(1) The CompuCell3D is a simulation environment based on cellular Potts model. I attended the CompuCell3D annual workshop and took lecture for using the CompuCell3D player and developing it. I will briefly report the workshop and talk you what I feel.
(You can download the manual of CompuCell3D and all presentation slides that shown in the workshop. www.compucell3d.org)
(2) In the early kidney development, a simple epithelial tube called ureteric bud is derived from the intermediate mesoderm and undergoes a complex process of growth and terminal bifid branching. Experimental studies have reported that the branching of the ureteric bud is induced mainly by local cell proliferation and chemotaxis. These phenomena are triggered by GDNF and the expression of which is localized in the mesenchyme near to the tips of the ureteric bud. In this study, we examine how the branching patterns to develop depends on different physical or chemical factors including cell proliferation rate and the intensity of chemotactic property. To model a simple tube branching in the early kidney development, we adopt an extended cellular Potts model. We conclude that a proper balance between cell mobility due to chemotaxis and cell proliferation is necessary for achieving normal Y-shape patterns. Kinked patterns are formed when cell proliferation rate is faster, and bloated patterns are formed when cell mobility is larger. The result reflects on the real situation when abnormal patterns appear. Further, we introduce a measure that can predict the branching patterns, named as "growth-chemotaxis ratio". We show the growth-chemotaxis ratio can represent the variety of branching patterns.
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