zhangxiao6776 / ready

A cross-platform implementation of various reaction-diffusion systems.

Ready

Ready is a program for exploring continuous and discrete cellular automata, including reaction-diffusion systems, on grids and arbitrary meshes. OpenCL is used as the computation engine, to take advantage of the many-core architectures on graphics cards and modern CPUs. OpenCL also allows rules to be written in a text format and compiled on the fly. Ready supports a compact XML-based file format so that images and rules can be shared easily.

Ready supports 1D, 2D and 3D data, as well as polygonal and polyhedral meshes.

Download Ready 0.8 here:

• Windows 64 bit (32 bit)
• MacOS (10.6+)
• Linux: build instructions in BUILD.txt

More details on the releases tab.

Changes, To-do list, Credits

For questions, join our mailing list. Or you can email [email protected].

Screenshots:

Press coverage:

• New Scientist, August 2012: "First gliders navigate ever-changing Penrose universe"

Citations:

• David H. Ackley , Elena S. Ackley. "The ulam Programming Language for Artificial Life" Artificial Life. Nov 2016, Vol. 22, No. 4: 431-450.
• Kawamata I., Yoshizawa S., Takabatake F., Sugawara K., Murata S. "Discrete DNA Reaction-Diffusion Model for Implementing Simple Cellular Automaton" In: Amos M., CONDON A. (eds) Unconventional Computation and Natural Computation. UCNC 2016. Lecture Notes in Computer Science, vol 9726. Springer, Cham.
• Shigeki Akiyama and Katsunobu Imai, "The corona limit of Penrose tilings is a regular decagon", Lecture Note in Computer Science 9664, M. Cook and T. Neary (Eds.): AUTOMATA 2016, pp. 35–48, 2016. DOI: 10.1007/978-3-319-39300-1
• John G. Maisey and John S. S. Denton. "Dermal Denticle Patterning in the Cretaceous Hybodont Shark Tribodus limae (Euselachii, Hybodontiformes), and Its Implications for the Evolution of Patterning in the Chondrichthyan Dermal Skeleton" Journal of Vertebrate Paleontology 36(5):e1179200, 2016 doi: http://dx.doi.org/10.1080/02724634.2016.1179200
• Elmeligy Abdelhamid SH, Kuhlman CJ, Marathe MV, Mortveit HS, Ravi SS "GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems" PLoS ONE 10(8):e0133660, 2015. https://doi.org/10.1371/journal.pone.0133660
• Nathanael Aubert and Olaf Witkowski. "Reaction-Diffusion Risk: Chemical Signaling in a Conquest Game" Late Breaking Proceedings of the European Conference on Artificial Life 2015, pp. 29-30, 2015.
• Kaier Wang, Moira L. Steyn-Ross, D. Alistair Steyn-Ross, Marcus T. Wilson, Jamie W. Sleigh, Yoichi Shiraishi. "Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK" BMC Systems Biology 8(14), 2014.
• Aubert, Nathanaël, Clément Mosca, Teruo Fujii, Masami Hagiya, and Yannick Rondelez. "Computer-assisted design for scaling up systems based on DNA reaction networks" Journal of The Royal Society Interface 11, no. 93, 2014.
• Millán, Emmanuel N., Paula Martínez, Graciela Verónica Gil Costa, María Fabiana Piccoli, Alicia Marcela Printista, Carlos Bederian, Carlos García Garino, and Eduardo M. Bringa. "Parallel implementation of a cellular automata in a hybrid CPU/GPU environment" In XVIII Congreso Argentino de Ciencias de la Computación. 2013.
• Adam P. Goucher. "Gliders in cellular automata on Penrose tilings", Journal of Cellular Automata, Volume 7, Number 5-6, p. 385-392, 2012.

Please cite Ready as:

Tim Hutton, Robert Munafo, Andrew Trevorrow, Tom Rokicki, Dan Wills. 
"Ready, a cross-platform implementation of various reaction-diffusion systems." 
https://github.com/GollyGang/ready

Blog coverage:

• The Christev Creative, April 2015: "Negative Worms in Reaction Diffusion"
• Tim's blog, December 2012: "Ready 0.5"
• GPU Science, September 2012: "Reaction-Diffusion by the Gray-Scott Model with OpenCL"
• Complex Projective 4-Space, August 2012: "Are you Ready?"
• Mikael Hvidtfeldt Christensen, August 2012: "Reaction-Diffusion Systems"
• Hacker News, July 2012: "First glider discovered in a cellular automata on an aperiodic tiling"
• Aperiodical.com, July 2012: "Ready: reaction-diffusion simulator" [2]
• Tim's blog, September 2010: "reaction-diffusion"

Other packages:

• TexRD (closed source)
• Visions of Chaos (closed source)
• CAPOW

Wanted rules: (help needed)

• K. Maginu, "Reaction-diffusion equation describing morphogenesis I. waveform stability of stationary wave solutions in a one dimensional model", Math. Biosci. 27:1/2 (1975), 17–98 http://dx.doi.org/10.1016/0025-5564(75)90026-7
• L.Decker 2003, derived from Maginu's (from TexRD)
• L.Decker 2002, derived from Ginzburg-Landau (from TexRD)
• L.Decker 1998, derived from Brusselator (from TexRD)

Videos: