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

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. RESULTS: This survey reviews the latest grid technologies from the viewpoints of computing grid, data grid and knowledge grid. Computing grid technologies have been matured enough to solve high-throughput real-world life scientific problems. Data grid technologies are strong candidates for realizing "resourceome" for bioinformatics. Knowledge grids should be designed not only from sharing explicit knowledge on computers but also from community formulation for sharing tacit knowledge among a community. CONCLUSION: Extending the concept of grid from computing grid to knowledge grid, it is possible to make use of a grid as not only sharable computing resources, but also as time and place in which people work together, create knowledge, and share knowledge and experiences in a community

A grid and cloud-based framework for high throughput bioinformatics

Recent advances in genome sequencing technologies have unleashed a flood of new data. As a result, the computational analysis of bioinformatics data sets has been rapidly moving from a labbased desktop computer environment to exhaustive analyses performed by large dedicated computing resources. Traditionally, large computational problems have been performed on dedicated clusters of high performance machines that are typically local to, and owned by, a particular institution. The current trend in Grid computing has seen institutions pooling their computational resources in order to offload excess computational work to remote locations during busy periods. In the last year or so, commercial Cloud computing initiatives have matured enough to offer a viable remote source of reliable computational power. Collections of idle desktop computers have also been used as a source of computational power in the form of ‘volunteer Grids’. The field of bioinformatics is highly dynamic, with new or updated versions of software tools and databases continually being developed. Several different tools and datasets must often be combined into a coherent, automated workflow or pipeline. While existing solutions are available for constructing workflows, there is a clear need for long-lived analyses consisting of many interconnected steps to be able to migrate among Grid and cloud computational resources dynamically. This project involved research into the principles underlying the design and architecture of flexible, high-throughput bioinformatics processes. Following extensive research into requirements gathering, a novel Grid-based platform, Microbase, has been implemented that is based on service-oriented architectures and peer-to-peer data transfer technology. This platform has been shown to be amenable to utilising a wide range of hardware from commodity desktop computers, to high-performance cloud infrastructure. The system has been shown to drastically reduce the bandwidth requirements of bioinformatics data distribution, and therefore reduces both the financial and computational costs associated with cloud computing. The system is inherently modular in nature, comprising a service based notification system, a data storage system scheduler and a job manager. In keeping with e-Science principles, each module can operate in physical isolation from each other, distributed within an intranet or Internet. Moreover, since each module is loosely coupled via Web services, modules have the potential to be used in combination with external service oriented components or in isolation as part of another system. In order to demonstrate the utility of such an open source system to the bioinformatics community, a pipeline of inter-connected bioinformatics applications was developed using the Microbase system to form a high throughput application for the comparative and visual analysis of microbial genomes. This application, Automated Genome Analyser (AGA) has been developed to operate without user interaction. AGA exposes its results via Web-services which can be used by further analytical stages within Microbase, by external computational resources via a Web service interface or which can be queried by users via an interactive genome browser. In addition to providing the necessary infrastructure for scalable Grid applications, a modular development framework has been provided, which simplifies the process of writing Grid applications. Microbase has been adopted by a number of projects ranging from comparative genomics to synthetic biology simulations.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Perspectives on distributed computing : thirty people, four user types, and the distributed computing user experience.

This report summarizes the methodology and results of a user perspectives study conducted by the Community Driven Improvement of Globus Software (CDIGS) project. The purpose of the study was to document the work-related goals and challenges facing today's scientific technology users, to record their perspectives on Globus software and the distributed-computing ecosystem, and to provide recommendations to the Globus community based on the observations. Globus is a set of open source software components intended to provide a framework for collaborative computational science activities. Rather than attempting to characterize all users or potential users of Globus software, our strategy has been to speak in detail with a small group of individuals in the scientific community whose work appears to be the kind that could benefit from Globus software, learn as much as possible about their work goals and the challenges they face, and describe what we found. The result is a set of statements about specific individuals experiences. We do not claim that these are representative of a potential user community, but we do claim to have found commonalities and differences among the interviewees that may be reflected in the user community as a whole. We present these as a series of hypotheses that can be tested by subsequent studies, and we offer recommendations to Globus developers based on the assumption that these hypotheses are representative. Specifically, we conducted interviews with thirty technology users in the scientific community. We included both people who have used Globus software and those who have not. We made a point of including individuals who represent a variety of roles in scientific projects, for example, scientists, software developers, engineers, and infrastructure providers. The following material is included in this report: (1) A summary of the reported work-related goals, significant issues, and points of satisfaction with the use of Globus software; (2) A method for characterizing users according to their technology interactions, and identification of four user types among the interviewees using the method; (3) Four profiles that highlight points of commonality and diversity in each user type; (4) Recommendations for technology developers and future studies; (5) A description of the interview protocol and overall study methodology; (6) An anonymized list of the interviewees; and (7) Interview writeups and summary data. The interview summaries in Section 3 and transcripts in Appendix D illustrate the value of distributed computing software--and Globus in particular--to scientific enterprises. They also document opportunities to make these tools still more useful both to current users and to new communities. We aim our recommendations at developers who intend their software to be used and reused in many applications. (This kind of software is often referred to as 'middleware.') Our two core recommendations are as follows. First, it is essential for middleware developers to understand and explicitly manage the multiple user products in which their software components are used. We must avoid making assumptions about the commonality of these products and, instead, study and account for their diversity. Second, middleware developers should engage in different ways with different kinds of users. Having identified four general user types in Section 4, we provide specific ideas for how to engage them in Section 5

