14831931
TRIPLES: a database of gene function in Saccharomyces cerevisiae
Using a novel multipurpose mini-transposon, we have generated a collection of defined mutant alleles for the analysis of disruption phenotypes, protein localization, and gene expression in Saccharomyces cerevisiae. To catalog this unique data set, we have developed TRIPLES, a Web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces. Encompassing over 250 000 data points, TRIPLES provides convenient access to information from nearly 7800 transposon-mutagenized yeast strains; within TRIPLES, complete data reports of each strain may be viewed in table format, or if desired, downloaded as tab-delimited text files. Each report contains external links to corresponding entries within the Saccharomyces Genome Database and International Nucleic Acid Sequence Data Library (GenBank). Unlike other yeast databases, TRIPLES also provides on-line order forms linked to each clone report; users may immediately request any desired strain free-of-charge by submitting a completed form. In addition to presenting a wealth of information for over 2300 open reading frames, TRIPLES constitutes an important medium for the distribution of useful reagents throughout the yeast scientific community. Maintained by the Yale Genome Analysis Center, TRIPLES may be accessed at http://ycmi.med.yale.edu/ygac/triples.htm
21095960
The TRIPLES database: a community resource for yeast molecular biology
TRIPLES is a web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces cerevisiae-a relational database housing nearly half a million data points generated from an ongoing study using large-scale transposon mutagenesis to characterize gene function in yeast. At present, TRIPLES contains three principal data sets (i.e. phenotypic data, protein localization data and expression data) for over 3500 annotated yeast genes as well as several hundred non-annotated open reading frames. In addition, the TRIPLES web site provides online order forms linked to each data set so that users may request any strain or reagent generated from this project free of charge. In response to user requests, the TRIPLES web site has undergone several recent modifications. Our localization data have been supplemented with approximately 500 fluorescent micrographs depicting actual staining patterns observed upon indirect immunofluorescence analysis of indicated epitope-tagged proteins. These localization data, as well as all other data sets within TRIPLES, are now available in full as tab-delimited text. To accommodate increased reagent requests, all orders are now cataloged in a separate database, and users are notified immediately of order receipt and shipment. Also, TRIPLES is one of five sites incorporated into the new functional analysis tool Function Junction provided by the Saccharomyces Genome Database. TRIPLES may be accessed from the Yale Genome Analysis Center (YGAC) homepage at http://ygac.med.yale.edu.
23929618
Organelle DB: an updated resource of eukaryotic protein localization and function
Organelle DB () is a web-accessible relational database presenting a supplemented catalog of organelle-localized proteins and major protein complexes. Since its release in 2004, Organelle DB has grown by 20% to encompass over 30 000 proteins from 138 eukaryotic organisms. Each protein in Organelle DB is presented with its subcellular localization, primary sequence and a detailed description of its function, as available. All records in Organelle DB have been annotated using controlled vocabulary from the Gene Ontology consortium. Protein localization data are inherently visual, and Organelle DB is a significant repository of biological images, housing 1500 micrographs of yeast cells carrying stained proteins. Furthermore, we report here the development of Organelle View, an extension of Organelle DB for the interactive visualization of organelles and subcellular structures in the budding yeast Saccharomyces cerevisiae. Organelle View offers a dimensional representation of a yeast cell; users can search Organelle View for proteins of interest, and the organelles housing these proteins will be highlighted in the cell image. Among other applications, Organelle View may serve as an educational aid engaging introductory biology students through a visually ‘fun’ interface. Organelle View can be accessed from the Organelle DB home page or directly at .
31048080
Advertising data analysis using rough sets model
This study explores the use of rough-set methods for marketing decision support systems in the retail business. A tutorial presentation of Rough Set Data Analysis (RSDA) in the context of knowledge discovery from time series databases is given. We show how an RSDA model can be used to develop a marketing decision support system which can capture the complex relationships between marketing factors, such as advertising and promotion, and the total impact on sales levels in order to find influential advertising strategies. This information is used by the business manager to make faster and better strategy decisions for the business to survive in the rapidly changing and competitive environments. The data set used for RSDA application example contains weekly investments in different media categories: TV, radio, cinema, morning press, evening press, popular press, special interest press, and outdoor posters; for seven makes of cars in the Swedish market.
