The superstructure toward open bioinformatics grid

Konagaya, Akihiko; Konishi, Fumikazu; Hatakeyama, Mariko; Satou, Kenji

doi:10.1007/bf03040955

Cited by 17 publications

(8 citation statements)

References 5 publications

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“…One of these is the Open Bioinformatics Grid (OBI Grid) (Konagaya, Konishi, Hatakeyama, & Satou, 2004) started in 2002. Its goal is to provide application tools such as distributed bioinformatics environments, scalable genome databases, genome annotation systems, and biochemical simulators, among others, to the social structure of virtual organization of the participating researchers and engineers.…”

Section: Grid Development and Biomedical Applications In Japanmentioning

confidence: 99%

A review of medical grids and their direction - A Swiss/Japanese perspective

Nakai¹,

Müller²,

Bagarinao³

et al. 2015

IJRSC

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This paper presents a general and comparative review of the advances of grid technologies in medical sciences since 2000, with a special emphasis on Europe and Japan. The EU has over the years funded several big projects in the Grid and now the cloud area, covering besides the high energy physics domain also bioinformatics and medical applications as in image analysis. Bioinformatics and pharmaceutical design have been the major targets of grid applications in Japan. Grids and clouds share many of the same goals and techniques, although clouds are more commercially oriented and privately provided services and grids are rather publicly initiated resource sharing platforms between institutions without strong economic objectives. In the future, merging these two may potentially solve inter-operation problems of grids, which have been limiting the propagation of biomedical grids.

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Section: Grid Development and Biomedical Applications In Japanmentioning

confidence: 99%

A review of medical grids and their direction - A Swiss/Japanese perspective

Nakai¹,

Müller²,

Bagarinao³

et al. 2015

IJRSC

View full text Add to dashboard Cite

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“…Grid is also attractive for the formation of community known as virtual organizations [8]. Such formation requires 'Ba', that Manuscript received February 13, 2006.…”

Section: Introductionmentioning

confidence: 99%

OBIGrid: towards the 'Ba' for sharing resources, services and knowledge for bioinformatics

Konagaya

2006

Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06)

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Open Bioinformatics Grid (OBIGrid) was established in 2002 for sharing the bioinformatics environment including computational resources, public databases, and bioinformatics application tools over the Internet. Grid is one of the most attractive cyber infrastructures for achieving scalability in the computation power and data storage necessary for bioinformatics. Grid also plays the role of 'Ba', the basis of virtual organizations in which people share time and place to work together. 'Ba' can extend beyond the boundaries of current grid computing by utilizing web service technologies for sharing databases, tools, and knowledge distributed all over the world.However, many issues regarding the widespread use of the web services have been raised, such as the semantic gap between bioinformatics workflows and the application programming interfaces provided by web services. The key to solving such issues is the bioinformatics ontology employed to establish interoperability among biological databases and bioinformatics application tools used by the web services. This paper proposes a design of bioinformatics ontology based on triadic relations among input-output data, commands, and databases, and demonstrates its feasibility in the automatic generation of bioinformatics workflows.

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“…Grid computing has been proposed as a potential solution to these requirements [12][13][14]. The Grid can be used to integrate genome data sources and computing resources to build integrated genome databases and powerful computing environments for genomic data processing, in particular for genome analysis and comparative genomics.…”

Section: Introductionmentioning

confidence: 99%

A grid-based system for microbial genome comparison and analysis

Sun¹,

Wipat²,

Pocock³

et al. 2005

CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.

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Genome comparison and analysis can reveal the structures and functions of genome sequences of different species. As more genomes are sequenced, genomic data sources are rapidly increasing such that their analysis is beyond the processing capabilities of most research institutes. The Grid is a powerful solution to support large-scale genomic data processing and genome analysis. This paper presents the Microbase project that is developing a Grid-based system for genome comparison and analysis, and discusses thefirst implementation ofthe system (called MicrobaseLite). MicrobaseLite uses a scalable computing environment to support computationally intensive microbial genome comparison and analysis, employing state-of-the-art technologies of Web Services, notification, comparative genomics and parallel computing. Microbase will support not only system-defined genome comparison and analysis but also user-defined, remotely conceived genome analysis.

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The superstructure toward open bioinformatics grid

Cited by 17 publications

References 5 publications

A review of medical grids and their direction - A Swiss/Japanese perspective

A review of medical grids and their direction - A Swiss/Japanese perspective

OBIGrid: towards the 'Ba' for sharing resources, services and knowledge for bioinformatics

A grid-based system for microbial genome comparison and analysis

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