Spare capacity allocation using shared backup path protection for dual link failures

This paper extends the spare capacity allocation (SCA) problem from single link failure [1] to dual link failures on mesh-like IP or WDM networks. The SCA problem pre-plans traffic flows with mutually disjoint one working and two backup paths using the shared backup path protection (SBPP) scheme. The aggregated spare provision matrix (SPM) is used to capture the spare capacity sharing for dual link failures. Comparing to a previous work by He and Somani [2], this method has better scalability and flexibility. The SCA problem is formulated in a non-linear integer programming model and partitioned into two sequential linear sub-models: one finds all primary backup paths first, and the other finds all secondary backup paths next. The results on five networks show that the network redundancy using dedicated 1+1+1 is in the range of 313-400%. It drops to 96-181% in 1:1:1 without loss of dual-link resiliency, but with the trade-off of using the complicated share capacity sharing among backup paths. The hybrid 1+1:1 provides intermediate redundancy ratio at 187-310% with a moderate complexity. We also compare the passive/active approaches which consider spare capacity sharing after/during the backup path routing process. The active sharing approaches always achieve lower redundancy values than the passive ones. These reduction percentages are about 12% for 1+1:1 and 25% for 1:1:1 respectively

Archon Genomics X PRIZE Validation Protocol

This document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches. The intent for the final version of this Validation Protocol is to become a useful standard by which to gauge the capabilities of whole genome sequencing technologies that emerge even after 2012

Topology optimization of freeform large-area metasurfaces

We demonstrate optimization of optical metasurfaces over $10^5$--$10^6$ degrees of freedom in two and three dimensions, 100--1000+ wavelengths ($\lambda$) in diameter, with 100+ parameters per $\lambda^2$. In particular, we show how topology optimization, with one degree of freedom per high-resolution "pixel," can be extended to large areas with the help of a locally periodic approximation that was previously only used for a few parameters per $\lambda^2$. In this way, we can computationally discover completely unexpected metasurface designs for challenging multi-frequency, multi-angle problems, including designs for fully coupled multi-layer structures with arbitrary per-layer patterns. Unlike typical metasurface designs based on subwavelength unit cells, our approach can discover both sub- and supra-wavelength patterns and can obtain both the near and far fields

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees.

BackgroundOne of the great advantages of next generation sequencing is the ability to generate large genomic datasets for virtually all species, including non-model organisms. It should be possible, in turn, to apply advanced computational approaches to these datasets to develop models of biological processes. In a practical sense, working with non-model organisms presents unique challenges. In this paper we discuss some of these challenges for ChIP-seq and RNA-seq experiments using the undomesticated tree species of the genus Populus.ResultsWe describe specific challenges associated with experimental design in Populus, including selection of optimal genotypes for different technical approaches and development of antibodies against Populus transcription factors. Execution of the experimental design included the generation and analysis of Chromatin immunoprecipitation-sequencing (ChIP-seq) data for RNA polymerase II and transcription factors involved in wood formation. We discuss criteria for analyzing the resulting datasets, determination of appropriate control sequencing libraries, evaluation of sequencing coverage needs, and optimization of parameters. We also describe the evaluation of ChIP-seq data from Populus, and discuss the comparison between ChIP-seq and RNA-seq data and biological interpretations of these comparisons.ConclusionsThese and other "lessons learned" highlight the challenges but also the potential insights to be gained from extending next generation sequencing-supported network analyses to undomesticated non-model species

Single Molecule Approaches to Mapping DNA Replication Origins

DNA replication is a fundamental process that is primarily regulated at the initiation step. In higher eukaryotes, the location and properties of replication origins are not well understood. Existing genome-wide approaches to map origins—such as nascent strand abundance mapping, Okazaki fragment mapping, or chromatin immunoprecipitation-based assays—average the behavior of a population of cells. However, due to cell-to-cell variability in origin usage, single molecule techniques are necessary to investigate the actual behavior of a cell. Here, I investigate the feasibility of using three single molecule, genome-wide technologies to map origins of replication. The Pacific Biosciences Single Molecule Real-Time (SMRT) sequencing technology, the BioNano Genomics Irys optical mapping technology, and the Oxford Nanopore Technologies MinION nanopore sequencing technology are promising approaches that can advance our understanding of DNA replication in higher eukaryotes