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A free textbook on Economic Principles in Cell Biology

How can a cell maintain itself as a living being? Living cells, shaped by billions of years of evolution, have developed many ways to adapt to their environment, e.g. by regulation of gene expression. But the rules of physics and chemistry enforce certain boundaries on what cells can achieve and how they can allocate their own resources. Our goal is to uncover some of these governing principles. Shaped by evolution, cells "do certain things right", and computational models of cells often assume that this "doing something right" can be described by evoking optimality principles. In our open textbook - to which anyone can contribute - we intend to give an overview of established approaches to "cellular economics", from descriptions of simple metabolic systems to cell growth, variability, and dynamic behaviour.

For more information about our book project, please see our website for (actual and potential) authors and this poster.

If you would like to join us for writing this free textbook, please get in touch!

Contributors

Please see our list of authors.

First preview version (January 2023 edition)

Starting in January 2023, you can find here a preview version of our book (with a small number of chapters and rudimentary layout). We will publish updated versions every 3 months. The text can be read and downloaded for free.

Read or download the entire book (pdf)

  1. Download the book pdf
  2. Read the book in your browser
    (depending on your internet connection, opening the pdf may take a while)

Download single chapters (pdf)

1. The cell as a factory

2. What makes up a cell


3. The dynamics of metabolic systems

4. The space of metabolic flux distributions

5. Optimal solutions of metabolic models

6. How to rate metabolic pathways by their enzyme efficiency

7. Large cell models


8. Cell behavior in the face of uncertainty


Computer exercises

Here you can find instructional jupyter notebooks

  1. Exercise "Flux balance analysis (FBA) of Escherichia coli core model"

Code

Here you can find python code accompanying the book

  1. Code for Voronoi treemaps

Lecture slides

Some of the chapters have been presented as lectures at the 2022 Summer school Economic Principles in Cell Bioloy at LPI Paris.
Numbers refer to chapter numbers. Lectures without a number will be featured in future editions of the book.

  1. -- Overview: Exploring the economy of the cell
  2. 2. What makes up a cell?
  3. -- Optimality problems in cells
  4. 3. A dynamic view of metabolism
  5. -- Balanced growth
  6. 4./5. Flux Balance Analysis
  7. 6. The cost of metabolic pathways
  8. -- Optimal metabolic states
  9. -- Self-replicator models (slides) (notes)
  10. 7. Resource allocation models
  11. -- Optimal cell behavior in time

Copyright

The book is published under the Creative Commons license CC BY-SA, which allows you to share and adapt (also for commercial purposes) if you give appropriate credit, provide a link to the license, and indicate if changes were made. If you remix, transform, or build upon the material, you must distribute your contributions under the same license CC BY-SA.

Contact

Anybody is welcome to contribute to our book! Please see our project page principlescellphysiology.org/book.html