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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.

To join us in writing this free and open textbook, please get in touch!


April 2023 release

Here you can find our current manuscript (which is still a "preview version"). We plan to release updated versions every 3 months.

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)

Single chapters (pdf)

1. The cell as a factory

2. What makes up a cell

3. The dynamics of metabolic systems

4. Metabolic flux distributions

5. Solutions of constraint-based metabolic models

6. Metabolic pathways and their enzyme efficiency

7. Models of growing cells

8. Large resource allocation models of cells

9. Optimal cell behavior in time

10. Metabolic diversity in cell populations

11. Control of cell division

12. Cell behavior in the face of uncertainty

Authors and financial support

Please see our list of authors and supporting institutions.

Lecture slides

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

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

Computer code and tutorials

Here you can find instructional jupyter notebooks

  1. Exercise "Flux balance analysis (FBA) of Escherichia coli core model"
  2. Jupyter notebooks covering different aspects of cell modeling (from ETH Systems Biology Course 2019)

Here you can find python code accompanying the book

  1. Code for Voronoi treemaps

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! If you're interested, please see our project page principlescellphysiology.org/book.html