The expansion of memory disaggregation, driven by data-centric applications, increases heterogeneity in memory systems. This shift enables the use of inexpensive, yet lifetime-limited, flash memory to be used as a memory expansion module. We argue that TRIM should be introduced into memory management systems to effectively respond to this transition. In this position paper, we explore the potential adoption of flash memory as memory expansion and present an analytical model that offers a straightforward yet rigorous evaluation of TRIM's effectiveness. Using this model and characteristics extracted from real-world workloads, we evaluate the effectiveness of TRIM in scalable memory systems and prove its necessity.

Abstract Motivation: Genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach that analyzes multiple individuals together. A compressed de Bruijn graph is a sophisticated data structure for representing the genomes of entire populations. It robustly encodes shared segments, simple single-nucleotide polymorphisms and complex structural variations far beyond what can be represented in a collection of linear sequences alone. Results: We explore deep topological relationships between suffix trees and compressed de Bruijn graphs and introduce an algorithm, splitMEM, that directly constructs the compressed de Bruijn graph in time and space linear to the total number of genomes for a given maximum genome size. We introduce suffix skips to traverse several suffix links simultaneously and use them to efficiently decompose maximal exact matches into graph nodes. We demonstrate the utility of splitMEM by analyzing the nine-strain pan-genome of Bacillus anthracis and up to 62 strains of Escherichia coli , revealing their core-genome properties. Availability and implementation: Source code and documentation available open-source http://splitmem.sourceforge.net . Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

MOTIVATION: Genome resequencing and short read mapping are two of the primary tools of genomics and are used for many important applications. The current state-of-the-art in mapping uses the quality values and mapping quality scores to evaluate the reliability of the mapping. These attributes, however, are assigned to individual reads and do not directly measure the problematic repeats across the genome. Here, we present the Genome Mappability Score (GMS) as a novel measure of the complexity of resequencing a genome. The GMS is a weighted probability that any read could be unambiguously mapped to a given position and thus measures the overall composition of the genome itself. RESULTS: We have developed the Genome Mappability Analyzer to compute the GMS of every position in a genome. It leverages the parallelism of cloud computing to analyze large genomes, and enabled us to identify the 5-14% of the human, mouse, fly and yeast genomes that are difficult to analyze with short reads. We examined the accuracy of the widely used BWA/SAMtools polymorphism discovery pipeline in the context of the GMS, and found discovery errors are dominated by false negatives, especially in regions with poor GMS. These errors are fundamental to the mapping process and cannot be overcome by increasing coverage. As such, the GMS should be considered in every resequencing project to pinpoint the 'dark matter' of the genome, including of known clinically relevant variations in these regions. AVAILABILITY: The source code and profiles of several model organisms are available at http://gma-bio.sourceforge.net

Due to the increasing oil prices, reducing the weight of future cars will be important. One way to do this is by replacing wired sensors and their cables with wireless sensors. This could reduce the weight of cars, thus improving fuel efficiency. The replacement is anticipated to reduce the weight of an average passenger vehicle by up to 50 kg. However, such a replacement raises security concerns due to the intrinsic vulnerability of wireless technologies. In addressing security problems for intra-car wireless sensor networks, existing methods, focusing on energy efficiency and providing a low security level, are unfortunately not applicable. Our research focuses on providing a real-time and a high security solution. In this paper, we make four main contributions. First, we propose a systematic methodology to select security algorithms for real-time wireless sensor networks. Second, we determine the most effective combination with respect to the execution time and the security level by using our methodology. Third, the reported results are shown to be directly applicable to off-the-shelf sensor products and real-time wireless sensor networks, since we evaluated the performance on a real sensor platform and the real-time requirements for a car are much more stringent than other real-time systems. Finally, we suggest a mathematical methodology to increase the security level which imposes a burden only to adversaries, not to sensors.