
B+ [88-90)
B [83-88)
B- [80-83)
C+ [78-80)
C [73-78)
C- [70-73)
F [0-70)

Course Objectives

Upon successful completion of BIFX547, students will be able to:

  • Effectively use agentic programming tools to create and maintain bioinformatics web tools

Attendance Policy

Students are required to attend every session and are expected to log on frequently to Blackboard and review the week’s course material. Attendance will be taken based on your participation in the class. Make up work will be assigned for excused absences.

In the event of severe weather resulting in the closure of Hood College and the cancellation of an in-person meeting, the class will be held virtually.

Professionalism

Professionalism is expected and required in all graduate courses; it is also one of the six core outcomes for all graduate degrees at Hood College. All students are expected to be prepared for class and to participate in activities or discussions in accordance with the course code of conduct.

In accordance with the College Catalog, the College generally permits the use of generative artificial intelligence (AI) tools for uses outlined in assignment descriptions for this course. See the course code of conduct for more information.

Accessibility Services and Wellness

This course is intended to be accessible for all students, including those with mental, physical, or cognitive disabilities, illnesses, injuries, impairments, or any other condition that tends to negatively affect one’s equal access to education. If at any point in the term, you find yourself not able to fully access the space, content, and experience of this course, you are welcome (and not required) to contact me by email, phone, or during office hours to discuss your specific needs. I also encourage you to contact the Office of Accessibility Services at 301-696-3569 or accessibilityservices@hood.edu. If you have a diagnosis or history of accommodations at a previous postsecondary institution, Accessibility Services can help you document your needs and create an accommodation plan. By partnering with Accessibility Services, you can ensure appropriate accommodations without disclosing your condition or diagnosis to course instructors.

Academic Success Services

Your success in my class is a priority. For this reason, I will be using the Blazer Navigate alert system as an early identification and intervention tool. If I notice you are struggling with issues such as attendance, class participation, or assignment/test performance, I may choose to send an Academic Alert through Blazer Navigate to connect you with appropriate campus resources. These referrals are designed to maximize your chances for success at Hood College, not as a reprimand or punishment. Please respond to any communications you may receive from me, your academic adviser, the graduate school or other campus offices regarding your academic progress in this course.

Holistic Wellness

Your holistic wellness is important to me. Consult College supports curated for you around the Eight Dimensions of Wellness at www.hood.edu/GradCare. If you are feeling anxious, stressed, worried or down during the semester or if you notice signs of emotional distress in someone else, please lean on support services freely available to all Hood students. Many campus resources are available including:

  • Hood Counseling Services – open M-F, 8:30AM-5:00PM, Apple Resource building, 1st floor, Room A. Make your appointment online at hood.edu/counseling, or drop in for a walk-in session on Mondays, Wednesdays, and Fridays between the hours of 11:00AM – 12:00PM. If you have questions about Counseling Services, email counselingservices@hood.edu.
  • Hood also has several connections to other mental health resources including the NeighborHood Counseling Training Center and Thriving Campus.
    If you or someone you know needs to talk to someone right now, text or call 9-8-8 for a free, confidential conversation with a trained counselor 24/7.

Important Contacts