5867882
Wavelength conversion in optical networks
In many models of optical routing, we are given a set of communication paths in a network, and we must assign a wavelength to each path so that paths sharing an edge receive different wavelengths. The goal is to assign as few wavelengths as possible in order to make as efficient use as possible of the optical bandwidth. A lot of work in the area of optical networks has considered the use of wavelength converters: if a node of a network contains a wavelength converter, any path that passes through this node may change its wavelength. Having converters at some of the nodes can reduce the number of wavelengths required for routing, down to the following natural congestion bound: even with converters, we will always need at least as many wavelengths as the maximum number of paths sharing a single edge. Thus Wilfong and Winkler defined a set S of nodes in a network to be sufficient if, placing converters at the nodes in S, every set of paths can be routed with a number of wavelengths equal to its congestion bound. They showed that finding a sufficient set of minimum size is NP-complete, even in planar graphs.In this paper, we provide a polynomial-time algorithm to find a sufficient set for an arbitrary directed network whose size is within a factor of 2 of minimum. We also observe that improving on the factor of 2 would lead to a corresponding improvement for the vertex cover problem. For the case of planar graphs, we provide a polynomial-time approximation scheme. The algorithms are based on connections between the minimum sufficient set problem and the undirected feedback vertex set problem. In particular, as a component of the algorithm on planar graphs, we develop the first polynomial-time approximation scheme for the undirected feedback vertex set problem in planar graphs, a result that we feel to be of interest in its own right.
2583878
A data streaming algorithm for estimating subpopulation flow size distribution
Statistical information about the flow sizes in the traffic passing through a network link helps a network operator to characterize network resource usage, infer traffic demands, detect traffic anomalies, and improve network performance through traffic engineering. Previous work on estimating the flow size distribution for the complete population of flows has produced techniques that either make inferences from sampled network traffic, or use data streaming approaches. In this work, we identify and solve a more challenging problem of estimating the size distribution and other statistical information about arbitrary subpopulations of flows. Inferring subpopulation flow statistics is more challenging than the complete population counterpart, since subpopulations of interest are often specified a posteriori (i.e., after the data collection is done), making it impossible for the data collection module to "plan in advance".Our solution consists of a novel mechanism that combines data streaming with traditional packet sampling to provide highly accurate estimates of subpopulation flow statistics. The algorithm employs two data collection modules operating in parallel --- a NetFlow-like packet sampler and a streaming data structure made up of an array of counters. Combining the data collected by these two modules, our estimation algorithm uses a statistical estimation procedure that correlates and decodes the outputs (observations) from both data collection modules to obtain flow statistics for any arbitrary subpopulation. Evaluations of this algorithm on real-world Internet traffic traces demonstrate its high measurement accuracy.
43715944
Performance Analysis and Scheduling of Stochastic Fork-Join Jobs in a Multicomputer System
The authors model a parallel processing system comprising several homogeneous computers interconnected by a communication network. Jobs arriving to this system have a linear fork-join structure. Each fork of the job gives rise to a random number of tasks that can be processed independently on any of the computers. Since exact analysis of fork-join models is known to be intractable, the authors resort to obtaining analytical bounds to the mean job response time of the fork-join job. For jobs with a single fork-join and, probabilistic allocation of tasks of the job to the N processors, they obtain upper and lower bounds to the mean job response time. Upper bounds are obtained using the concept of associated random variables and are found to be a good approximation to the mean job response time. A simple lower bound is obtained by neglecting queueing delays. They also find two lower bounds that include queueing delays. For multiple fork-join jobs, they study an approximation based on associated random variables. Finally, two versions of the join-the-shortest-queue (JSQ) allocation policy (i.e., JSQ by batch and JSQ by task) are studied and compared, via simulations and diffusion limits. >
38260906
An Efficient SuperGrid Protocol for High Availability and Load Balancing
Recently there has been a resurgence of interest in quorum-based methods for maintaining consistency of a group of replicated servers as a way to achieve load balancing in addition to high availability. We describe a SuperGrid protocol that performs well for small number of items (less than 100) and evaluate its performance analytically and through simulation experiments. Although it has been shown that it is possible to construct quorum systems where the load is O(1//spl radic/N) and the availability is exp(-/spl Omega/(/spl radic/N)), these asymptotic results do not perform very well when the number of items is relatively small. In such cases, our results show that the Supergrid protocol outperforms the recent Crumbling Walls protocol and the Paths system. It is also simple and easy to implement.