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

A Lightweight Multilevel Markup Language for Connecting Software Requirements and Simulations

[Context] Simulation is a powerful tool to validate specified requirements especially for complex systems that constantly monitor and react to characteristics of their environment. The simulators for such systems are complex themselves as they simulate multiple actors with multiple interacting functions in a number of different scenarios. To validate requirements in such simulations, the requirements must be related to the simulation runs. [Problem] In practice, engineers are reluctant to state their requirements in terms of structured languages or models that would allow for a straightforward relation of requirements to simulation runs. Instead, the requirements are expressed as unstructured natural language text that is hard to assess in a set of complex simulation runs. Therefore, the feedback loop between requirements and simulation is very long or non-existent at all. [Principal idea] We aim to close the gap between requirements specifications and simulation by proposing a lightweight markup language for requirements. Our markup language provides a set of annotations on different levels that can be applied to natural language requirements. The annotations are mapped to simulation events. As a result, meaningful information from a set of simulation runs is shown directly in the requirements specification. [Contribution] Instead of forcing the engineer to write requirements in a specific way just for the purpose of relating them to a simulator, the markup language allows annotating the already specified requirements up to a level that is interesting for the engineer. We evaluate our approach by analyzing 8 original requirements of an automotive system in a set of 100 simulation runs

Histopathological image analysis : a review

Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe

Your Smart Home Can't Keep a Secret: Towards Automated Fingerprinting of IoT Traffic with Neural Networks

The IoT (Internet of Things) technology has been widely adopted in recent years and has profoundly changed the people's daily lives. However, in the meantime, such a fast-growing technology has also introduced new privacy issues, which need to be better understood and measured. In this work, we look into how private information can be leaked from network traffic generated in the smart home network. Although researchers have proposed techniques to infer IoT device types or user behaviors under clean experiment setup, the effectiveness of such approaches become questionable in the complex but realistic network environment, where common techniques like Network Address and Port Translation (NAPT) and Virtual Private Network (VPN) are enabled. Traffic analysis using traditional methods (e.g., through classical machine-learning models) is much less effective under those settings, as the features picked manually are not distinctive any more. In this work, we propose a traffic analysis framework based on sequence-learning techniques like LSTM and leveraged the temporal relations between packets for the attack of device identification. We evaluated it under different environment settings (e.g., pure-IoT and noisy environment with multiple non-IoT devices). The results showed our framework was able to differentiate device types with a high accuracy. This result suggests IoT network communications pose prominent challenges to users' privacy, even when they are protected by encryption and morphed by the network gateway. As such, new privacy protection methods on IoT traffic need to be developed towards mitigating this new issue