22168621
BLAST++ : A Tool for BLASTing Queries in Batches
BLAST is the standard tool that molecular biologists use to search for sequence similarity in genomic (and protein) databases. It employs a brute force approach of comparing a query sequence against every database sequence - for each pair of the sequences to be matched, BLAST searches for short fixed-length word pairs (seeds) in the sequences and then extends them to higher-scoring regions. To search multiple queries, the basic approach is to run BLAST on each of the queries one at a time. This is clearly inefficient and fails to exploit common subsequences that the collection of queries may share. In this paper, we propose a new genome search tool, BLAST++, that allows multiple, say K, queries to be searched against a database concurrently. The design of BLAST++ is based on our observation that the seed searching step of BLAST is a bottleneck that consumes more than 80% of the total response time! BLAST++ essentially treats a collection of queries as a single virtual query so that the seed searching step needs to be performed only once for common subsequences. We implemented BLAST++ as an extension of the NCBI BLAST, and evaluated its performance. Our study shows that the results obtained by BLAST++ are identical to that obtained by executing BLAST on each of the K queries, but the single-process version of BLAST++ completes the processing in a much shorter time, about only 25% of the original single-process version of NCBI BLAST.
20063786
Implementation of a graphics design framework on the Web
We propose a client-server graphics design framework and implement a room design system using CORBA. We have integrated technologies used in distributed computation (Java and CORBA) and computer graphics (VRML). To support multiuser collaborative design, we propose a supplier-consumer communication approach and implement it using the event service in CORBA. Our system can be applied in electronic commerce to improve the existing systems by allowing customers to select furniture and to visualize the whole furnished room in 3D.
16399618
Fast filter-and-refine algorithms for subsequence selection
Large sequence databases, such as protein, DNA and gene sequences in biology, are becoming increasingly common. An important operation on a sequence database is approximate subsequence matching, where all subsequences that are within some distance from a given query string are retrieved. This paper proposes a filter-and-refine algorithm that enables efficient approximate subsequence matching in large DNA sequence databases. It employs a bitmap indexing structure to condense and encode each data sequence into a shorter index sequence. During query processing, the bitmap index is used to filter out most of the irrelevant subsequences, and false positives are removed in the final refinement step. Analytical and experimental studies show that the proposed strategy is capable of reducing response time substantially while incurring only a small space overhead.
16268564
FreeRank: implementing independent ranking service for multiplayer online games
Ranking is necessary for multiplayer online games to provide players with self-complacence and reference for choosing game counterparts. Most existing ranking solutions are tightly coupled with game applications of client-server architectures. In this paper, a novel scheme named FreeRank is proposed as a ranking service independent to specific architecture and detailed implementation of each individual game application. Based on a certificate-based framework and a reputation-based score-computing algorithm. FreeRank resolves the challenge of cheating prevention. Preliminary analysis and simulation results show that FreeRank is feasible and effective.
10926021
Agora: Grid Community in Vega Grid
In grid environment, how to organize, discover and use grid resources is one of the basic research problems. In this paper, we introduce a new concept called agora, which refers grid community in our Vega grid project. We propose a principle on agora as one of the basic design principles of Vega grid, which is the community principle. We give a detailed definition of the agora as a 4-tuple(S, O, C, P), representing the set of Subject, Object, Context, and Policy respectively. Our research methodology is comparative studies, drawing an analog between the grid and other platform systems such as OS, CPU, and MPI. We also study some properties about the agora, for example, grid law of inertia. This agora approach could be used to unify the grid invariability and dynamic variability effectively, develop the appropriate technology to support the dynamic and open properties of the grid, and deal with the complexity in the grid more efficiently.
14490221
Exploiting Request Characteristics to Improve Performance of Web Services Based Business Applications
Web Services and workflow have been widely adopted in building complicated business systems. In these systems, high security concern is claimed. But frequent authentication and computing-intensive encoding and decoding operation bring extra workload to the systems and greatly impact the performance of Web Services and workflow engine, especially under heavy load. In this paper, we propose Requests Automated Binding Mechanism, RABM, to automatically pack the requests from multiple clients but to a common target service in a short time period into one SOAP message, then sent by the workflow engine at runtime. Extra security operation costs are reduced without modifying of application programs. We use the Travel Service provided by W3C to evaluate RABM. As the experiment result shows, we can achieve up to 130% improvement of throughput and lower the average response time to 41%1.
10887257
Foundations of SMS commerce success: lessons from SMS messaging and co-opetition
As a convenient and low-cost mobile communication technology, short messaging service (SMS) is experiencing very rapid growth. It is reported that 700 million mobile phone users worldwide sent 20 to 30 billion SMS messages every month in 2001. At the same time, SMS commerce applications have emerged to provide mobile users consumer-oriented services. The huge SMS messaging customer base serves as the potential SMS commerce customer base according to K. Kellett and A. Linde (2001) . However, the bloom in messaging business does not automatically lead to the success of general SMS commerce applications. In this paper, we analyzed SMS developments in three different countries to derive three success indicators for SMS messaging and relate them to the success of SMS commerce. Based on the proposed SMS application framework, we postulate four additional hypothesized success factors that could uniquely contribute to the success of SMS commerce. Our findings provide practical implications for promoting SMS commerce applications successfully.
4427518
On the stability of rational, heterogeneous interdomain route selection
The recent discovery of instability caused by the interaction of local routing policies of multiple ASes has led to extensive research on the subject. However, previous studies analyze stability under a specific route selection algorithm. In this paper, instead of studying a specific route selection algorithm, we study a general class of route selection algorithms which we call rational route selection algorithms. We present a sufficient condition to guarantee routing convergence in a heterogeneous network where each AS runs any rational route selection algorithm. Applying our general results, we study the potential instability of a network where the preference of an AS depends on not only its egress routes to the destinations but also its inbound traffic patterns (i.e., the distribution of incoming traffic from its neighbors). We show that there exist networks which will have persistent route oscillations even when the ASes strictly follow the constraints imposed by business considerations, and adopt any rational route selection algorithms.