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 course meetings. Lectures will not be recorded. Laptops are not allowed during lecture except when announced. 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.
- 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 Edpage 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 AM on Fridays. Homework is submitted as separate problems via Canvas. If the problem does not involve any computation, it must be in PDF format. If computation is involved, submit your solution as a Jupyter notebook. If the total computation time of the notebook exceeds one minute, also convert your notebook (with all cells having been executed) to HTML and submit that as well. Follow the file naming conventions below, where #.# denotes the homework problem number.
- No computation: lastname_firstname_#.#.pdf
- With computation that executes in less than one minute: lastname_firstname_#.#.ipynb
- With computation that executes in more than one minute: Submit a single ZIP File, lastname_firstname_#.#.zip, where the ZIP file contains two files, lastname_firstname_#.#.ipynb and lastname_firstname_#.#.html.
You have six grace days for the term. Grace days are spent as you submit late homework. For example, if you submit a homework within 24 hours of the due time, you spend one grace day, between 24 and 48 hours, you spend two, etc. Late homework will no longer be accepted after you spend your grace days. No homework will be accepted after June 9. If you have legitimate reasons for homework extensions, you may write the course staff and we will grant them at our discretion. Homework extensions do not result in spent grace days.
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 large language models (LLMs; examples include ChatGPT and GPT-4) or any other code- or prose-generating software.
Grading
Your final grade will be determined from your homework.