Lectures
We have lectures from 11:00-11:50 AM on Mondays, Wednesdays, and Fridays in 100 Chen. All students are expected to attend all lectures. Lectures will not be recorded. Laptops are not allowed during lecture except when announced and cell phones are never allowed. Tablets may only be used for notetaking purposes. There are many reasons why we have this policy, some of which you can read about here.
Textbooks and reading materials
All course content can be accessed at https://biocircuits.github.io. We also have one suggested textbook for the course:
- U. Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, 2nd Ed., CRC Press, 2020.
The following books are also useful.
- D. Del Vecchio and R. M. Murray, Biomolecular Feedback Systems. This book is also a great resource. You can get PDFs from the book wiki.
- U. Alon, Systems Medicine: Physiological Circuits and the Dynamics of Disease, CRC Press, 2024.
- Phillips, Kondev, Theriot, and Garcia, Physical Biology of the Cell, 2nd Ed., Garland Scientific, 2012. This book has good analysis of physical bases for the regulation of gene expression.
- S. Strogatz, Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering, 2nd Ed., Westview Press, 2014. This book gives a good pedagogical background on the analysis of dynamical systems.
Email and Ed
We will use Ed for discussions on the course content and homework. You can access the class Ed page here. When you post anonymously on Ed, you are anonymous to students, but not to the course staff. You can also post private messages on Ed that are visible only to the course staff. For matters regarding personal issues you do not feel comfortable using the Ed platform to share, please contact the course staff directly via email.
Homework
We will have weekly homeworks, typically due at 10:30 PM on Thursdays. Homework is submitted with a separate submission for each problem via Canvas. Follow the file submission and naming conventions below, where #.# denotes the homework problem number as listed on Canvas.
- No computation: Submit a single PDF with the file name lastname_firstname_#.#.pdf
- With computation: Submit two separate files, a PDF, and the Jupyter notebook that generated the PDF. If you're having issues exporting to PDF, export as HTML, then open in browser and download or print the PDF from there. The file names are lastname_firstname_#.#.pdf and lastname_firstname_#.#.ipynb.
You are expected to turn homework in on time. There are no extensions. This is not meant to be cruel. It is meant to prevent students from falling behind the pace. Late homeworks are eligible for up to 50% credit up to three days late. All homeworks have to be turned in to pass the class (even if more than 3 days late), but the lowest-scored problem will be dropped from your grade calculation.
If you have a CASS accommodation, you need to communicate it to the instructors within the first week of class, or within the first week after the accommodation is issued if issued during the term. If your accommodation allows for extra time on coursework, you need to let course staff know you will be exercising that accommodation at least 24 hours before the homework is due or as soon as reasonably practicable.
No homework will be accepted after June 5.
Unless otherwise noted on a particular problem set, you may discuss homework with other students in the course. In fact, you are encouraged to do so. Naturally, the submitted homework must be your own original work. If you do work with collaborators, please indicate with whom you collaborated on your submission.
Of course, you may not refer to homework materials from previous editions of this course. If you happen to find the solution to a very similar problem online or elsewhere, you may not refer to it.
You may not use any chatbots, large language models (LLMs; examples include ChatGPT, Claude, Copilot, etc.), AI, or any other code- or prose-generating software unless specifically directed to in a problem statement. We have found that policing AI usage has become impossible. We therefore will not be scrutinizing your homework for AI usage. It is not in your best interest, nor that of the Caltech community, for you to use AI for your homework. It will stunt your learning and make the final exam, which counts 30% of your grade, very difficult. Please adhere to this policy.
Final exam
We will have an in-person final exam. The timing of the exam will be finalized before the end of the fifth week of class.
Grading
Your final grade will be determined from your homework (70%) and the final exam (30%). Any serious Honor Code violations will result in failure of the course.