33547700
Collaborative and interactive room design on the web
Design on the Web raises challenging questions concerning how users interact with objects, applications, and other users. In this work, we propose a collaborative and interactive client-server design framework and implement a room design system for our study. We have integrated technologies used in distributed computation (Java and CORBA) and computer graphics (VRML). It divides the design process into three tiers. First, collaborative and interactive design, viewing, and publishing. Second, scene generation. Third, scene database management. 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.
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.
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.
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.
465231
BLAST++: BLASTing queries in batches
UNLABELLED
BLAST++ is a tool that is integrated with NCBI BLAST, allowing multiple, say K, queries to be searched against a database concurrently. The results obtained by BLAST++ are identical to that obtained by executing BLAST on each of the K queries, but BLAST++ completes the processing in a much shorter time.


AVAILABILITY
http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++


SUPPLEMENTARY INFORMATION
http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++
7017728
Indexing Genomic Databases for Fast Homology Searching
Genomic sequence databases has been widely used by molecular biologists for homology searching. However, as amino acid and nucleotide databases are growing in size at an alarming rate, traditional brute force approach of comparing a query sequence against each of the database sequences is becoming prohibitively expensive. In this paper, we re-examine the problem of searching for homology in large protein databases. We proposed a novel filter-and-refine approach to speed up the search process. The scheme operates in two phases. In the filtering phase, a small set of candidate database sequences (as compared to all sequences in the database) is quickly identified. This is realized using a signature-based scheme. In the refinement phase, the query sequence is matched against the sequences in the candidate set using any local alignment strategies. Our preliminary experimental results show that the proposed method results in significant savings in computation without sacrificing on the accuracy of the answers as compared to FASTA.
14889815
Understanding the Session Durability in Peer-to-Peer Storage System
This paper emphasizes that instead of long-term availability and reliability, the short-term session durability analysis will greatly impact the design of the real large-scale Peer-to-Peer storage system. In this paper, we use a Markov chain to model the session durability, and then derive the session durability probability distribution. Subsequently, we show the difference between our analysis and the traditionalMean Time to Failure (MTTF) analysis, from which we conclude that the misuse of MTTF analysis will greatly mislead our understanding of the session durability. We further show the impact of session durability analysis on the real system design. To our best knowledge, this is the first time ever to discuss the effects of session durability in large-scale Peer-to-Peer storage system.
21956342
Architectural design and implementation of highly available and scalable medical system with IBM Websphere middleware
Medical systems require the end-to-end high availability and scalability. There are many components in a medical system, and each individual component contributes to the overall system availability and scalability. We present the formulas to assess the overall system availability and capacity planning, and we architect approaches and technologies to make all components highly available in all tiers by clustering, workload management, and replication. We discuss how to unify all medical systems and design the uniform framework for different kinds of medical systems to hook up with this framework so that we can maintain a highly available and highly scalable system with ease. We use the n-tier distributed component based architecture and J2EE technologies as well as Web services to interact with .NET and others. We discuss how to program in the framework for high availability and scalability and how to upgrade application software without service interruption to achieve continuous availability. We show how to add or reduce hardware capacity in each tier and how to maintain hardware and software without service interruption as well as how to balance the capacity and availability among tiers.
35188491
Requirement and Design Analysis for the Post-Trauma Mobile Psychology Service
In 2008, a serious earthquake struck Sichuan province. Tens of thousands of people in disaster areas have suffered injuries both in physical and mental aspects. Thus, a Post-Trauma Mobile Service (PTMS) is launched and implemented in Sichuan province, which creates a new mode of long-distance psychological counseling service. This study discusses the comparisons between mobile-based and traditional psychological counseling method, indicating that mobile-based method is a significant experiment both in the post-disaster psychological assistance work and mobile communication service. Besides, requirement analysis is explored, which guides the work of PTMS system design. The system design is described in three stages including architecture design, service mode design and industry chain analysis, in which online and offline service mode are highlighted. This study presents the implementation of PTMS service, which shows that the mobile-based platform and service mode have acceptable psychometric properties, equivalent with paper-based method.
1622406
Structure Analysis and SNR-Variance Evolution for Parallel Concatenated Coded IDMA Systems
This paper is concerned with parallel concatenated coded interleave-division multiple-access (IDMA) systems. We briefly present the transmitter/receiver structure of these systems and propose an efficient SNR-variance evolution scheme for bit-error-rate (BER) performance evaluation. The proposed evolution scheme is also useful for system performance optimization. Numerical results show that the BER performance curves obtained by simulation and evolution are quite close when the data length is long enough.
9889663
Feature Similarity Based Redundancy Reduction for Gene Selection
this paper we propose a feature similarity based redundancy reduction (FSRR) algorithm for high-dimensional gene expression data analysis. FSRR has two steps. First, the relevance of each feature is evaluated. Second, based on the relevance, the redundant features are removed by feature similarity. The efficiency and effectiveness of our algorithm is established through an experimental study using gene expression data. Four state-of-art feature ranking algorithms and three feature similarity measures are compared and discussed in our work. The results indicate that our algorithm has the capability of finding a well-suited feature set and improving the classification accuracy.