Generative AI technologies such as ChatGPT, Claude, GitHub Copilot, NoteBookLM and TritonGPT (see next section) are rapidly becoming part of professional practice in bioinformatics. In this course, I will encourage you to engage with these tools, and in some assignments you will be required to use them. Learning to use AI effectively is an emerging skill, and I will provide resources and guidance as required. I am also available to discuss effective and ethical AI use strategies during office hours.

Expectations for AI Use

Encouraged Use: You may use AI to explore ideas, test knowledge, generate code, improve writing, or visualize concepts. AI can help you experiment, avoid simple errors, and deepen your engagement with the course material.

Critical Responsibility: AI outputs may contain errors, bias, or repetition, and often need refinement. You are responsible for validating information, testing code thoroughly, and ensuring your final submission meets the standards of the course.

Documentation and Transparency is key: For your assignments, including the find-a-gene project, include a short paragraph at the end of your assignment explaining how you used AI and provide the key prompts. For code, include the prompt(s) and significant parts of the AI’s response in your comments. Transparency is key: we are learning how to use these tools effectively together.

Things to Keep in Mind

Garbage in, garbage out: Minimal prompts will produce low-quality results. Refining prompts takes thought and practice.

AI is not a fact-checker: Assume that factual information, numbers, or citations may be wrong unless you verify them independently.

AI is not always appropriate: Use it when it enhances your work, but recognize when other tools, resources, and your own reasoning are more suitable.

Why We Do This

Our goal as a learning community is not only to master the course content, but also to understand how emerging AI tools can augment and support our research, study, and professional performance. By using AI openly, responsibly, and critically, we are preparing for the environments you will encounter in your academic and professional futures.

Custom TritonGPT AI assistant for BIMM143

This quarter you will have access to a custom AI instructional assistant powered by TritonGPT, our campus-built and secure generative AI. This is powered by OpenAI’s leading model and is seeded with custom BIMM143 specific information.

How to Access It:

• Go to https://tritongpt.ucsd.edu.
• Click Explore Assistants in the left-hand menu.
• Scroll and look for “BIMM143 Grant - Student Assistant”.
• Click Pin to add it to your sidebar and drag it to the top of the list for quick access going forward.
• Ask away, e.g. “what is lab 2 all about?”, “what is the answer to q19 in lab 1?”, “what is a porphyrin group?”, “what are the due dates for assignments?”, etc.

What It Can Do:

This custom BIMM143 AI assistant is designed to support your learning in a Socratic, teaching-focused way. It’s designed not to just answer your questions, but to help guide your thinking, reinforce course concepts, and clarify material. Its responses are based on our course materials - which is super cool! Have a look at the examples in this TritonGPT_example.pdf. It can also help you review, quiz yourself, and think through challenging topics and general in-class/homework problems.

Feedback:

This pilot is focused on exploring responsible and helpful uses of AI in teaching and learning, and your input is essential. Please try out different models (like GPT-5 or LLaMA 3 Scout) to see how their responses compare. Use the thumbs up or thumbs down icons to rate responses and add optional comments when you can. This helps us understand what’s working and what isn’t.

If you run into any tech issues, please reach out to me and the custom email ai-pilots@ucsd.edu. This will create a ServiceNow ticket and be routed to the appropriate ITS team.

Some important information about privacy & safety to bear in mind: Nothing you submit is used to train the AI models. I do have access to a general (anonymous) dashboard showing what students are asking, so I can see where people might be struggling and adjust my teaching accordingly. These prompts are never linked to any particular student. If you have any questions or concerns, please don’t hesitate to reach out.

Ethics Code

You are encouraged to collaborate with your fellow students and, as described above, to use generative AI tools as part of your learning process. However, you are ultimately responsible and accountable for all material you submit. This means:

• You must understand and be able to explain any work you submit;
• You must verify the accuracy of any AI-generated content;
• You must document your use of AI and collaboration as specified above;
• You must not misrepresent others’ work (human or AI) as solely your own unaided effort.

In short: use the tools available to you, but own the result intellectually.

“Academic Integrity is expected of everyone at UC San Diego. This means that you must be honest, fair, responsible, respectful, and trustworthy in all of your actions. Lying, cheating or any other forms of dishonesty will not be tolerated because they undermine learning and the University’s ability to certify students’ knowledge and abilities.  Thus, any attempt to get, or help another get, a grade by cheating, lying or dishonesty will be reported to the Academic Integrity Office and will result sanctions.

Sanctions can include an F in this class and suspension or dismissal from the University. So, think carefully before you act. Before you act, ask yourself the following questions: a) is my action honest, fair, respectful, responsible & trustworthy and, b) is my action authorized by the instructor?  If you are unsure, don’t ask a friend—ask your instructor, instructional assistant, or the Academic Integrity Office”.

You can learn more about academic integrity at academicintegrity.ucsd.edu (Source: UCSD Academic Integrity Office, 2025)

Code of Conduct

We are dedicated to providing a harassment-free learning experience for everyone, regardless of gender, age, sexual orientation, disability, physical appearance, body size, race, or religion (or lack thereof). We do not tolerate harassment of class participants in any form. Sexual language and imagery is not appropriate for any class venue, including talks, labs, parties, Twitter and other online media. Class participants violating these rules may be sanctioned or expelled from class at the discretion of the class organisers.

This Code of Conduct taken from http://confcodeofconduct.com/.

Need help?

You can reach the course director, Barry Grant, at bjgrant@ucsd.edu. You can also talk to any of the IAs if you need immediate help, or (in an emergency) call 911.