Goo

Goo is an open-source Python library to simulate cells, tissues and embryos in Blender.

It allows for the simulation of a collection of growing, self-replicating, autonomous and interacting agents in order to simulate biological tissues. Goo currently supports mechanical interactions of cells by adapting and extending the physics engine built into Blender, but will later support cell-cell communication and biocircuits including gene regulatory networks and signalling pathways.

Users can takes advantage of Blender’s rendering engines to render simulations in their preferred format, lighting, background and so much more.

Goo is hosted on Github at https://github.com/smegason/Goo.

Getting started

• Installation
  • Dependencies
  • Install dependencies in Blender
  • MacOS/Linux
  • Windows
• Example scripts
  • Writing your first simulation script
  • Cell division based a threshold volume
  • Random cell motion in a confined sphere
• Hardware recommendations
  • GPU
• Running Goo on O2
• Documentation
  • goo.cell
  • goo.molecule
  • goo.division
  • goo.force
  • goo.handler
  • goo.reloader
  • goo.simulator
  • goo.utils

Contributing

• Developer’s guide
  • Contributing to the codebase
  • Testing your code
  • Update the documentation
• Learning resources
  • Learn Blender
  • Learn Blender’s Python API
  • Learn Goo

Acknowledgments

• Citing goo
• Contributors

News

Goo v1.0 is here! This is the first stable release after refactoring the codebase to be more efficient and close to Python. More information.

Goo was presented at the 2023 Blender Conference in Amsterdam! More information.