979117
The software architecture of a distributed problem-solving environment
This paper describes the functionality and software architecture of a generic problem-solving environment (PSE) for collaborative computational science and engineering. A PSE is designed to provide transparent access to heterogeneous distributed computing resources, and is intended to enhance research productivity by making it easier to construct, run, and analyze the results of computer simulations. Although implementation details are not discussed in depth, the role of software technologies such as CORBA, Java, and XML is outlined. An XML-based component model is presented. The main features of a Visual Component Composition Environment for software development, and an Intelligent Resource Management System for scheduling components, are described. Some prototype implementations of PSE applications are also presented. Copyright 2000 John Wiley & Sons, Ltd.
7274224
Wrapping MPI-based legacy codes as Java/CORBA components
Abstract Techniques for wrapping an MPI-based molecular dynamics (MD) simulation code as Java/CORBA components, for use within a distributed component based problem solving environment (CB-PSE), is presented. A legacy code for simulating a Lennard–Jones fluid is first wrapped as a single CORBA object, followed by division of the code into computational sub-units, where each sub-unit is wrapped as a CORBA object containing MPI calls, and run on a cluster of workstations — enabling different MPI implementations to inter-operate. Using a Java implementation, users can submit simulation tasks through a Web based interface, without needing to know implementation details of the legacy code, or the exact interaction between sub-units within the code. We provide performance comparisons of wrapping the entire MD code as a single object versus wrapping sub-units within it, and offer a simple performance model to explain our findings.
45224109
Service Matchmaking and Discovery with Rough Sets
The past few years have seen the Grid is evolving as a service-oriented computing infrastructure. It is foreseen that various resources in a Grid environment will be exposed as services for use by a wider user community. Service discovery becomes an issue of vital importance for utilising Grid facilities. This paper presents Rosse, a Rough Sets based Search Engine for service discovery that can deal with uncertainty of service properties when matching service advertisements with service requests. The evaluation results show that Rosse is more effective in service discovery compared with other mechanisms such as UDDI keyword matching and OWL-S matchmaking.
1974621
Engineering high-performance legacy codes as CORBA components for problem-solving environments
This paper describes techniques used to leverage high-performance legacy codes as CORBA components to a distributed problem-solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high-performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element-based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high-performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user's desktop computing environment can be extended to a high-performance computing environment using a cluster of workstations or a parallel computer.
5393650
PaDDMAS: parallel and distributed data mining application suite
Discovering complex associations, anomalies and patterns in distributed data sets is gaining popularity in a range of scientific, medical and business applications. Various algorithms are employed to perform data analysis within a domain, and range from statistical to machine learning and AI based techniques. Several issues need to be addressed however to scale such approaches to large data sets, particularly when these are applied to data distributed at various sites. As new analysis techniques are identified, the core tool set must enable easy integration of such analytical components. Similarly, results from an analysis engines must be sharable, to enable storage, visualisation or further analysis of results. We describe the architecture of PaDDMAS, a component based system for developing distributed data mining applications. PaDDMAS provides a tool set for combining pre-developed or custom components using a dataflow approach, with components performing analysis, data extraction or data management and translation. Each component is wrapped as a Java/CORBA object, and has an interface defined in XML. Components can be serial or parallel objects, and may be binary or contain a more complex internal structure. We demonstrate a prototype using a neural network analysis algorithm.
14345064
A Wrapper Generator for Wrapping High Performance Legacy Codes as Java/CORBA Components
This paper describes a Wrapper Generator for wrapping high performance legacy codes as Java/CORBA components for use in a distributed component-based problem- solving environment. Using the Wrapper Generator we ave automatically wrapped an MPI-based legacycode as a single CORBA object, and implemented a problem- solving environment for molecular dynamic simulations. Performance comparisons between runs of the CORBA object and the original legacy code on a cluster of workstations and on a parallel computer are also presented.
17270817
Grid Computing in China
Abstract
Grid computing presents a new trend to distributed computation and Internet applications, which can construct a virtual single image of heterogeneous resources, provide uniform application interface and integrate widespread computational resources into super, ubiquitous and transparent aggregation. In the adoption of Grid computing, China, who is facing more resource heterogeneity and other specific demands, has put much effort on both research and practical utilization. In this paper, we introduce the major China Grid research projects and their perspective applications. First we give the overview of the four government-sponsored programs in Grid, namely the China National Grid, ChinaGrid, NSFC Grid, and ShanghaiGrid. Then we present six representative ongoing Grid systems in details, which are categorized into Grid middleware and Grid application. This paper provides the general picture of Grid computing in China, and shows the great efforts, devotion and confidence in China to use Grid technology to boost the society, economics and scientific research.

7887955
PatternHunter: faster and more sensitive homology search
MOTIVATION
Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation.


RESULTS
We present a new homology search algorithm 'PatternHunter' that uses a novel seed model for increased sensitivity and new hit-processing techniques for significantly increased speed. At Blast levels of sensitivity, PatternHunter is able to find homologies between sequences as large as human chromosomes, in mere hours on a desktop.


AVAILABILITY
PatternHunter is available at http://www.bioinformaticssolutions.com, as a commercial package. It runs on all platforms that support Java. PatternHunter technology is being patented; commercial use requires a license from BSI, while non-commercial use will be free.
14969576
Semi-Supervised Regression with Co-Training
In many practical machine learning and data mining applications, unlabeled training examples are readily available but labeled ones are fairly expensive to obtain. Therefore, semi-supervised learning algorithms such as co-training have attracted much attention. Previous research mainly focuses on semi-supervised classification. In this paper, a co-training style semi-supervised regression algorithm, i.e. COREG, is proposed. This algorithm uses two k-nearest neighbor regressors with different distance metrics, each of which labels the unlabeled data for the other regressor where the labeling confidence is estimated through consulting the influence of the labeling of unlabeled examples on the labeled ones. Experiments show that COREG can effectively exploit unlabeled data to improve regression estimates.
879315
Kolmogorov Random Graphs and the Incompressibility Method
We investigate topological, combinatorial, statistical, and enumeration properties of finite graphs with high Kolmogorov complexity (almost all graphs) using the novel incompressibility method. Example results are (i) the mean and variance of the number of (possibly overlapping) ordered labeled subgraphs of a labeled graph as a function of its randomness deficiency (how far it falls short of the maximum possible Kolmogorov complexity) and (ii) a new elementary proof for the number of unlabeled graphs.
17266656
General Consistency Management Within the Development of Ontology-Driven Web Information System
This paper proposes a general consistency management methodology within ontology-driven WIS development. The contributions of this paper are follows: 1) introduces the concept structures for representing model ontologies, mappings ontology and their instances. These ontologies and their instances greatly enhance the representation and reasoning capabilities of mapping and also simplify the manipulation 2) Defines and implements a series of general operators to manipulate mapping and model ontologies. 3) Formalizes the consistency management problem and gives an algorithm basing on general operators. 4) Implements a prototype and integrates it with WISE.