Peptide-based hidden Markov model for peptide fingerprint mapping.

Peptide-based hidden Markov model for peptide fingerprint mapping.

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Date: December 2004
Creator: Yang, Dongmei
Description: Peptide mass fingerprinting (PMF) was the first automated method for protein identification in proteomics, and it remains in common usage today because of its simplicity and the low equipment costs for generating fingerprints. However, one of the problems with PMF is its limited specificity and sensitivity in protein identification. Here I present a method that shows potential to significantly enhance the accuracy of peptide mass fingerprinting, using a machine learning approach based on a hidden Markov model (HMM). This method is applied to improve differentiation of real protein matches from those that occur by chance. The system was trained using 300 examples of combined real and false-positive protein identification results, and 10-fold cross-validation applied to assess model discrimination. The model can achieve 93% accuracy in distinguishing correct and real protein identification results versus false-positive matches. The receiver operating characteristic (ROC) curve area for the best model was 0.833.
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A Netcentric Scientific Research Repository

A Netcentric Scientific Research Repository

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Date: December 2006
Creator: Harrington, Brian
Description: The Internet and networks in general have become essential tools for disseminating in-formation. Search engines have become the predominant means of finding information on the Web and all other data repositories, including local resources. Domain scientists regularly acquire and analyze images generated by equipment such as microscopes and cameras, resulting in complex image files that need to be managed in a convenient manner. This type of integrated environment has been recently termed a netcentric sci-entific research repository. I developed a number of data manipulation tools that allow researchers to manage their information more effectively in a netcentric environment. The specific contributions are: (1) A unique interface for management of data including files and relational databases. A wrapper for relational databases was developed so that the data can be indexed and searched using traditional search engines. This approach allows data in databases to be searched with the same interface as other data. Fur-thermore, this approach makes it easier for scientists to work with their data if they are not familiar with SQL. (2) A Web services based architecture for integrating analysis op-erations into a repository. This technique allows the system to leverage the large num-ber of existing tools by wrapping them ...
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Adaptive planning and prediction in agent-supported distributed collaboration.

Adaptive planning and prediction in agent-supported distributed collaboration.

Date: December 2004
Creator: Hartness, Ken T. N.
Description: Agents that act as user assistants will become invaluable as the number of information sources continue to proliferate. Such agents can support the work of users by learning to automate time-consuming tasks and filter information to manageable levels. Although considerable advances have been made in this area, it remains a fertile area for further development. One application of agents under careful scrutiny is the automated negotiation of conflicts between different user's needs and desires. Many techniques require explicit user models in order to function. This dissertation explores a technique for dynamically constructing user models and the impact of using them to anticipate the need for negotiation. Negotiation is reduced by including an advising aspect to the agent that can use this anticipation of conflict to adjust user behavior.
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Mediation on XQuery Views

Mediation on XQuery Views

Date: December 2006
Creator: Peng, Xiaobo
Description: The major goal of information integration is to provide efficient and easy-to-use access to multiple heterogeneous data sources with a single query. At the same time, one of the current trends is to use standard technologies for implementing solutions to complex software problems. In this dissertation, I used XML and XQuery as the standard technologies and have developed an extended projection algorithm to provide a solution to the information integration problem. In order to demonstrate my solution, I implemented a prototype mediation system called Omphalos based on XML related technologies. The dissertation describes the architecture of the system, its metadata, and the process it uses to answer queries. The system uses XQuery expressions (termed metaqueries) to capture complex mappings between global schemas and data source schemas. The system then applies these metaqueries in order to rewrite a user query on a virtual global database (representing the integrated view of the heterogeneous data sources) to a query (termed an outsourced query) on the real data sources. An extended XML document projection algorithm was developed to increase the efficiency of selecting the relevant subset of data from an individual data source to answer the user query. The system applies the projection algorithm ...
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Analysis of Web Services on J2EE Application Servers

