Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum

H2O: An Autonomic, Resource-Aware Distributed Database System

This paper presents the design of an autonomic, resource-aware distributed database which enables data to be backed up and shared without complex manual administration. The database, H2O, is designed to make use of unused resources on workstation machines. Creating and maintaining highly-available, replicated database systems can be difficult for untrained users, and costly for IT departments. H2O reduces the need for manual administration by autonomically replicating data and load-balancing across machines in an enterprise. Provisioning hardware to run a database system can be unnecessarily costly as most organizations already possess large quantities of idle resources in workstation machines. H2O is designed to utilize this unused capacity by using resource availability information to place data and plan queries over workstation machines that are already being used for other tasks. This paper discusses the requirements for such a system and presents the design and implementation of H2O.Comment: Presented at SICSA PhD Conference 2010 (http://www.sicsaconf.org/

A Survey of Parallel Data Mining

With the fast, continuous increase in the number and size of databases, parallel data mining is a natural and cost-effective approach to tackle the problem of scalability in data mining. Recently there has been a considerable research on parallel data mining. However, most projects focus on the parallelization of a single kind of data mining algorithm/paradigm. This paper surveys parallel data mining with a broader perspective. More precisely, we discuss the parallelization of data mining algorithms of four knowledge discovery paradigms, namely rule induction, instance-based learning, genetic algorithms and neural networks. Using the lessons learned from this discussion, we also derive a set of heuristic principles for designing efficient parallel data mining algorithms

Distributed Object Medical Imaging Model

Abstract- Digital medical informatics and images are commonly used in hospitals today,. Because of the interrelatedness of the radiology department and other departments, especially the intensive care unit and emergency department, the transmission and sharing of medical images has become a critical issue. Our research group has developed a Java-based Distributed Object Medical Imaging Model(DOMIM) to facilitate the rapid development and deployment of medical imaging applications in a distributed environment that can be shared and used by related departments and mobile physiciansDOMIM is a unique suite of multimedia telemedicine applications developed for the use by medical related organizations. The applications support realtime patients’ data, image files, audio and video diagnosis annotation exchanges. The DOMIM enables joint collaboration between radiologists and physicians while they are at distant geographical locations. The DOMIM environment consists of heterogeneous, autonomous, and legacy resources. The Common Object Request Broker Architecture (CORBA), Java Database Connectivity (JDBC), and Java language provide the capability to combine the DOMIM resources into an integrated, interoperable, and scalable system. The underneath technology, including IDL ORB, Event Service, IIOP JDBC/ODBC, legacy system wrapping and Java implementation are explored. This paper explores a distributed collaborative CORBA/JDBC based framework that will enhance medical information management requirements and development. It encompasses a new paradigm for the delivery of health services that requires process reengineering, cultural changes, as well as organizational changes

UTILISING NETWORKED WORKSTATIONS TO ACCELERATE DATABASE QUERIES

The rapid growth in the size of databases and the advances made in Query Languages has resulted in increased SQL query complexity submitted by users, which in turn slows down the speed of information retrieval from the database. The future of high performance database systems lies in parallelism. Commercial vendors´ database systems have introduced solutions but these have proved to be extremely expensive. This paper investagetes how networked resources such as workstations can be utilised by using Parallel Virtual Machine (PVM) to Optimise Database Query Execution. An investigation and experiments of the scalability of the PVM are conducted. PVM is used to implement palallelism in two separate ways: (i) Removes the work load for deriving and maintaining rules from the data server for Semantic Query Optimisation, therefore clears the way for more widespread use of SQO in databases [16], [5]. (ii) Answers users queries by a proposed Parallel Query Algorithm PQA which works over a network of workstations, coupled with a sequential Database Management System DBMS called PostgreSql on the prototype called Expandable Server Architecture ESA [11], [12], [21], [13]. Experiments have been conducted to tackle the problems of Parallel and Distributed systems such as task scheduling, load balance and fault tolerance