Software

Please properly cite the following software and papers when using or referencing them in any published work.

Cassandra D.M. Churchill (University of Alberta), Philip Winter (University of Alberta), Jack A. Tuszynski (University of Alberta), Michael Levin (Tufts University):

• EDeN - Electroceutical Design Environment (2021)
• EDeN interface implemented by Stefano Rosa

Alexander Mordvintsev (Google), Eyvind Niklasson (Google), and Ettore Randazzo (Google):

• Growing Neural Cellular Automata: Differentiable Model of Morphogenesis (2020)

Erik Hoel (Tufts University) and Brennan Klein (Northeastern University):

• Analyzing causal emergence in networks (2019)

Franz Kuchling (Tufts University):

• MorphoBayes - Bayesian modeling of morphogenesis (2019)

Douglas Moore (Tufts University/ASU):

• Moore, D., and McMillen, P., (2019):
  CAIM: information analysis of imaging data
• Moore, D., Levin, M., and Walker, S., (2016):
  "Inform: A Cross Platform C library for Information Analysis of Dynamical Systems"
• Moore, D., Levin, M., and Walker, S., (2016):
  "PyInform: A Python Wrapper for the Inform Information Analysis Library"
• Moore, D., Levin, M., and Walker, S., (2016):
  "Cellular: A simple, extensible cellular automaton library"
• Moore, D., Levin, M., and Walker, S., (2016):
  "Annette: A recurrent artificial neural network library"
• Moore, D., Levin, M., and Walker, S., (2016):
  "Neato: An implementation Ken Stanley’s NeuroEvolution of Augmenting Topologies"

Cuong Nguyen (Allen Discovery Center at Tufts University):

• Nguyen, C., and Levin, M., (2017):
  "Baccountant: a software package for quantifying bacterial colony growth"
  For Windows (.zip file) | For Mac (.zip file) | Learn how to use the software (video tutorials)

Alexis Pietak (Allen Discovery Center at Tufts University):

• Pietak, A., and Levin, M., (2019):
  "PLIMBO (Planarian Interface for Modelling Body Organization)"
• Pietak, A., and Levin, M., (2016):
  "BETSE - BioElectric Tissue Simulation Engine"

Cecil Curry:

• "BETSEE: a front-end GUI for the BETSE package

Micah Brodsky (Tufts University/MIT):

• Brodsky, M., Pietak, A., and Levin, M., (2017):
  "GABEE - Genetic Algorithm for Bio-Electric Exploration"

Chris Fields:

• Fields, C. and Levin, M., (2018):
  "Somatic cells protect stem cells from a lethal environment"
• Fields, C. and Levin, M., (2018):
  "Neoblast competition simulation"

Daniel Lobo (Tufts University/University of Maryland):

• Planform - planarian regeneration expert system
• Limbform - limb regeneration expert system
• Planarian regeneration simulation software