With the number of fully sequenced genomes increasing steadily, there is greater interest in performing large-scale phylogenomic analyses from large numbers of individual gene families. Maximum likelihood (ML) has been shown repeatedly to be one of the most accurate methods for phylogenetic construction. Recently, there have been a number of algorithmic improvements in maximum-likelihood-based ...

The InterCondor system is an implementation of the concept of InterGrid. InterGrid is from the comparison of Internet and Grid. With the reference to the idea of Internet, which integrates different local networks into a global network with a certain protocol, InterGrid utilizes a set of Grid services to manage resources such as data, algorithms, and local Grid pools. In this paper we present t...

This paper present GC3Pie [7], a python library to ease the development of scalable and robust High Throughput data analysis tools. Most of the current distributed computing middlewares as well as most of the in-house grown scripts fall short in reaching the scaling and reliability factors required by the ever growing demand of large data analysis. GC3Pie provides mechanisms to automitise the e...

Teragrid resources are often used when high-performance computing is required. We describe our experiences in using Teragrid resources in a high-throughput manner, generating a significant number of CPU cycles over a long time span. In particular, we discuss using Teragrid resources as part of a larger computational grid to perform computations in an ongoing attempt to solve an open problem in ...

Conventional resource management systems use a system model to describe resources and a centralized scheduler to control their allocation. We argue that this paradigm does not adapt well to distributed systems, particularly those built to support high-throughput computing. Obstacles include heterogeneity of resources, which make uniform allocation algorithms difficult to formulate, and distribu...

High-performance and low-cost sensors are critical devices for high-throughput analyses of bio-samples in medical diagnoses and life sciences. In this paper, we demonstrate photonic crystal nanolaser sensor, which detects the adsorption of biomolecules from the lasing wavelength shift. It is a promising device, which balances a high sensitivity, high resolution, small size, easy integration, si...

Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively...

To realize the full potential of a high-performance computing system with a reconfigurable interconnect, there is a need to design algorithms for computing a topology that will allow for a high-throughput load distribution, while simultaneously partitioning the computational task graph of the application for the computed topology. In this paper, we propose a new framework that exploits such rec...

Many high performance computing applications require computing both sparse matrix-vector product (SMVP) and sparse matrix-transpose vector product (SMTVP) for better overall performance. Under such a circumstance, it is critical to maintain a similarly high throughput for these two computing patterns with the underlying sparse matrix encoded in a single storage format. The compressed sparse blo...

Cloud computing provides an elastic, as-a-Service resource abstraction with a usage-based payment model, and is emerging as an attracting computing paradigm. This is especially true for computing intensive application workflows with high-throughput requirements, such as those involving large-scale image datasets. In this paper, we investigate the usage of cloud computing to support a medical im...