Ipsj Digital Courier最新文献_第2页

A Distributed-Processing System for Accelerating Biological Research Using Data-Staging 利用数据分期加速生物研究的分布式处理系统

Ipsj Digital Courier Pub Date : 2008-03-15 DOI: 10.2197/IPSJDC.4.250

Y. Kido, S. Seno, S. Date, Y. Takenaka, H. Matsuda

{"title":"A Distributed-Processing System for Accelerating Biological Research Using Data-Staging","authors":"Y. Kido, S. Seno, S. Date, Y. Takenaka, H. Matsuda","doi":"10.2197/IPSJDC.4.250","DOIUrl":"https://doi.org/10.2197/IPSJDC.4.250","url":null,"abstract":"The number of biological databases has been increasing rapidly as a result of progress in biotechnology. As the amount and heterogeneity of biological data increase, it becomes more difficult to manage the data in a few centralized databases. Moreover, the number of sites storing these databases is getting larger, and the geographic distribution of these databases has become wider. In addition, biological research tends to require a large amount of computational resources, i.e., a large number of computing nodes. As such, the computational demand has been increasing with the rapid progress of biological research. Thus, the development of methods that enable computing nodes to use such widely-distributed database sites effectively is desired. In this paper, we propose a method for providing data from the database sites to computing nodes. Since it is difficult to decide which program runs on a node and which data are requested as their inputs in advance, we have introduced the notion of “data-staging” in the proposed method. Data-staging dynamically searches for the input data from the database sites and transfers the input data to the node where the program runs. We have developed a prototype system with data-staging using grid middleware. The effectiveness of the prototype system is demonstrated by measurement of the execution time of similarity search of several-hundred gene sequences against 527 prokaryotic genome data.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"163 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114180455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Generalized Hidden Markov Model Approach to Transmembrane Region Prediction with Poisson Distribution as State Duration Probabilities 以泊松分布为状态持续概率的跨膜区域预测的广义隐马尔可夫模型方法

Ipsj Digital Courier Pub Date : 2008-03-15 DOI: 10.2197/IPSJDC.4.193

T. Kaburagi, Takashi Matsumoto

{"title":"A Generalized Hidden Markov Model Approach to Transmembrane Region Prediction with Poisson Distribution as State Duration Probabilities","authors":"T. Kaburagi, Takashi Matsumoto","doi":"10.2197/IPSJDC.4.193","DOIUrl":"https://doi.org/10.2197/IPSJDC.4.193","url":null,"abstract":"We present a novel algorithm to predict transmembrane regions from a primary amino acid sequence. Previous studies have shown that the Hidden Markov Model (HMM) is one of the powerful tools known to predict transmembrane regions; however, one of the conceptual drawbacks of the standard HMM is the fact that the state duration, i.e., the duration for which the hidden dynamics remains in a particular state follows the geometric distribution. Real data, however, does not always indicate such a geometric distribution. The proposed algorithm utilizes a Generalized Hidden Markov Model (GHMM), an extension of the HMM, to cope with this problem. In the GHMM, the state duration probability can be any discrete distribution, including a geometric distribution. The proposed algorithm employs a state duration probability based on a Poisson distribution. We consider the two-dimensional vector trajectory consisting of hydropathy index and charge associated with amino acids, instead of the 20 letter symbol sequences. Also a Monte Carlo method (Forward/Backward Sampling method) is adopted for the transmembrane region prediction step. Prediction accuracies using publicly available data sets show that the proposed algorithm yields reasonably good results when compared against some existing algorithms.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"908 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132601711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Maintaining Multiple Populations with Different Diversities for Evolutionary Optimization Based on Probability Models 基于概率模型的多种群多样性维持进化优化

Ipsj Digital Courier Pub Date : 2008-03-15 DOI: 10.2197/IPSJDC.4.268

Takayuki Higo, K. Takadama

引用次数: 3

Exploring Factors Effecting the Continuance of Purchasing Behavior in Internet Shopping: Extrinsic Benefits and Intrinsic Benefits 网络购物中影响购买行为持续的因素:外在利益与内在利益

Ipsj Digital Courier Pub Date : 2008-02-15 DOI: 10.2197/IPSJDC.4.91

K. Atchariyachanvanich, H. Okada, N. Sonehara

引用次数: 20

Merging String Sequences by Longest Common Prefixes 按最长公共前缀合并字符串序列

Ipsj Digital Courier Pub Date : 2008-02-15 DOI: 10.2197/IPSJDC.4.69

Waihong Ng, K. Kakehi

引用次数: 14

d-ACTM/VT: A Distributed Virtual AC Tree Detection Method d-ACTM/VT:分布式虚拟交流树检测方法

Ipsj Digital Courier Pub Date : 2008-02-15 DOI: 10.2197/IPSJDC.4.79

N. Kawaguchi, H. Shigeno, Ken-ichi Okada

引用次数: 2

Web Resource Categorization by Detecting Potential Relations 通过检测潜在关系对Web资源进行分类

Ipsj Digital Courier Pub Date : 2008-02-15 DOI: 10.2197/IPSJDC.4.103

Minghua Pei, Kotaro Nakayama, T. Hara, S. Nishio

引用次数: 0

Design and Implementation of an Inter-Device Authentication Framework Guaranteeing Explicit Ownership 保证明确所有权的设备间认证框架的设计与实现

Ipsj Digital Courier Pub Date : 2008-02-06 DOI: 10.2197/IPSJDC.4.114

Manabu Hirano, T. Okuda, S. Yamaguchi

{"title":"Design and Implementation of an Inter-Device Authentication Framework Guaranteeing Explicit Ownership","authors":"Manabu Hirano, T. Okuda, S. Yamaguchi","doi":"10.2197/IPSJDC.4.114","DOIUrl":"https://doi.org/10.2197/IPSJDC.4.114","url":null,"abstract":"Future networks everywhere will be connected to innumerable Internet-ready home appliances. A device accepting connections over a network must be able to verify the identity of a connecting device in order to prevent device spoofing and other malicious actions. In this paper, we propose a security mechanism for an inter-device communication. We state the importance of a distingushing and binding mechanism between a device's identity and its ownership information to realize practical inter-device authentication. In many conventional authentication systems, the relationship between the device's identity and the ownership information is not considered. Therefore, we propose a novel inter-device authentication framework guaranteeing this relationship. Our prototype implementation employs a smart card to maintain the device's identity, the ownership information and the access control rules securely. Our framework efficiently achieves secure inter-device authentication based on the device's identity, and authorization based on the ownership information related to the device. We also show how to apply our smart card system for inter-device authentication to the existing standard security protocols.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129029853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Automatic Construction of Program Transformation Templates 程序转换模板的自动构建

Ipsj Digital Courier Pub Date : 2008-01-15 DOI: 10.2197/IPSJDC.4.44

Yuki Chiba, Takahito Aoto, Y. Toyama

引用次数: 4

Evaluation of the Integration Effect of Content Location and Request Routing in Content Distribution Networks 内容分发网络中内容定位与请求路由集成效果评价

Ipsj Digital Courier Pub Date : 2008-01-15 DOI: 10.2197/IPSJDC.4.1

H. Miura, M. Yamamoto

引用次数: 0