VTechWorks staff will be away for the Thanksgiving holiday beginning at noon on Wednesday, November 27, through Friday, November 29. We will resume normal operations on Monday, December 2. Thank you for your patience.

Browsing by Author "Struble, Craig A."

Now showing 1 - 4 of 4
  • Collaboration Transparency in Java through Event Broadcasting
    Begole, James M.A.; Struble, Craig A.; Shaffer, Clifford A. (Department of Computer Science, Virginia Polytechnic Institute & State University, 1997-02-01)
    Widespread use of the Internet for education and research is yielding many opportunities for network-based synchronous collaboration. For example, the Java runtime environment provides a platform independent vehicle for new collaborative applications. While many toolkits are becoming available that support development of collaborative applications, they do not enable collaborative use of existing single-user Java applets, a process called collaboration transparency. This paper discusses two approaches to collaboration transparency: display broadcasting and event broadcasting. We then consider the suitability of each within the context of the Java runtime environment. Unfortunately, simple modifications to the standard Java class libraries as they are currently implemented are not sufficient to support collaboration transparency. We describe the problems and suggest solutions.
  • Thumbnail Image
    Critical Issues in the Processing of cDNA Microarray Images
    Jouenne, Vincent Y. (Virginia Tech, 2001-06-28)
    Microarray technology enables simultaneous gene expression level monitoring for thousands of genes. While this technology has now been recognized as a powerful and cost-effective tool for large-scale analysis, the many systematic sources of experimental variations introduce inherent errors in the extracted data. Data is gathered by processing scanned images of microarray slides. Therefore robust image processing is particularly important and has a large impact on downstream analysis. The processing of the scanned images can be subdivided in three phases: gridding, segmentation and data extraction. To measure the gene expression levels, the processing of cDNA microarray images must overcome a large set of issues in these three phases that motivates this study. This study presents automatic gridding methods and compares their performances. Two segmentation techniques already used, the Seeded Region Growing Algorithm and the Mann-Whitney Test, are examined. We present limitations of these techniques. Finally, we studied the data extraction method used in MicroArray Suite (MS), a microarray analysis software, via synthetic images and explain its intricacies.
  • Thumbnail Image
    Studying the Functional Genomics of Stress Responses in Loblolly Pine With the Expresso Microarray Experiment Management System
    Heath, Lenwood S.; Ramakrishnan, Naren; Sederoff, Ronald R.; Whetten, Ross W.; Chevone, Boris I.; Struble, Craig A.; Jouenne, Vincent Y.; Chen, Dawei; van Zyl, Leonel; Grene, Ruth (Hindawi, 2002-01-01)
    Conception, design, and implementation of cDNA microarray experiments present avariety of bioinformatics challenges for biologists and computational scientists. The multiplestages of data acquisition and analysis have motivated the design of Expresso, asystem for microarray experiment management. Salient aspects of Expresso includesupport for clone replication and randomized placement; automatic gridding, extraction ofexpression data from each spot, and quality monitoring; flexible methods of combiningdata from individual spots into information about clones and functional categories; and theuse of inductive logic programming for higher-level data analysis and mining. Thedevelopment of Expresso is occurring in parallel with several generations of microarrayexperiments aimed at elucidating genomic responses to drought stress in loblolly pineseedlings. The current experimental design incorporates 384 pine cDNAs replicated andrandomly placed in two specific microarray layouts. We describe the design of Expresso aswell as results of analysis with Expresso that suggest the importance of molecularchaperones and membrane transport proteins in mechanisms conferring successfuladaptation to long-term drought stress.
  • Thumbnail Image
    System Resource Sharing for Synchronous Collaboration
    Begole, James M.A.; Struble, Craig A.; Shaffer, Clifford A.; Smith, R. B. (Department of Computer Science, Virginia Polytechnic Institute & State University, 1999-09-01)
    We describe problems associated with accessing data resources external to the application, which we term externalities, in replicated synchronous collaborative applications (e.g., a multiuser text editor). Accessing externalities such as les, databases, network connections, environment variables and the system clock is not as straightforward in replicated collaborative software as in single-user applications and centralized collaborative systems. We describe ad hoc solutions that have been used previously. Our primary objection to the ad hoc solutions is that the developer must program dierent behavior into the dierent replicas of a multi-user application, which increases the cost and complexity of development. We introduce a novel general approach to accessing externalities uniformly in a replicated collaborative system. The approach uses a semi-replicated architecture where the actual externality resides at a single location and is accessed via replicated proxies. The proxies multiplex input to and output from the single instance of the externality. This approach facilitates the creation of replicated synchronous groupware in two ways: (1) developers use the same mechanisms as in traditional single-user applications (2) developers program all replicas to execute the same behavior. We describe a general design for proxied access to read{only, write{only and read{write externalities. We discuss the tradeos of this semi- replicated approach over full, literal replication and the class of applications to which this approach can be successfully applied. We also describe details of a prototype implementation of this approach within a replicated collaboration-transparency system, called Flexible JAMM (Java Applets Made Multi-user).