We developed Tilescope, a fully integrated data processing pipeline for analyzing high-density tilingarray data http://tilescope.gersteinlab.org. In a completely automated fashion, Tilescope will normalize signals between channels and across arrays, combine replicate experiments, score each array element, and identify genomic features. The program is designed with a modular, three-tiered archit...

It is crucial to explore the chemical and biological space covered by patent documents. In order to recognize chemical and biological entities, a recognition system is developed on the basis of open-source machine learning and natural language processing (NLP) toolkits. The system processing pipeline consists of three major components: pre-processing (sentence detection, tokenization), recognit...

In this paper, the impact of demosaicing on gradient extraction is studied and a gradient-based feature pipeline based raw Bayer pattern images proposed. It shown both theoretically experimentally that are applicable to central difference algorithms with negligible performance degradation, as long arrangement color filter array (CFA) patterns matches operators. The constancy assumption, which w...

Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that...

The finite element method (FEM) is a widely employed numerical technique for approximating the solution of partial differential equations (PDEs) in various science and engineering applications. Many of these applications benefit from fast execution of the FEM pipeline. One way to accelerate the FEM pipeline is by exploiting advances in modern computational hardware, such as the many-core stream...

A three-dimensional (3-D) shape measurement system that can simultaneously achieve 3-D shape acquisition, reconstruction, and display at 30 frames per second (fps) with 480,000 measurement points per frame is presented. The entire processing pipeline was realized on a graphics processing unit (GPU) without the need of substantial central processing unit (CPU) power, making it achievable on a po...

Horizontal auger boring (HAB) is a widely used trenchless technology for the high-accuracy installation of gravity or pressure pipelines on line and grade. Differing from other pipeline installations, HAB requires a more precise and automated guidance system for use in a practical project. This paper proposes an economic and enhanced automated optical guidance system, based on optimization rese...

We have developed PGPG (Pipeline Generator for Programmable GRAPE), a software which generates the low-level design of the pipeline processor and communication software for FPGA-based computing engines (FBCEs). An FBCE typically consists of one or multiple FPGA (Field-Programmable Gate Array) chips and local memory. Here, the term “Field-Programmable” means that one can rewrite the logic implem...

This paper presents a clocking pipeline technique referred to as a single-pulse pipeline (PP-Pipeline) and applies it to the problem of mapping pipelined circuits to a Field Programmable Gate Array (FPGA). A PP-pipeline replicates the operation of asynchronous micropipelined control mechanisms using synchronous-orientated logic resources commonly found in FPGA devices. Consequently, circuits wi...

Within the last decade the high costs and complexity of Next Generation Sequencing (NGS) data organization put pressure on NGS data centres to organize convenient IT service infrastructures for automatic data management, processing and analyses. Our market analysis showed that existing applications processing NGS data were insufficiently documented, not extensible or strongly dependent on the u...