DevoWorm
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 Harvesting Wildtype Nematodes: a protocol
Poster  YouTube Animation
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​WormWorx App (for Android)  

Google Play
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​WormSim Demo  
YouTube
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Open DevoCell   Herokuapp
​Flocking Boids (collective behavior demo)
T.E. Portegys, K. M. Greenan (2003). "Managing Flocking Objects with an Octree Spanning a Parallel Message-Passing Computer Cluster", International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'03)

We investigate the management of flocking mobile objects using a parallel message-passing computer cluster. An octree, a data structure well-known for use in managing a 3D space, is adapted to “span” the cluster. Objects are distributed in the tree, and partitions of the tree are distributed among the processors in such a way that a minimum of global information is required to be shared by the processors. When objects move, the tree is modified accordingly; this in turn may cause partitions to migrate processors. Two constraints drive the distribution algorithm: (1) minimizing message traffic by clustering nearby objects on the same processor, and (2) processor load-balancing. Boids, flocking artificial life forms, embody the objects in this study. The performance of the system is measured in terms of the inter-processor message traffic as a function of the number, interactivity, and mobility of objects. An application of the scheme allows external clients to view objects in specified spatial loci. 
​Paper (pdf).
Simulation (C++/OpenGL) code (zip).
Lab (C++/PVM/OpenGL) code (zip). 
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​CAST Alignment Demo
CAST (Code Alignment Search Tool) alignments and scores between Caenorhabditis elegans, Ciona Intestinalis, and Axolotl (Ambystoma mexicanum)  

Alicea, B. and Gordon, R. (2016). Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development Via Differentiation Trees of Embryos [invited]. Biology, 5(3), 33. Paper  Supplemental Data

​Example Computations and Summary Statistics (xlsx).
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Genotype-to-Phenotype Programs
First proposed in: Alicea, B. (2007). Towards a theory of human intraspecific variation for ergonomics and human modeling. Society for Automotive Engineering (SAE) Digital Human Modeling, #2007-01-2461.
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Epistatic Program and Output
Paired Variance
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  • Home
  • Project Overview
    • Slack Channel
    • DevoLearn/DevoGraph
    • DevoWorm @ Huggingface
  • People
  • Education, Notebooks, and Media
    • Background
    • DevoZoo
    • DevoWormML
    • Jupyter Notebooks
    • Media and Public Lectures
    • Google Summer of Code
  • Academic Output
    • Publications
    • Devoworm @ Github
    • Data Sources
    • Demos
  • Affiliations
    • OpenWorm Foundation
    • Orthogonal Research and Education Laboratory
  • Schedule/Join