Modelling and simulation of multicellular systems using the Cellular Potts model
In this part of the course the students will learn how to model and simulate multicellular and multiscale systems using the cellular Potts model and the software Morpheus: https://morpheus.gitlab.io/ It consists of a 90 minutes lecture followed by two hands-on sessions of 80 minutes each.
Lecture 14 Oct, 8:30-10:00: Modelling multicellular systems using the cellular Potts model.
Hands-on sessions 16 Oct 8:30-12:00: 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)
I attach to this mail the whole section II of the book, which is all about the cellular Potts model, in case students have time and special interest in the topic.
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/) in their own laptops. In case of problems, contact Alvaro Köhn-Luque (alvaro.kohn-luque@medisin.uio.no)
Assignment text
1. Cell sorting
2. Tumor growth (xml file)
3. Networks (movie)
Links about the CPM:
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