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.
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.
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.
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.
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.
16993770
Service matchmaking with rough sets
With the wide adoption of open grid services architecture (OGSA) and Web services resource framework (WSRF), the grid is emerging as a service-oriented computing infrastructure for engineers and scientists to solve data and computationally intensive problems. It is envisioned that computing resources in a future grid environment will be exposed as services. Service discovery becomes an issue of vital importance for a wider uptake of the grid. This paper presents RSSM, a rough sets based service matchmaking algorithm for service discovery with an aim to tolerate uncertainty in identifying service properties. The evaluation results show that the RSSM algorithm is more effective in service discovery compared with other mechanisms such as UDDI and OWLS.
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.
53306617
Human-Machine Collaborative Systems for Microsurgical Applications
Human-machine collaborative systems (HMCSs) are systems that amplify or assist human capabilities during the performance of tasks that require both human judgment and robotic precision. We examine the design and performance of HMCSs in the context of microsurgical procedures such as vitreo-retinal eye surgery. Three specific problems considered are: (1) development of systems tools for describing and implementing HMCSs, (2) segmentation of complex tasks into logical components given sensor traces of human task execution, and (3) measurement and evaluation of HMCS performance. These components can be integrated into a complete workstation with the ability to automatically “parse” traces of user activities into task models, which are loaded into an execution environment to provide the user with assistance using on-line recognition of task states. The major contributions of this work include an XML task graph modeling framework and execution engine, an algorithm for real-time segmentation of user actions using continuous hidden Markov models, and validation techniques for analyzing the performance of HMCSs.
1076701
Integrated Intermediate Waveband and Wavelength Switching for Optical WDM Mesh Networks
As wavelength-division multiplexing (WDM) evolves towards practical applications in optical transport networks, waveband switching (WBS) has been introduced to cut down the operational costs and to reduce the complexities and sizes of network components, e.g., optical cross-connects (OXCs). This paper considers the routing, wavelength assignment and waveband assignment (RWWBA) problem in a WDM network supporting mixed waveband and wavelength switching. First, the techniques supporting waveband switching are studied, where a node architecture enabling mixed waveband and wavelength switching is proposed. Second, to solve the RWWBA problem with reduced switching costs and improved network throughput, the cost savings and call blocking probabilities along intermedi- ate waveband-routes are analyzed. Our analysis reveals some important insights about the cost savings and call blocking probability in relation to the fiber capacity, the candidate path, and the traffic load. Third, based on our analysis, an online integrated intermediate WBS algorithm (IIWBS) is proposed. IIWBS determines the waveband switching route for a call along its candidate path according to the node connectivity, the link utilization, and the path length information. In addition, the IIWBS algorithm is adaptive to real network applications under dynamic traffic requests. Finally, our simulation results show that IIWBS outperforms a previous intermediate WBS algorithm and RWA algorithms in terms of network throughput and cost efficiency.
3204350
A New Approach to Formal Language Theory by Kolmogorov Complexity
We present a new approach to formal language theory using Kolmogorov complexity. The main results presented here are an alternative for pumping lemma(s), a new characterization for regular languages, and a new method to separate deterministic context-free languages and nondeterministic context-free languages. The use of the new "incompressibility arguments" is illustrated by many examples. The approach is also successful at the high end of the Chomsky hierarchy since one can quantify nonrecursiveness in terms of Kolmogorov complexity.
54297489
Iso-Map: Energy-Efficient Contour Mapping in Wireless Sensor Networks
Contour mapping is a crucial part of many wireless sensor network applications. Many efforts have been made to avoid collecting data from all the sensors in the network and producing maps at the sink, which is proven to be inefficient. The existing approaches (often aggregation based), however, suffer from heavy transmission traffic and incur large computational overheads on each sensor node. We propose Iso-Map, an energy-efficient protocol for contour mapping, which builds contour maps based solely on the reports collected from intelligently selected ?isoline nodes? in wireless sensor networks. Iso-Map achieves high-quality contour mapping while significantly reducing the generated traffic from O(n) to O(?n), where n is the total number of sensor nodes in the field. The pernode computation overhead is also restrained as a constant. We conduct comprehensive trace-driven simulations to verify this protocol, and demonstrate that Iso-Map outperforms the previous approaches in the sense that it produces contour maps of high fidelity with significantly reduced energy cost.