A GPU Implementation for Two-Dimensional Shallow Water Modeling

In this paper, we present a GPU implementation of a two-dimensional shallow water model. Water simulations are useful for modeling floods, river/reservoir behavior, and dam break scenarios. Our GPU implementation shows vast performance improvements over the original Fortran implementation. By taking advantage of the GPU, researchers and engineers will be able to study water systems more efficiently and in greater detail.Comment: 9 pages, 1 figur

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Piko: A Framework for Authoring Programmable Graphics Pipelines

Photo shows a group of cross-country skiers in the vicinity of Snowbird, Little Cottonwood Canyon, Uta

Staged Metaprogramming for Shader System Development

The shader system for a modern game engine comprises much more than just compilation of source code to executable kernels. Shaders must also be exposed to art tools, interfaced with engine code, and specialized for performance. Engines typically address each of these tasks in an ad hoc fashion, without a unifying abstraction. The alternative of developing a more powerful compiler framework is prohibitive for most engines.In this paper, we identify staged metaprogramming as a unifying abstraction and implementation strategy to develop a powerful shader system with modest effort. By using a multi-stage language to perform metaprogramming at compile time, engine-specific code can consume, analyze, transform, and generate shader code that will execute at runtime. Staged metaprogramming reduces the effort required to implement a shader system that provides earlier error detection, avoids repeat declarations of shader parameters, and explores opportunities to improve performance.To demonstrate the value of this approach, we design and implement a shader system, called Selos, built using staged metaprogramming. In our system, shader and application code are written in the same language and can share types and functions. We implement a design space exploration framework for Selos that investigates static versus dynamic composition of shader features, exploring the impact of shader specialization in a deferred renderer. Staged metaprogramming allows Selos to provide compelling features with a simple implementation

Author's personal copy A stochastic model for the development of Bateson-Dobzhansky-Muller incompatibilities that incorporates protein interaction networks

a b s t r a c t Speciation is characterized by the development of reproductive isolating barriers between diverging groups. Intrinsic post-zygotic barriers of the type envisioned by Bateson, Dobzhansky, and Muller are deleterious epistatic interactions among loci that reduce hybrid fitness, leading to reproductive isolation. The first formal population genetic model of the development of these barriers was published by Orr in 1995, and here we develop a more general model of this process by incorporating finite protein-protein interaction networks, which reduce the probability of deleterious interactions in vivo. Our model shows that the development of deleterious interactions is limited by the density of the protein-protein interaction network. We have confirmed our analytical predictions of the number of possible interactions given the number of allele substitutions by using simulations on the Saccharomyces cerevisiae proteinprotein interaction network. These results allow us to define the rate at which deleterious interactions are expected to form, and hence the speciation rate, for any protein-protein interaction network