Goo

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

Goo was designed as a platform to model collections of growing, self-replicating, autonomous, and interacting agents, enabling the exploration of tissue organization. It connects together cellular biomechanics, molecular diffusion in the extracellular environment and gene regulatory networks at the cell-level.

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
• Example scripts
  • 1. Writing your first script: a tutorial
  • 2. Modeling growing cell doublets with differential adhesion
  • 3. Cell division based on volume growth
  • 4. Random cell mixing
  • 5. Blinking cells and the repressilator
  • 6. Controlling cell motility with gene concentration
• API documentation
  • goo.cell
  • goo.division
  • goo.force
  • goo.growth
  • goo.molecule
  • goo.gene
  • goo.handler
  • goo.simulator
  • goo.reloader
  • goo.boundary
  • goo.utils
• Hardware recommendations
  • GPU

Contributing

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

Acknowledgments

• Citing goo
• Contributors

News

Goo v1.1.0 is here! This release includes new features to simulate extracellular diffusion and gene regulatory networks. More information.

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.