Analysis of Web Services on J2EE Application Servers

Date: May 2004
Creator: Gosu, Adarsh Kumar
Description: The Internet became a standard way of exchanging business data between B2B and B2C applications and with this came the need for providing various services on the web instead of just static text and images. Web services are a new type of services offered via the web that aid in the creation of globally distributed applications. Web services are enhanced e-business applications that are easier to advertise and easier to discover on the Internet because of their flexibility and uniformity. In a real life scenario it is highly difficult to decide which J2EE application server to go for when deploying a enterprise web service. This thesis analyzes the various ways by which web services can be developed & deployed. Underlying protocols and crucial issues like EAI (enterprise application integration), asynchronous messaging, Registry tModel architecture etc have been considered in this research. This paper presents a report by analyzing what various J2EE application servers provide by doing a case study and by developing applications to test functionality.
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Automatic Tagging of Communication Data

Automatic Tagging of Communication Data

Date: August 2012
Creator: Hoyt, Matthew Ray
Description: Globally distributed software teams are widespread throughout industry. But finding reliable methods that can properly assess a team's activities is a real challenge. Methods such as surveys and manual coding of activities are too time consuming and are often unreliable. Recent advances in information retrieval and linguistics, however, suggest that automated and/or semi-automated text classification algorithms could be an effective way of finding differences in the communication patterns among individuals and groups. Communication among group members is frequent and generates a significant amount of data. Thus having a web-based tool that can automatically analyze the communication patterns among global software teams could lead to a better understanding of group performance. The goal of this thesis, therefore, is to compare automatic and semi-automatic measures of communication and evaluate their effectiveness in classifying different types of group activities that occur within a global software development project. In order to achieve this goal, we developed a web-based component that can be used to help clean and classify communication activities. The component was then used to compare different automated text classification techniques on various group activities to determine their effectiveness in correctly classifying data from a global software development team project.
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A Pattern Oriented Data Structure for Interactive Computer Music

A Pattern Oriented Data Structure for Interactive Computer Music

Date: May 2011
Creator: Lockhart, Adam
Description: This essay describes a pattern oriented data structure, or PODS, as a system for storing computer music data. It organizes input by sequences or patterns that recur, while extensively interlinking the data. The interlinking process emulates cognitive models, while the pattern processing draws specifically from music cognition. The project aims at creating open source external objects for the Max/MSP software environment. The computer code for this project is in the C and Objective-C computer programming languages.
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An analysis of motivational cues in virtual environments.

An analysis of motivational cues in virtual environments.

Access: Use of this item is restricted to the UNT Community.
Date: December 2003
Creator: Voruganti, Lavanya
Description: Guiding navigation in virtual environments (VEs) is a challenging task. A key issue in the navigation of a virtual environment is to be able to strike a balance between the user's need to explore the environment freely and the designer's need to ensure that the user experiences all the important events in the VE. This thesis reports on a study aimed at comparing the effectiveness of various navigation cues that are used to motivate users towards a specific target location. The results of this study indicate some significant differences in how users responded to the various cues.
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Modeling Changes in End-user Relevance Criteria : An Information Seeking Study

Modeling Changes in End-user Relevance Criteria : An Information Seeking Study

Date: May 1998
Creator: Bateman, Judith Ann
Description: This study examines the importance of relevance criteria in end-user evaluation of valuable or high relevant information.
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Information Seeking in a Virtual Learning Environment

Information Seeking in a Virtual Learning Environment

Date: August 1999
Creator: Byron, Suzanne M.
Description: Duplicating a time series study done by Kuhlthau and associates in 1989, this study examines the applicability of the Information Search Process (ISP) Model in the context of a virtual learning environment. This study confirms that students given an information seeking task in a virtual learning environment do exhibit the stages indicated by the ISP Model. The six-phase ISP Model is shown to be valid for describing the different stages of cognitive, affective, and physical tasks individuals progress through when facing a situation where they must search for information to complete an academic task in a virtual learning environment. The findings in this study further indicate there is no relationship between the amount of computer experience subjects possess and demonstrating the patterns of thoughts, feelings, and actions described by the ISP Model. The study demonstrates the ISP Model to be independent of the original physical library environments where the model was developed. An attempt is made to represent the ISP model in a slightly different manner that provides more of the sense of motion and interaction among the components of thoughts, feelings, and action than is currently provided for in the model. The study suggests that the development of non-self-reporting ...
Contributing Partner: UNT Libraries
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