The cellular Potts model (CPM), and the software package CompuCell3D, simulate cellular patterns on a computer. They represent each cell as a set of pixels, like in experimental pictures. They can thus describe cell shapes with the same precision as experiments. Since they are detailed enough to describe sub-cellular details, and quick enough to compute thousands (and sometimes millions) of cells, they are truly multi-scale.
They are used in a large variety of numerical studies of either foams or biological tissues. They are flexible and can include several physical or biological ingredients. For instance, in foams they simulate structure, coarsening and slow rheology. In biology they simulate plant or animal tissues, cell colonies, or multicellular spheroids (also called aggregates), with ingredients such as adhesion, growth, division, cortical contraction, chemotaxy, or membrane fluctuations.
The workshop is opened to anybody who could be interested, from beginners to advanced users.
It will take place on June 28 and 29th, 2012.
NOTE : there will be two different locations.
Thursday, June 28th, 2012 : in Univ. Paris 6 “Marie and Pierre Curie”, Jussieu campus. See Map and Info. Tower 15, 3rd floor, 15-16, room 309
Friday, June 29th, 2012 : in Univ. Paris 7 “Denis Diderot”, Paris Rive Gauche campus, Condorcet B building. See Map and Info. 6th floor, room 631B - Kandinsky
| Thursday 28th | Univ. Marie et Pierre Curie, Jussieu, tower 15, 3rd floor, 15-16, room 309 | ||
|---|---|---|---|
| 9 h | François Graner | Motivations, history, principle | |
| 10 h | Jos Käfer | How to start, applications to biological tissues | |
| 11 h | Gilberto Thomas | The CompuCell3D package, applications to cellular structures | |
| 12 h | Lunch | ||
| 14 h | Verônica Grieneisen | “Making heads and tails of cell polarity” | |
| 15 h 30 | Benoît Vianay | “Micropatterned substrates to simplify single cell spreading and modeling” | |
| 16 h | Marc Durand | “Effect of temperature on a foam's topological disorder” | |
| 16 h 20 | Stan Marée | “Cell surface mechanics and the cellular Potts model” | |
| 16 h 50 | François Graner | “Growth laws and self-similar growth regimes of coarsening 2D foams” | |
| 17 h 10 | Boris Guirao | “Role of oriented cell rearrangements in cell packing of drosophila wing” | |
| 17 h 40 | Jean-Louis Martiel | “How actin network dynamics control the onset of actin-based motility” | |
| 17 h 55 | Closure | Short discussion | |
| Friday 29th | Univ. Paris Diderot, Condorcet building, 6th floor, room 631B - Kandinsky | ||
|---|---|---|---|
| 9 h 30 | Chair : Stan Marée | Recent advances, open questions, possible applications, perspectives and improvements | |
| 14 h | Gilberto Thomas | CompuCell tutorials for beginners can be arranged upon request | |
There is no formal registration. Please feel free to participate any session, and change your mind until the last minute. 
The GdR Mousses provides 1000 euros. They are mostly used to fund the trip and lodging of two foreign participants.
Sandwiches will be provided on Thursday noon in the cafeteria in front of room 309; you can contribute by bringing your own food if you wish.
This workshop is part of the “GdR Mousses” (or more precisely: Groupe de Recherches “Mousses et Emulsions”), which is a CNRS-funded consortium of french laboratories studying foams and emulsions.
An introduction to Potts model simulations can be found in the book Les mousses - structure et dynamique (Belin, collection Échelles, 2010); English version, “Foams: Structure and Dynamics”, edited by S. Cox (Oxford University Press, Oxford, to appear, ISBN 978-0-19-966289-0).
Nature Methods (March 2012) presents on its cover applications of the cellular Potts model.
On July 5th, 2012 at 14 h, James Glazier will give a talk at Amphithéâtre Lacassagne, Institut Curie, 11 rue Marie et Pierre Curie, 75005 Paris, entitled “Applying Multi-Scale, Multi-Cell Modeling of Pathological Neovascularization in the Retina and Solid Tumors to Suggest Novel Treatment Strategies”.
He will organise the annual CompuCell training session on July 30th - August 3rd 2012.
On June 1st, in Amsterdam (NL), there has been a NCSB Tutorial: Multiscale, Cell-based Modelling in Biological Development and Cancer based on Cellular Potts model (CPM) and the software package CompuCell3D.
There will be a workshop on multiscale modeling of cancer at the Lorentz Center in November 2012.
There should be a CompuCell workshop in Brazil in 2013 - more details later.
François Graner: francois.graner (at) univ-paris-diderot.fr
Thanks to Carole Philippe-Barache, Luis Almeida, Ibrahim Cheddadi, Cyprien Gay and Marc Durand.