Uji Efektivitas Pupuk Majemuk (10 : 6 : 20 : 2) 5 % Mikro Nutrient Pada Tanaman Jagung

Pupuk merupakan salah satu sarana produksi penting dalam meningkatkan produksi tanaman karena pupuk dapat menyediakan hara dalam memperbaiki pertumbuhan dan hasil tanaman, terutama bagi lahan lahan pertanaman yang kurang mengandung unsur hara makro seperti N,P dan K serta hara mikro. Kurangnya ketersediaan hara bagi tanaman dapat disebabkan oleh penggunaan lahan secara intensif sehingga tanah tidak mampu menyediakan hara yang cukup bagi pertumbuhan dan hasil tanaman. Oleh sebab itu untuk mempertahankan pertumbuhan dan hasil yang baik bagi tanaman perlu dilakukan tambahan nutrisi dari pupuk terutama unsur N, P, dan K. Penelitian dengan metode percobaan telah dilaksanakan di Kabupaten Pasaman Barat, Sumatera Barat dengan jenis tanah aluvial, di Laboratgorium Agronomi Jurusan Budidaya Pertanian dan di Laboratorium Ilmu Tanah, Fakultas Pertanian, Universitas Andalas, Padang pada bulan Agustus sampai Desember 2015. Rancangan yang digunakan adalah Acak Kelompok (RAK) dengan lima perlakuan dan empat ulangan. Masing-masing perlakuan yaitu tanpa pemupukan, pupuk tunggal Urea 300 kg/ha, SP-36 200 kg/ha, KCl 100 kg/ha,pupuk majemuk (10:6:20:2) 1.380 kg/ha, pupuk majemuk (10:6:20:2) 750 kg/ha + Urea 135 kg/ha, pupuk majemuk (10:6:20:2) 300 kg/ha + Urea 200 kg/ha. Hasil penelitian menunjukkan bahwa perlakuan pemupukan secara efektif dapat memperbaiki pertumbuhan dan hasil tanaman jagung. Pemberian pupuk tunggal (Urea 300 kg/ha, SP36 200 kg/ha, KCl 100 kg/ha), pupuk majemuk (10:6:20:2) (1380 kg/ha), kombinasi pupuk majemuk (10:6:20:2) 750 kg/ha + 135 Urea/ha, serta kombinasi pupuk majemuk (10:6:20:2) 300 kg/ha + Urea 200 kg/ha secara nyata dapat meningkatkan bobot pipilan kering tanaman jagung berturut turut 4,2 ton/ha, 4,8 ton/ha, 4,1 ton/ha dan 4,5 ton/ha. Kata kunci: pupuk majemuk , mikro nutrient, jagun

Biology

Low levels of secretory IgA (SIgA) and transient IgA deficiency have been associated with an increased risk for allergy, but data are conflicting. The aim was to assess the relationship between salivary SIgA antibody levels at 1 yr and wheezing at age four in a birth cohort, in particular the possible protective role of salivary SIgA in sensitized children. Saliva samples were obtained from all children (n = 67) with a positive skin prick test (SPT) at 1 yr and 212 children with a negative SPT. In all, 200 of these children responded to questionnaires at 4 yrs and 183 were skin prick tested at that age. The levels of salivary SIgA and salivary IgA antibodies to the most common food allergen egg and inhalant allergen cat were analyzed by ELISA. Serum was analyzed for IgE antibodies to egg and cat. Development of late-onset wheezing was associated with low SIgA levels in children with positive SPT to at least one allergen both at 1 and 4 yrs of age (p = 0.04), as well as in children with circulating IgE antibodies to egg or cat at 1 yr (p = 0.02). None of nine persistently sensitized children with SIgA levels in the upper quartile developed wheezing, when compared to 10/20 children with lower levels (p = 0.01). Older siblings, more than three infections during infancy, at least one smoking parent, and male gender, were all associated with SIgA in the upper quartile. In conclusion, high levels of SIgA antibodies in sensitized infants were associated with significantly less late-onset wheezing, supporting a protective role against development of asthmatic symptoms. Recurrent infections and other factors supporting an increased microbial pressure during infancy were associated with high levels of salivary SIgA.This is the authors’ version of:Anna Sandin, Bengt Bjorksten, Malin Fagerås Böttcher, Erling Englund, Maria Jenmalm and Lennart Braback, High salivary secretory IgA antibody levels are associated with less late-onset wheezing in IgE-sensitized infants, 2011, Pediatric Allergy and Immunology, (22), 5, 477-481.http://dx.doi.org/10.1111/j.1399-3038.2010.01106.xCopyright: John Wiley and Sonshttp://www.wiley.com