BioGRID - An European grid for molecular biology

Bała, Piotr; Pytliński, Jarosław; Nazaruk, Mirosław

doi:10.1109/hpdc.2002.1029942

Cited by 14 publications

(7 citation statements)

References 4 publications

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“…The UNICORE Architecture The UNICORE client checks the correctness of the work and warns users immediately to correct errors. The main grid tools and application projects using UNICORE as their low-level middleware include: Euro Grid [18] and its applications-Bio Grid [19], Metro Grid and CAE Grid, Grid interoperability Project (GRIP) [20], Open Mol Grid [19] and Japanese NAREGI (National Research Grid Initiative) [22].…”

Section: Figure 2: a Layered Grid Architecture And Componentsmentioning

confidence: 99%

Global Grids and Package Toolkits at 4 Grid Middleware Technologies

Sundaram*

2019

IJEAT

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Grid is an infrastructure that involves the integrated and collaborative use of computers, networks, databases and scientific instruments owned and managed by many organizations. Grid applications often involve large amounts of data and/or computer resources that require a secure resource sharing throughout the organization. This makes grid operation and deployment a complex undertaking. Grid middleware provides users with seamless computer skills and uniform access to resources in the heterogeneous grid. A number of toolkits and systems have been developed, most of which are the result of academic research projects worldwide. This chapter focuses on four of these intermediaries: UNICORE, Globus, Legion and Grid bus. It also presents our implementation of a UNICORE resource broker because it did not support this functionality. A comparison of these systems is included based on the architecture, the implementation model and a number of other functions.

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Section: Figure 2: a Layered Grid Architecture And Componentsmentioning

confidence: 99%

Global Grids and Package Toolkits at 4 Grid Middleware Technologies

Sundaram*

2019

IJEAT

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“…Such projects in Europe include Biotechnology Information and Knowledge Grid (BIOGRID) [48], Grid Basic Local Alignment Search Tool (Grid-BLAST) or (DataGridBlast) project [49], Biotechnology Grid (BioGrid) project [28], BioInformatics and Genomics GRID for European Research (BIGGER) [50], Open Computing GRID Molecular Science and Engineering (OpenMolGRID) [51]. Some projects in France focused on the same concern such as the Realization and Use of a Grid for Bio-computing (RUGBI) based on European DataGrid (EDG) [40], GenoGrid [52], and the Grid Protein Pattern Scanning (GriPPS) [53].…”

Section: Biomedical Imagingmentioning

confidence: 99%

Bioinformatics and Healthcare Computing Models and Services on Grid Initiatives for Data Analysis and Management

Mazari

2014

2014 3rd International Conference on Advanced Computer Science Applications and Technologies

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Grid platforms serve a wide range of activities in life sciences, bioinformatics, engineering, healthcare and other industries. This paper identifies the key bioinformatics and healthcare computing models and services on grid initiatives and classifies and describes their current use in the industry. Based on what has been reported by the literature, the paper identifies eight key areas of interests and eleven models where bioinformatics and healthcare oriented services are available. The efforts of this work will assist in determining areas of interests for end-users of grid technologies and highlighting future grid studies and research toward further grid services developments.

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“…Various databases of gene/protein sequences, gene expressions, and related analysis tools help scientists determine whether and how a particular molecule is directly involved in a disease process. That, in turn, aids in the discovery of new and better drug targets [18,22].…”

Section: Mpiblastmentioning

confidence: 99%

G‐BLAST: a Grid‐based solution for mpiBLAST on computational Grids

Yang

Han

Kan

2008

Concurrency and Computation

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SUMMARYOver the past few years, research and development in bioinformatics (e.g. genomic sequence alignment) has grown with each passing day fueling continuing demands for vast computing power to support better performance. This trend usually requires solutions involving parallel computing techniques because cluster computing technology reduces execution times and increases genomic sequence alignment efficiency. One example, mpiBLAST is a parallel version of NCBI BLAST that combines NCBI BLAST with message passing interface (MPI) standards. However, as most laboratories cannot build up powerful cluster computing environments, Grid computing framework concepts have been designed to meet the need. Grid computing environments coordinate the resources of distributed virtual organizations and satisfy the various computational demands of bioinformatics applications. In this paper, we report on designing and implementing a BioGrid framework, called G-BLAST, that performs genomic sequence alignments using Grid computing environments and accessible mpiBLAST applications. G-BLAST is also suitable for cluster computing environments with a server node and several client nodes. G-BLAST is able to select the most appropriate work nodes, dynamically fragment genomic databases, and self-adjust according to performance data. To enhance G-BLAST capability and usability, we also employ a WSRF Grid Service Portal and a Grid Service GUI desk application for general users to submit jobs and host administrators to maintain work nodes.

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BioGRID - An European grid for molecular biology

Cited by 14 publications

References 4 publications

Global Grids and Package Toolkits at 4 Grid Middleware Technologies

Global Grids and Package Toolkits at 4 Grid Middleware Technologies

Bioinformatics and Healthcare Computing Models and Services on Grid Initiatives for Data Analysis and Management

G‐BLAST: a Grid‐based solution for mpiBLAST on computational Grids

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