Genomedia a middleware platform for distributed genomic information

Gros, Pierre-Emmanuel; Férey, Nicolas; Hérisson, Joan; Gherbi, Rachid

doi:10.1109/ictta.2004.1307853

Cited by 3 publications

(5 citation statements)

References 2 publications

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“…We have developed a genomic database called GenoMEDIA (Gros, Férey, Hérisson & Gherbi, 2004) that stores annotated DNA sequences containing information about DNA sequences and gene positions and names. Thanks to SQL queries, the ADN-Viewer can download any requested annotated sequence in order to augment the visualization ( Figure 6).…”

Section: Interfacing the Adn-viewer With A Genomic Databasementioning

confidence: 99%

3D Visualization and Virtual Exploration of Genomic Sequences

et al. 2005

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In this paper, we address the potential offered by Virtual Reality for 3D modeling and immersive visualization of large genomic sequences. The representation of the 3D structure of DNA allows biologists to observe and analyze genomes in an interactive way at different levels. We developed a powerful software platform that provides a new point of view for sequences analysis: ADN-Viewer. Nevertheless, a classical eukaryotic chromosome of 40 million base pairs requires about 6 Gbytes of 3D data. In order to manage these huge amounts of data in real-time, we designed various scene management algorithms and immersive human-computer interaction for user-friendly data exploration.

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Section: Interfacing the Adn-viewer With A Genomic Databasementioning

confidence: 99%

3D Visualization and Virtual Exploration of Genomic Sequences

et al. 2005

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“…Our framework GenoMEDIA (Gros, Ferey, Hérisson, & Gherbi, 2004) is close in term of goals to DiscoveryLink approach, but it achieves its aims in a different manner. Like DiscoveryLink, we used SQL as a federator language (Agha,1986;Williams,1997).…”

Section: Introductionmentioning

confidence: 99%

Combining applications and remote databases view in a common SQL distributed genomic database

Gros¹,

Hérisson²,

Férey³

et al. 2005

Data Sci. J.

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“…The goal of Lydia is to offer integration and collaboration facilities between Services [2]. Like CORBA, Lydia uses a script language for interface description called LDL (Lydia Description Language), describing the functionalities of a given Service that can be compiled into several languages (presently we compile LDL to C/C++ and Java).…”

Section: Lydiamentioning

confidence: 99%

“…Users do not have to use the database link into the SQL statements. In this paper, we will present shortly the Lydia [2] concept, our service integration middleware. This will allow the reader to better understand its connections with Antje on the GenoMEDIA platform.…”

Section: Introductionmentioning

confidence: 99%

“…1 the user sends a query to the DBMS, like 'select gene from CDS Aeropyrum pernix'. 2 The DBMS tries to retrieve information from the view, and calls the function executeAntje with the query in parameter. 3-4 Antje retrieves from the DBMS the maximum memory consumed by this query (in order to match the memory available by the JVM and the memory needed to answer the query).…”

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confidence: 99%

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Combining Applications and Databases Integration Approaches in a Common Distributed Genomic Platform

Gros

Hérisson

Férey

et al.

19th International Conference on Advanced Information Networking and Applications (AINA'05) Volume 1 (AINA Papers)

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Many databases and software tools are currently available for accessing genomic data. In general, each tool uses a different type of data in exchange protocols, and usually they offer specific services. Our system approach, named GenoMEDIA, addresses the problem of integrating these heterogeneous databases and software utilities within a generic distributed platform. GenoMEDIA provides two specific middleware, named Lydia and Antje, for this integration. Lydia offers facilities for working simultaneously with a variety of Services and Databases; Antje is designed to allow users to manage multiple heterogeneous remote databases in a uniform vision. The aim of this paper is to present GenoMEDIA and how heterogeneous databases and remote services are integrated, in particular how Antje was designed, implemented and tested with various genomic databases

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Genomedia a middleware platform for distributed genomic information

Cited by 3 publications

References 2 publications

3D Visualization and Virtual Exploration of Genomic Sequences

3D Visualization and Virtual Exploration of Genomic Sequences

Combining applications and remote databases view in a common SQL distributed genomic database

Combining Applications and Databases Integration Approaches in a Common Distributed Genomic Platform

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