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HIVToolbox, an integrated web application for investigating HIV.

Sargeant D, Deverasetty S, Luo Y, Villahoz Baleta A, Zobrist S, Rathnayake V, Russo JC, Vyas J, Muesing MA, Schiller MR - PLoS ONE (2011)

Bottom Line: HIV-1 integrase protein was used as a case study to show the utility of this application.We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories.Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America.

ABSTRACT
Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories. Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site. Weblink: [http://hivtoolbox.bio-toolkit.com].

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Diagram of software architecture of HIVToolbox.
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pone-0020122-g007: Diagram of software architecture of HIVToolbox.

Mentions: HIVToolbox is a web-based application built as a Java 2 Enterprise Edition servlet that pulls data from a server-side MySQL relational database. The application retrieves data from tables of the database (Fig. 6) and stores the data in a number of “beans”, Java objects that correspond to query results of data in the tables of the database. Beans are easily stored and retrieved by the application. The majority of the application's data processing and calculations are performed on the server to minimize time transmitting data over the internet to the end user. The overall architecture of HIVToolbox is shown in Fig. 7.


HIVToolbox, an integrated web application for investigating HIV.

Sargeant D, Deverasetty S, Luo Y, Villahoz Baleta A, Zobrist S, Rathnayake V, Russo JC, Vyas J, Muesing MA, Schiller MR - PLoS ONE (2011)

Diagram of software architecture of HIVToolbox.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102074&req=5

pone-0020122-g007: Diagram of software architecture of HIVToolbox.
Mentions: HIVToolbox is a web-based application built as a Java 2 Enterprise Edition servlet that pulls data from a server-side MySQL relational database. The application retrieves data from tables of the database (Fig. 6) and stores the data in a number of “beans”, Java objects that correspond to query results of data in the tables of the database. Beans are easily stored and retrieved by the application. The majority of the application's data processing and calculations are performed on the server to minimize time transmitting data over the internet to the end user. The overall architecture of HIVToolbox is shown in Fig. 7.

Bottom Line: HIV-1 integrase protein was used as a case study to show the utility of this application.We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories.Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America.

ABSTRACT
Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories. Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site. Weblink: [http://hivtoolbox.bio-toolkit.com].

Show MeSH