Advances in Networking Software

The six articles in this special section focus on advancements in networking software. Networking and communications systems are currently undergoing a substantive transformation on several fronts, promising substantially lower cost, simplified operations, and dramatically faster innovation cycles as traditional barriers to the deployment of innovations are removed. Where in the past networking functions were predominantly implemented using purpose-built hardware, custom protocols, and firmware images, those networking functions are increasingly instantiated through software that is abstracted from hardware, freely programmable, and relying on algorithmic invocation of generic application programming interfaces (APIs). This transformation is best summarized as “softwarization” of the network, which is, in turn, realized through advances in networking software. These articles exemplify this transformation, providing an excellent cross-section across these facets

Enveloping Sophisticated Tools into Process-Centered Environments

We present a tool integration strategy based on enveloping pre-existing tools without source code modifications or recompilation, and without assuming an extension language, application programming interface, or any other special capabilities on the part of the tool. This Black Box enveloping (or wrapping) idea has existed for a long time, but was previously restricted to relatively simple tools. We describe the design and implementation of, and experimentation with, a new Black Box enveloping facility intended for sophisticated tools --- with particular concern for the emerging class of groupware applications

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved