Updates in metabolomics tools and resources: 2014-2015

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table

Statistical structures for internet-scale data management

Efficient query processing in traditional database management systems relies on statistics on base data. For centralized systems, there is a rich body of research results on such statistics, from simple aggregates to more elaborate synopses such as sketches and histograms. For Internet-scale distributed systems, on the other hand, statistics management still poses major challenges. With the work in this paper we aim to endow peer-to-peer data management over structured overlays with the power associated with such statistical information, with emphasis on meeting the scalability challenge. To this end, we first contribute efficient, accurate, and decentralized algorithms that can compute key aggregates such as Count, CountDistinct, Sum, and Average. We show how to construct several types of histograms, such as simple Equi-Width, Average-Shifted Equi-Width, and Equi-Depth histograms. We present a full-fledged open-source implementation of these tools for distributed statistical synopses, and report on a comprehensive experimental performance evaluation, evaluating our contributions in terms of efficiency, accuracy, and scalability

Computing infrastructure issues in distributed communications systems : a survey of operating system transport system architectures

The performance of distributed applications (such as file transfer, remote login, tele-conferencing, full-motion video, and scientific visualization) is influenced by several factors that interact in complex ways. In particular, application performance is significantly affected both by communication infrastructure factors and computing infrastructure factors. Several communication infrastructure factors include channel speed, bit-error rate, and congestion at intermediate switching nodes. Computing infrastructure factors include (among other things) both protocol processing activities (such as connection management, flow control, error detection, and retransmission) and general operating system factors (such as memory latency, CPU speed, interrupt and context switching overhead, process architecture, and message buffering). Due to a several orders of magnitude increase in network channel speed and an increase in application diversity, performance bottlenecks are shifting from the network factors to the transport system factors.This paper defines an abstraction called an "Operating System Transport System Architecture" (OSTSA) that is used to classify the major components and services in the computing infrastructure. End-to-end network protocols such as TCP, TP4, VMTP, XTP, and Delta-t typically run on general-purpose computers, where they utilize various operating system resources such as processors, virtual memory, and network controllers. The OSTSA provides services that integrate these resources to support distributed applications running on local and wide area networks.A taxonomy is presented to evaluate OSTSAs in terms of their support for protocol processing activities. We use this taxonomy to compare and contrast five general-purpose commercial and experimental operating systems including System V UNIX, BSD UNIX, the x-kernel, Choices, and Xinu

Forman-Ricci flow for change detection in large dynamic data sets

We present a viable solution to the challenging question of change detection in complex networks inferred from large dynamic data sets. Building on Forman's discretization of the classical notion of Ricci curvature, we introduce a novel geometric method to characterize different types of real-world networks with an emphasis on peer-to-peer networks. Furthermore we adapt the classical Ricci flow that already proved to be a powerful tool in image processing and graphics, to the case of undirected and weighted networks. The application of the proposed method on peer-to-peer networks yields insights into topological properties and the structure of their underlying data.Comment: Conference paper, accepted at ICICS 2016. (Updated version