Learning Resources
Build-a-Books: These are links to curated collections of papers, organized as chapters, which can be thought of as advanced textbooks on specific subjects. The collections are curated by lab members, maintained in Dropbox, and can be accessed below:
Build-a-Book: Cellular Energy in Context
Link: Cellular Bioenergetics (Biothermokinetics)
This book is about how metabolism works as a 'constitutive regime' that drives all biological activity. There is a strong focus on foundational thermodynamics in non-equilibrium systems and experimental methods for learning things about such systems. ATP and the phospho-group transfer potential are chosen as an important model system to frame the discussion.
Build-a-Book: The Action of Predicting
Link: Cellular Biocomputation
This book is about models of computation and how they might be applied to the physiology of cells, cell collectives, and even organisms. There is a strong focus on the idea that 'cognition' can be quantitatively defined, and that computation is a fundamental part of biology, not simply an analogy to human designed machines.
Coding Resources: These are links to Python language programming materials. They are hosted on our lab GitHub page. They are formatted in Jupyter notebooks. We recommend using the Anaconda Python distribution.
Coding Resource: PyoChem I
Link: PyoChem I
Learn fundamentals of scientific computing for biochemistry using Python in Jupyter Notebooks.