WormSim Demo YouTube
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.
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.
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).
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).
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
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Paired Variance
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