Cactus Tools for Grid Applications

Cactus is an open source problem solving environment designed for scientists and engineers. Its modular structure facilitates parallel computation across different architectures and collaborative code development between different groups. The Cactus Code originated in the academic research community, where it has been developed and used over many years by a large international collaboration of physicists and computational scientists. We discuss here how the intensive computing requirements of physics applications now using the Cactus Code encourage the use of distributed and metacomputing, and detail how its design makes it an ideal application test-bed for Grid computing. We describe the development of tools, and the experiments which have already been performed in a Grid environment with Cactus, including distributed simulations, remote monitoring and steering, and data handling and visualization. Finally, we discuss how Grid portals, such as those already developed for Cactus, will open the door to global computing resources for scientific users.     

Separation of cellular nonpolar neutral lipids by normal-phase chromatography and analysis by electrospray ionization mass spectrometry

Neutral lipids are an important class of hydrophobic compounds found in all cells that play critical roles from energy storage to signal transduction. Several distinct structural families make up this class, and within each family there are numbers of individual molecular species. A solvent extraction protocol has been developed to efficiently isolate neutral lipids without complete extraction of more polar phospholipids. Normal-phase HPLC was used for the separation of cholesteryl esters (CEs), monoalkylether diacylglycerols, triacylglycerols, and diacylglycerols in a single HPLC run from this extract. Furthermore, minor lipids such as ubiquinone-9 could be detected in RAW 264.7 cells. Molecular species that make up each neutral lipid class can be analyzed both qualitatively and quantitatively by on-line LC-MS and LC-MS/MS strategies. The quantitation of >20 CE molecular species revealed that challenging RAW 264.7 cells with a Toll-like receptor 4 agonist caused a >20-fold increase in the content of CEs within cells, particularly those CE molecular species that contained saturated (14:0, 16:0, and 18:1) fatty acyl groups. Longer chain CE molecular species did not change in response to the activation of these cells.     

The next meta-challenge for Bioinformatics

The direct sequencing of uncultivable organisms present in complex biological and environmental samples has opportunities to discover new life forms and metabolic processes. This transformational field, known as metagenomics, is generating massive amounts of molecular information that can overwhelm the performance of conventional analysis and visualization algorithms. Here, I briefly highlight some of the emerging challenges this new discipline presents to the computational biology community and point some of the opportunities to develop applications that can translate metagenomic information into biomedical, agricultural, environmental, and industrial applications.     

多维背包问题的DNA计算

提出了一种基于DNA计算的求解多维背包问题的算法,该算法分两个阶段执行,第一个阶段采用试管方法,分别求出满足各个约束方程的可行域;第二个阶段采用表面方法,对第一个阶段求出的多个可行域取交集,即得满足整个约束方程组的可行域,再比较该可行域中各可行解对应的目标函数值,进而得到最优解。并通过实例分析验证了该算法的有效性和正确性,该算法将试管方法和表面方法结合使用,充分利用了两种方法各自的优点。     

A Distributed Multi-Storage Resource Architecture and I/O Performance Prediction for Scientific Computing

I/O intensive applications have posed great challenges to computational scientists. A major problem of these applications is that users have to sacrifice performance requirements in order to satisfy storage capacity requirements in a conventional computing environment. Further performance improvement is impeded by the physical nature of these storage media even when state-of-the-art I/O optimizations are employed.In this paper, we present a distributed multi-storage resource architecture, which can satisfy both performance and capacity requirements by employing multiple storage resources. Compared to a traditional single storage resource architecture, our architecture provides a more flexible and reliable computing environment. This architecture can bring new opportunities for high performance computing as well as inherit state-of-the-art I/O optimization approaches that have already been developed. It provides application users with high-performance storage access even when they do not have the availability of a single large local storage archive at their disposal. We also develop an Application Programming Interface (API) that provides transparent management and access to various storage resources in our computing environment. Since I/O usually dominates the performance in I/O intensive applications, we establish an I/O performance prediction mechanism which consists of a performance database and a prediction algorithm to help users better evaluate and schedule their applications. A tool is also developed to help users automatically generate performance data stored in databases. The experiments show that our multi-storage resource architecture is a promising platform for high performance distributed computing.     

