Supplementary Material For "A Framework For Three-Dimensional Simulation of Morphogenesis", submitted to ACM Transactions on Computational Biology and Bioinformatics.

  • Preprint of Paper (PDF)
  • Download Page
  • README for Linux (TEXT)
  • README for Windows (HTML)
  • GPL License (BasicUtils, XercesUtils, XMLCereal) (TEXT)
  • Apache License (Xerces) (TEXT)
  • Input and Output Files for 3D Chick Limb Growth Simulation (ZIP)
  • Input Files For Chickenlimb without Growth (TAR , 16.1 M) README (TEXT, 450 B)



  • Overview of CompuCell3D Configuration File and How To Run CompuCell3D (TEXT)
  • Extending CompuCell3D: Configuration File Objects (TEXT)


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    Supplementary Material For "BIOLOGO: A Domain Specific Language For Morphogenesis", submitted to ACM Transactions on Programming Languages and Systems.

  • README (TEXT)
  • Preprint of Paper (PDF)
  • Cell Sort Validation Simulation (XML)
  • Chickenlimb Validation Simulation (XML)
  • Chickenlimb with Domain Growth Validation Simulation (XML)
  • Dictyostelium Discoideum Validation Simulation (XML)

    * Note: You will need to install CompuCell3D by following the instructions on the CompuCell Wiki page. Instructions are described in more detail in the first supplementary material, for our paper to ACM TCBB. Documents below may also help (and are also linked above).




  • Overview of CompuCell3D Configuration File and How To Run CompuCell3D (TEXT)
  • Extending CompuCell3D: Configuration File Objects (TEXT)
    		•