Trends in life science grid: from computing grid to knowledge grid

Konagaya, Akihiko

doi:10.1186/1471-2105-7-s5-s10

Cited by 19 publications

(15 citation statements)

References 35 publications

(31 reference statements)

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“…Not every programmer codes in the same way, and it may be that they have a tacit, rather than codified, understanding of how the system is structured and how it is to be maintained. While Konagaya (2006) has argued that knowledge grids could be designed 'for sharing tacit knowledge among a community', the individual stylization of programming can nevertheless cause problems for long-term maintenance of biological databases.…”

Section: Maintenancementioning

confidence: 99%

Socio-Cultural characteristics of usability of bioinformatics databases and tools

Douglas

Goulding

Ferris

et al. 2011

Interdisciplinary Science Reviews

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With the increasing importance of the usability of bioinformatics systems and databases, this paper examines the socio-cultural characteristics that may affect the usability of such tools. We understand socio-cultural characteristics to be the norms, values, and beliefs that mediate the interactions between the structures and institutions of science (i.e. disciplines, universities, funding organizations), and its practitioners. These factors are not necessarily distinct from the technical features of a database, but do nevertheless affect the context in which one chooses to use a particular set of tools. We have developed three socio-cultural characteristics of bioinformatics database usability: accessibility, utility, and portability. By 'accessibility', we mean the social and cultural attributes that make resources open and available for use, such as intellectual property arrangements or institutional reputation and prestige. 'Utility' in this context means the perceived usefulness of a database, which can be determined by non-technical matters such as trust and taste. 'Portability' refers to the social aspects of criteria such as maintenance funding, and input and storing standards that allow a database 56 CONOR DOUGLAS et al. to move through space and time. In this article, we call for a social science research programme on these -and other -socio-cultural characteristics to usability. We invite researchers in human-computer interaction, bioinformatics, usability engineering and other areas to extend their work to examine the social contexts in which these systems are used, and the sociocultural factors that mediate their use. Such a research programme would increase the multidisciplinary nature of these emergent fields, and help address the complexities of work in the post-genomic era.

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Section: Maintenancementioning

confidence: 99%

Socio-Cultural characteristics of usability of bioinformatics databases and tools

Douglas

Goulding

Ferris

et al. 2011

Interdisciplinary Science Reviews

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“…Grid technology allows users to have access to services without knowledge of, or expertise with, or control of the infrastructure which supports them. Recently, grid technology has been embraced by the field of biomedicai informatics [20] for research purposes particularly in imaging informatics and translational clinical research [21]. Grid computing applied to the public health domain has currently been on the rise and each of these study has demonstrated the potential benefits of leveraging grid technology in the public health domain [22][23][24][25][26].…”

Section: Introductionmentioning

confidence: 99%

Implementing public health analytical services: Grid enabling of MetaMap

Davis

Price

Facelli

2013

Proceedings of the 26th IEEE International Symposium on Computer-Based Medical Systems

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Public health data could be used to assist with public health surveillance and decision support. However, in most cases data has to be transformed into a coded format to make it computable and amiable to quasi real time analytical processing. Natural language processing (NLP) systems, which aim to accurately extract and encode biomedicai information in a Standardformat, have a great potential in surveillance. NLP methods are complex, difficult, and

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“…A virtual grid resource specification captures the desired resources for an application, and its explicit resource structure can be used by the application designer to express parallelism, communication, and other forms of optimization. The primary goal of grid computing platforms is to seamlessly multiplex distributed computational resources with its associated providers and end users across wide area networks [12]. In traditional computing environments, resources are multiplexed based on typical operating systems confined to limited resources.…”

Section: Introductionmentioning

confidence: 99%

A comparative analysis of dynamic grids vs. virtual grids using the A3pviGrid framework

Shankaranarayanan¹,

Amaldas²

2010

Bioinformation

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With the proliferation of Quad/Multi-core micro-processors in mainstream platforms such as desktops and workstations; a large number of unused CPU cycles can be utilized for running virtual machines (VMs) as dynamic nodes in distributed environments. Grid services and its service oriented business broker now termed cloud computing could deploy image based virtualization platforms enabling agent based resource management and dynamic fault management. In this paper we present an efficient way of utilizing heterogeneous virtual machines on idle desktops as an environment for consumption of high performance grid services. Spurious and exponential increases in the size of the datasets are constant concerns in medical and pharmaceutical industries due to the constant discovery and publication of large sequence databases. Traditional algorithms are not modeled at handing large data sizes under sudden and dynamic changes in the execution environment as previously discussed. This research was undertaken to compare our previous results with running the same test dataset with that of a virtual Grid platform using virtual machines (Virtualization). The implemented architecture, A3pviGrid utilizes game theoretic optimization and agent based team formation (Coalition) algorithms to improve upon scalability with respect to team formation. Due to the dynamic nature of distributed systems (as discussed in our previous work) all interactions were made local within a team transparently. This paper is a proof of concept of an experimental mini-Grid test-bed compared to running the platform on local virtual machines on a local test cluster. This was done to give every agent its own execution platform enabling anonymity and better control of the dynamic environmental parameters. We also analyze performance and scalability of Blast in a multiple virtual node setup and present our findings. This paper is an extension of our previous research on improving the BLAST application framework using dynamic Grids on virtualization platforms such as the virtual box.

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Trends in life science grid: from computing grid to knowledge grid

Abstract: Background: Grid computing has great potential to become a standard cyberinfrastructure for life sciences which often require high-performance computing and large data handling which exceeds the computing capacity of a single institution.

Cited by 19 publications

References 35 publications

Socio-Cultural characteristics of usability of bioinformatics databases and tools

Socio-Cultural characteristics of usability of bioinformatics databases and tools

Implementing public health analytical services: Grid enabling of MetaMap

A comparative analysis of dynamic grids vs. virtual grids using the A3pviGrid framework

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