File and Object Replication in Data Grids

Data replication is a key issue in a Data Grid and can be managed in different ways and at different levels of granularity: for example, at the file level or object level. In the High Energy Physics community, Data Grids are being developed to support the distributed analysis of experimental data. We have produced a prototype data replication tool, the Grid Data Mirroring Package (GDMP) that is in production use in one physics experiment, with middleware provided by the Globus Toolkit used for authentication, data movement, and other purposes. We present here a new, enhanced GDMP architecture and prototype implementation that uses Globus Data Grid tools for efficient file replication. We also explain how this architecture can address object replication issues in an object-oriented database management system. File transfer over wide-area networks requires specific performance tuning in order to gain optimal data transfer rates. We present performance results obtained with GridFTP, an enhanced version of FTP, and discuss tuning parameters.     

CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing

Estimating taxonomic content constitutes a key problem in metagenomic sequencing data analysis. However, extracting such content from high-throughput data of next-generation sequencing is very time-consuming with the currently available software. Here, we present CloudLCA, a parallel LCA algorithm that significantly improves the efficiency of determining taxonomic composition in metagenomic data analysis. Results show that CloudLCA (1) has a running time nearly linear with the increase of dataset magnitude, (2) displays linear speedup as the number of processors grows, especially for large datasets, and (3) reaches a speed of nearly 215 million reads each minute on a cluster with ten thin nodes. In comparison with MEGAN, a well-known metagenome analyzer, the speed of CloudLCA is up to 5 more times faster, and its peak memory usage is approximately 18.5% that of MEGAN, running on a fat node. CloudLCA can be run on one multiprocessor node or a cluster. It is expected to be part of MEGAN to accelerate analyzing reads, with the same output generated as MEGAN, which can be import into MEGAN in a direct way to finish the following analysis. Moreover, CloudLCA is a universal solution for finding the lowest common ancestor, and it can be applied in other fields requiring an LCA algorithm.     

An HPLC-CAD/fluorescence lipidomics platform using fluorescent fatty acids as metabolic tracers

Fluorescent lipids are important tools for live imaging in cell culture and animal models, yet their metabolism has not been well-characterized. Here we describe a novel combined HPLC and LC-MS/MS method developed to characterize both total lipid profiles and the products of fluorescently labeled lipids. Using this approach, we found that lipids labeled with the fluorescent tags, 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene (BODIPY FL), 4,4-difluoro-5-(2-thienyl)-4-bora-3a,4a-diaza-s-indacene [BODIPY(558/568)], and dipyrrometheneboron difluoride undecanoic acid (TopFluor) are all metabolized into varying arrays of polar and nonpolar fluorescent lipid products when they are fed to larval zebrafish. Quantitative metabolic labeling experiments performed in this system revealed significant effects of total dietary lipid composition on fluorescent lipid partitioning. We provide evidence that cholesterol metabolism in the intestine is important in determining the metabolic fates of dietary FAs. Using this method, we found that inhibitors of dietary cholesterol absorption and esterification both decreased incorporation of dietary fluorescent FAs into cholesterol esters (CEs), suggesting that CE synthesis in enterocytes is primarily responsive to the availability of dietary cholesterol. These results are the first to comprehensively characterize fluorescent FA metabolism and to demonstrate their utility as metabolic labeling reagents, effectively coupling quantitative biochemistry with live imaging studies.     

Structure-activity relationship study of β-oxidation resistant indole-based 5-oxo-6,8,11,14-eicosatetraenoic acid (5-oxo-ETE) receptor antagonists

5-Oxo-6,8,11,14-eicosatetraenoic acid (5-oxo-ETE) is formed from 5S-hydroxy-6,8,11,14-eicosatetraenoic acid (5-HETE) by the 5-lipoxygenase (5-LO) pathway under conditions associated with oxidative stress. 5-Oxo-ETE is an important pro-inflammatory mediator, which stimulates the migration of eosinophils via a selective G-protein coupled receptor, known as the OXE receptor (OXE-R). Previously, we designed and synthesized structural mimics of 5-oxo-ETE such as 1 using an indole scaffold. In the present work, we added various substituents at C-3 of this moiety to block potential β-oxidation of the 5-oxo-valerate side chain, and investigated the structure-activity relationships of the resulting novel β-oxidation-resistant antagonists. Cyclopropyl and cyclobutyl substituents were well tolerated in this position, but were less potent as the highly active 3S-methyl compound. It seems likely that 3-alkyl substituents can affect the conformation of the 5-oxovalerate side chain containing the critical keto and carboxyl groups, thereby affecting interaction with the OXE-receptor.