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At least 973 records · Page 54

Modular HPC I/O characterization with Darshan

Contemporary high-performance computing (HPC) applications encompass a broad range of distinct I/O strategies and are often executed on a number of different compute platforms in their lifetime. These large-scale HPC platforms employ increasingly complex I/O subsystems to provide a suitable level of I/O performance to applications. Tuning I/O workloads for such a system is nontrivial, and the results generally are not portable to other HPC systems. I/O profiling tools can help to address this challenge, but most existing tools only instrument specific components within the I/O subsystem that provide a limited perspective on I/O performance. The increasing diversity of scientific applications and computing platforms calls for greater flexibililty and scope in I/O characterization.

Snyder, Shane↗

Modular Semantic Tagging of Medline Abstracts and its Use in Inferring Regulatory Networks

We describe MedstractPlus, a resource for mining relations from the Medline bibliographic database that is currently under construction. It was built on the remains of Medstract, a previously created resource that included a biorelation server and an acronym database. MedstractPlus uses simple and scalable natural language processing modules to structure text, is designed with reusability and extendibility in mind, and adheres to the philosophy of the Linguistic Annotation Framework. We show how MedstractPlus has been used to provide seeds for a novel approach to inferring transcriptional regulatory networks from gene expression data.

59 BASIC BIOLOGICAL SCIENCES↗

Modular Spiking Neural Circuits for Mapping Long Short-Term Memory on a Neurosynaptic Processor

Due to the distributed and asynchronous nature of neural computation through low-energy spikes, brain-inspired hardware systems offer high energy efficiency and massive parallelism. One such platform is the IBM TrueNorth neurosynaptic system. Recently, TrueNorth compatible representation learning algorithms have emerged, achieving close to the state-of-the-art performance in various data sets. However, its application in temporal sequence processing models, such as recurrent neural networks (RNNs), is still only at the proof of concept level. There is an inherent difficulty in capturing temporal dynamics of an RNN using spiking neurons, which is only exasperated by the hardware constraints in connectivity and synaptic weight resolution. This paper presents a design flow that overcomes these difficulties and maps a special case of recurrent networks called long short-term memory (LSTM) onto a spike-based platform. The framework utilizes various approximation techniques, such as activation discretization, weight quantization, and scaling and rounding, spiking neural circuits that implement the complex gating mechanisms, and a store-and-release technique to enable neuron synchronization and faithful storage. While the presented techniques can be applied to map LSTM to any spiking neural network (SNN) simulator/emulator, here we choose the TrueNorth chip as the target platform by adhering to its hardware constraints. Three LSTM applications, parity check, extended Reber grammar, and question classification, are evaluated. The tradeoffs among accuracy, performance, and energy tradeoffs achieved on TrueNorth are demonstrated. Finally, this is compared with the performance on an SNN platform without hardware constraints, which represents the upper bound of the achievable accuracy.

97 MATHEMATICS AND COMPUTING↗

PhytoPET: Design and initial results of modular PET for plant biology

We have developed a positron emission tomography (PET) system designed specifically for plant imaging in Phytotron at Duke University. Initial evaluation of a PhytoPET system to image the biodistribution of the positron emitting tracer {sup 11}C in live plants is presented. The mechanical arrangement of the detectors is designed to accommodate the unpredictable and random distribution in space of the plant parts such as stems, leaves, and roots. Prototyping such a system requires a completely new PET system design strategy different from preclinical and clinical applications. This PhytoPET design allows flexible arrangements of PET detectors based on individual standalone detector modules built from single 5 cm × 5 cm Hamamatsu H8500 position sensitive photomultiplier tubes. Each H8500 is coupled to a L YSO:Ce scintillator array composed of 48 × 48 elements that are 10 mm thick with a 1 mm pitch. Initial results provide planar PET images from two different arrangements (1 × 4 or 2 × 2) for flexible imaging capability.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Development of Packaging and Modular Control of Thermoelectric Clothes Dryer, With Performance Evaluation

This paper provides an overview of a thermoelectric heat pump clothes dryer which was developed with the aim of reducing the significant primary energy consumption attributed to residential electric clothes drying in the United States (623 TBtu/yr). The use of thermoelectric modules in place of the conventional electric resistance heater resulted in a 40% reduction in the energy consumption of the system, compared to the minimum energy efficiency standard. This was achieved for the first time for a standard test load of 8.45 lb, using a clothes dryer prototype with a thermoelectric heat pump module as the sole heating mechanism. The current experimental prototype was developed after extensive modeling, system design and control optimization, and experimental system-level evaluation of control parameters. The demonstration of improved energy consumption has laid the foundation for future development of this technology.

Patel, Viral↗

BioBits™ Explorer: A modular synthetic biology education kit

Hands-on demonstrations greatly enhance the teaching of science, technology, engineering, and mathematics (STEM) concepts and foster engagement and exploration in the sciences. While numerous chemistry and physics classroom demonstrations exist, few biology demonstrations are practical and accessible due to the challenges and concerns of growing living cells in classrooms. We introduce BioBits™ Explorer, a synthetic biology educational kit based on shelf-stable, freeze-dried, cell-free (FD-CF) reactions, which are activated by simply adding water. The FD-CF reactions engage the senses of sight, smell, and touch with outputs that produce fluorescence, fragrances, and hydrogels, respectively. We introduce components that can teach tunable protein expression, enzymatic reactions, biomaterial formation, and biosensors using RNA switches, some of which represent original FD-CF outputs that expand the toolbox of cell-free synthetic biology. The BioBits™ Explorer kit enables hands-on demonstrations of cutting-edge science that are inexpensive and easy to use, circumventing many current barriers for implementing exploratory biology experiments in classrooms.

59 BASIC BIOLOGICAL SCIENCES↗

Submicrosecond linear pulse transformer for 800 kV voltage with modular low-inductance primary power supply

A pulsed power source with voltage amplitude up to 800 kV for fast charging (350–400 ns) of the forming line of a high-current nanosecond accelerator is developed. The source includes capacitive energy storage and a linear pulse transformer. The linear transformer consists of a set of 20 inductors with circular ferromagnetic cores surrounded by primary windings inside of which a common stock adder of voltage with film-glycerol insulation is placed. The primary energy storage consists of ten modules, each of which is a low-inductance assembly of two capacitors with a capacitance of 0.35 μF and one gas switch mounted in the same frame. The total energy stored in capacitors is 5.5 kJ at the operating voltage of 40 kV. According to test results, the parameters of the equivalent circuit of the source are the following: shock capacitance = 17.5 nF, inductance = 2 μH, resistance = 3.2 Ω.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