Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Stochastic chemical kinetics describes the time evolution of a wellstirred chemically reacting system in a way that takes into account the fact that molecules come in whole numbers and exhibit some degree of randomness in their dynamical behavior. Researchers are increasingly using this approach to chemical kinetics in the analysis of cellular systems in biology, where the small molecular populations of only a few reactant species can lead to deviations from the predictions of the deterministic differential equations of classical chemical kinetics. After reviewing the supporting theory of stochastic chemical kinetics, I discuss some recent advances in methods for using that theory to make numerical simulations. These include improvements to the exact stochastic simulation algorithm (SSA) and the approximate explicit tau-leaping procedure, as well as the development of two approximate strategies for simulating systems that are dynamically stiff: implicit tau-leaping and the slow-scale SSA.

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Stochastic Simulation of Chemical Kinetics

In recent years, indoor positioning has emerged as a critical function in many end-user applications; including military, civilian, disaster relief and peacekeeping missions. In comparison with outdoor environments, sensing location information in indoor environments requires a higher precision and is a more challenging task in part because various objects reflect and disperse signals. Ultra WideBand (UWB) is an emerging technology in the field of indoor positioning that has shown better performance compared to others. In order to set the stage for this work, we provide a survey of the state-of-the-art technologies in indoor positioning, followed by a detailed comparative analysis of UWB positioning technologies. We also provide an analysis of strengths, weaknesses, opportunities, and threats (SWOT) to analyze the present state of UWB positioning technologies. While SWOT is not a quantitative approach, it helps in assessing the real status and in revealing the potential of UWB positioning to effectively address the indoor positioning problem. Unlike previous studies, this paper presents new taxonomies, reviews some major recent advances, and argues for further exploration by the research community of this challenging problem space.

https://www.mdpi.com/1424-8220/16/5/707/pdf

Ultra Wideband Indoor Positioning Technologies: Analysis and Recent Advances.

Data centers are critical, energy-hungry infrastructures that run large-scale Internet-based services. Energy consumption models are pivotal in designing and optimizing energy-efficient operations to curb excessive energy consumption in data centers. In this paper, we survey the state-of-the-art techniques used for energy consumption modeling and prediction for data centers and their components. We conduct an in-depth study of the existing literature on data center power modeling, covering more than 200 models. We organize these models in a hierarchical structure with two main branches focusing on hardware-centric and software-centric power models. Under hardware-centric approaches we start from the digital circuit level and move on to describe higher-level energy consumption models at the hardware component level, server level, data center level, and finally systems of systems level. Under the software-centric approaches we investigate power models developed for operating systems, virtual machines and software applications. This systematic approach allows us to identify multiple issues prevalent in power modeling of different levels of data center systems, including: i) few modeling efforts targeted at power consumption of the entire data center ii) many state-of-the-art power models are based on a few CPU or server metrics, and iii) the effectiveness and accuracy of these power models remain open questions. Based on these observations, we conclude the survey by describing key challenges for future research on constructing effective and accurate data center power models.

Data Center Energy Consumption Modeling: A Survey

No wonder you activities are, reading will be always needed. It is not only to fulfil the duties that you need to finish in deadline time. Reading will encourage your mind and thoughts. Of course, reading will greatly develop your experiences about everything. Reading molecular biology of the gene is also a way as one of the collective books that gives many advantages. The advantages are not only for you, but for the other peoples with those meaningful benefits.

Molecular Biology of the Gene.

This paper proposes a hardware accelerator for Cholesky decomposition on FPGAs by designing a single triangular linear equation solver. Good performance is achieved by reordering the computation of Cholesky factorization algorithms and thus alleviating the data dependency. The dedicated hardware architecture for solving triangular linear equations is designed and implemented for different accuracy requirements using customized precisions. Compared to the software on the Intel Xeon quad core microprocessor, our design achieves a speedup of 7~13.

High Performance Reconfigurable Computing for Cholesky Decomposition

The theory of Compressed Sensing (CS) is applied to Ultra-Wideband (UWB) positioning systems to obtain high resolution UWB pulses and achieve high performance. A Fast Orthogonal Matching Pursuit (FOMP) algorithm is proposed and embedded in the Time Difference Of Arrival (TDOA) algorithm for fast object positioning. Our pipelined FOMP TDOA algorithm outperforms the traditional serial OMP TDOA method. Simulation results have demonstrated that the CS-based UWB positioning system using the FOMP TDOA algorithm has the potential to achieve sub-mm positioning accuracy while still using very low sampling rate ADCs. Additionally, results are not sensitive to the tag location relative to base stations which is unavoidable drawback of geometrical dilution of accuracy in the sequential sampling method.

Compressive sensing TDOA for UWB positioning systems

In performance modeling of parallel synchronous iterative applications, the longest individual execution time among parallel processors determines the iteration time and often must be estimated for performance analysis. This involves the mean maximum calculation which has been a challenge in computer modeling for a long time. For large systems, numerical methods are not suitable because of heavy computation requirements and inaccuracy caused by rounding. On the other hand, previous approximation methods face challenges of accuracy and generality, especially for heterogeneous computing environments. This paper presents an interesting property of extreme values to enable Effective Mean Maximum Approximation (EMMA). Compared to previous mean maximum execution time approximation methods, this method is more accurate and general to different computational environments.

An Effective Execution Time Approximation Method for Parallel Computing

A Space-Time Turbo Bayesian Compressed Sensing (STTBCS) algorithm is proposed for Ultra-Wideband (UWB) systems in this paper. Based on the sparsity of UWB signals, the STTBCS algorithm provides an efficient approach for integrating spatial and temporal redundancies. A space-time structure is also designed for exploiting and transferring the spatial and temporal \emph{a priori} information for signal reconstructions in the framework of Bayesian Compressed Sensing (BCS). Simulation results using experimental UWB echo signals demonstrate that our STTBCS algorithm achieves good performance for UWB systems, compared with the traditional BCS and multitask BCS algorithms.

Space-Time Turbo Bayesian Compressed Sensing for UWB Systems

Dedicated hardware implementations of artificial neural networks promise to provide faster, lower-power operation when compared to software implementations executing on microprocessors, but rarely do these implementations have the flexibility to adapt and train online under dynamic conditions. A typical design process for artificial neural networks involves offline training using software simulations and synthesis and hardware implementation of the obtained network offline. This paper presents a design of block-based neural networks (BbNNs) on FPGAs capable of dynamic adaptation and online training. Specifically the network structure and the internal parameters, the two pieces of the multiparametric evolution of the BbNNs, can be adapted intrinsically, in-field under the control of the training algorithm. This ability enables deployment of the platform in dynamic environments, thereby significantly expanding the range of target applications, deployment lifetimes, and system reliability. The potential and functionality of the platform are demonstrated using several case studies.

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Gregory D. Peterson

Papers

High Performance Reconfigurable Computing for Cholesky Decomposition

Compressive sensing TDOA for UWB positioning systems

An Effective Execution Time Approximation Method for Parallel Computing

Space-Time Turbo Bayesian Compressed Sensing for UWB Systems

Evolvable block-based neural network design for applications in dynamic environments