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NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions,(More)
The Technical Note series provides an outlet for a variety of NCAR manuscripts that contribute in specialized ways to the body of scientific knowledge but which are not suitable for journal, monograph, or book publication. Reports in this series are issued by the NCAR Scientific Divisions ; copies may be obtained on request from the Publications Office of(More)
The Technical Note series provides an outlet for a variety of NCAR manuscripts that contribute in specialized ways to the body of scientific knowledge but which are not suitable for journal, monograph, or book publication. Reports in this series are issued by the NCAR Scientific Divisions ; copies may be obtained on request from the Publications Office of(More)
<i>Map-matching</i> is the process of aligning a sequence of observed user positions with the road network on a digital map. It is a fundamental pre-processing step for many applications, such as moving object management, traffic flow analysis, and driving directions. In practice there exists huge amount of low-sampling-rate (e.g., one point every 2--5(More)
Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer(More)
A survey of the dog genome sequence (6.22 million sequence reads; 1.5x coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. More than 650 million base pairs (>25%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for(More)
In this paper, we propose a new computational model for visual saliency derived from the information maximization principle. The model is inspired by a few well acknowledged biological facts. To compute the saliency spots of an image, the model first extracts a number of sub-band feature maps using learned sparse codes. It adopts a fully-connected graph(More)
The complete genome sequence of Geobacillus thermodenitrificans NG80-2, a thermophilic bacillus isolated from a deep oil reservoir in Northern China, consists of a 3,550,319-bp chromosome and a 57,693-bp plasmid. The genome reveals that NG80-2 is well equipped for adaptation into a wide variety of environmental niches, including oil reservoirs, by(More)
Neural Machine Translation (NMT) is an end-to-end learning approach for automated translation, with the potential to overcome many of the weaknesses of conventional phrase-based translation systems. Unfortunately, NMT systems are known to be computationally expensive both in training and in translation inference – sometimes prohibitively so in the case of(More)
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative(More)