Homework Assignments

3) Programming Assignment

posted Jul 31, 2018, 1:21 PM by Alexander Wolff   [ updated Jul 31, 2018, 1:22 PM ]

Because so much of physics, chemistry, and biology depends on computational resources, we believe that learning how to program is an essential part of your PhD training. As a result, all of you are required to complete a summer project before physically attending bootcamp. In particular, we will ask you to begin learning Python, a commonly used programming language in the life sciences, using Rosalind, a series of bio-oriented online programming exercises.  Additionally, everyone is required to complete a project building a Ramachandran plot using Python.

Action items:

1. If you have never coded in Python before, install it.

2. Learn and practice Python using Rosalind. You will need to enroll in the class with this link. Once you are on the class page, there will be a number of questions for you to work your way through as practice. The questions are sorted in order of increasing difficulty. If the earlier questions are not challenging, you may move to later questions. It is recommended that you complete at least 3 tasks of your choice per week.

3. Complete the Python project, attached below. It is broken up in steps to help you organize your time, but you should begin the project by early August so that you have time to complete it before the start of bootcamp. Again, if you have any questions or get stuck, email us. We realize if you have never programmed before, this may be challenging. However, we are here to help you through it and will be checking in with you every week to see how you are progressing.

The intent is that you spend a little bit of time every day practicing Python coding so that you are proficient in the basics by the time you reach UCSF in the fall. If you are new to Python, we highly encourage you to get started right away. Python takes some time to learn, especially if you have no prior coding background. 

Happy coding!

2) Biology Reading Assignment

posted Jul 9, 2018, 2:28 PM by Alexander Wolff   [ updated Jul 9, 2018, 2:38 PM ]

If your background in biology is limited (ie: you can you count the number of biology courses you've taken on one hand), we recommend reading the first few chapters of a molecular biology textbook to get acquainted with the fundamentals. A great option is Molecular Biology of the Cell. We're partial to this book, because four of the authors hail from UCSF:

An older, used copy can save you plenty of money, and will still get the fundamentals across. We think that chapters 1-3 are especially important, but reading chapters 4-7 would also be helpful.

1) Read "What is Life?" by Erwin Schrödinger

posted Jul 9, 2018, 1:57 PM by Alexander Wolff   [ updated Jul 9, 2018, 1:58 PM ]

This is a short book that we’ll discuss during lunch on our first day of bootcamp. While the text is old, it is surprisingly insightful. Schrödinger speculates about the separation between life and non-life life from the perspective of a physicist. In doing so, he made surprisingly accurate predictions, and influenced a generation of molecular biologists. If you want a preview, check out this highlight by Matthew Cobb in The Guardian.

PDFs of the book are available online, or you can pick up a paper copy.

1-3 of 3