Cellular Potts model (CPM)

Modelling and simulation of multicellular systems using the cellular Potts model

• Hands-on sessions 4 Nov 12:15-16:00: Getting Started with Morpheus. Simulation and analysis of simple models.
• Pre-Assignment:
  1. Before the lecture, students should read at least Chapter II.2: The Cellular Potts Model and Biophysical Properties of Cells, Tissues and Morphogenesis in this book: https://www.springer.com/gp/book/9783764381011 (free download from UiO)
  2. For the practical sessions, students should install the software Morpheus (https://morpheus.gitlab.io/#download) and Gnuplot (https://sourceforge.net/projects/gnuplot/files/gnuplot/) on their laptops.

• Original 1992 CPM paper by Graner and Glacier in PRL: https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.69.2013
• 1997 paper by Hogeweg extending the CPM to account for chemotaxis and applied to Dictyostelium social life: https://www.sciencedirect.com/science/article/pii/S0022519396902374
• Book including full section about CPM (free download from UiO). In particular, the first two chapters  of that section (Magnetization to morphogenesis and CPM and Biophysical properties of cells) are specially interesting readings for a course in biophysics. https://www.springer.com/gp/book/9783764381011
• Morpheus software: https://morpheus.gitlab.io/, https://academic.oup.com/bioinformatics/article/30/9/1331/234757
• Morpheus tutorial by Walter de Back: https://gitlab.com/wdeback/Workshop-Morpheus/blob/master/tutorial-intro/README.md
• Introductory slides to multicellular models and Morpheus: https://gitlab.com/wdeback/Workshop-Morpheus/tree/master/slides
• CompuCell3D software: http://www.compucell3d.org/FrontPage, https://www.sciencedirect.com/science/article/pii/B9780123884039000138
• Cellular Potts modeling of complex multicellular behaviors
  in tissue morphogenesis
• Cellular Potts modeling of tumor growth, tumor invasion,
  and tumor evolution