Goo is a modeling environment for creating physics based simulations of biological cells, tissues, and whole embryos. Goo contains built-in models for basic cell properties such as growth, division, and adhesion. Goo creates realistic models of cells in 3D based on surface meshes enclosing compresible fluid. Goo is meant to fill a void in currently available models such as vertex and particle based models which are too simplified to capture essential featuers of cells, are often 2D, and can be difficult for new users to use.
Goo is built on top of Blender, which is a truly amazing open source computer graphics project empoyering scientists with a user-friendly 3D modeling and simulation environment. Goo provides a library of helper functions in Python for modeling cells with user defined properties that are used inside the scripting environment and GUI of Blender. Physics and rendering are handled by Blender. In combination Goo and Blender allow cell-based simulations to be interacted with via Python scripts and through a GUI.
Goo is open source and currently being developed by Sean Megason’s group at Harvard University - http://www.digitalfish.org/.
Our grand Driving Biological Problem is to simulate the first 24 hours of zebrafish development. Our initial efforts are focussed on cleavage stage. We hope that Goo will be useful for simulating other biological tissues and for understanding morphogenesis, embryonic development, growth of organoids, tissue engineering, and artificial life.
Contributors: Antoine Ruzette1,2, Kali Konstantinopoulos3, Michael Mitsch3, Drew Willis3, Daniel Oo4, Ahmed Almaghasilah1,5, Nenghan Lin2, Vanshika Bidhan2, Jiangli Gui2, Julie De Man2, and Sean Megason1
1Harvard University, 2KU Leuven, 3Indiana University, 4Amhrest University, 5University of Maine
