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7 Cyberinfrastructure and Data Acquisition
Pages 227-246

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From page 227...
... · Data repositories that are well curated and that store and make available to all researchers large volumes and many types of biological data, both in raw form and as associated derived products. Such repositories must store data, of course, but they must also organize, manage, and document these 1 "Revolutionizing Science and Engineering Through Cyberinfrastructure: Report of the NSF Blue-Ribbon Advisory Panel on Cyberinfrastructure," 2003, available at http://www.communitytechnology.org/nsf_ci_report/report.pdf.
From page 228...
... Also, they are likely to have a major role in ensuring the data interoperability necessary when data collected in one context are made available for use in another. · Digital libraries that contain the intellectual legacy of biological researchers and provide mechanisms for sharing, annotating, reviewing, and disseminating knowledge in a collaborative context.
From page 229...
... For NSF BIO to underestimate the importance of cyberinfrastructure for biology, or fail to provide fuel over the entire journey, would severely retard progress and be very damaging for the entire national and international biological sciences community. SOURCE: Adapted from Subcommittee on 21st Century Biology, NSF Directorate for Biological Sciences Advisory Committee, Building a Cyberinfrastructure for the Biological Sciences 2005 and Beyond: A Roadmap for Consolidation and Exponentiation, a workshop report, July 14-15, 2003.
From page 230...
... The discussion below focuses primarily on computing and networking. Box 7.2 Examples of Possible Elements of a Cyberinfrastructure for Biology Pacific Rim Application and Grid Middleware Assembly The Pacific Rim Application and Grid Middleware Assembly (PRAGMA)
From page 231...
... NEON is a continental-scale research instrument consisting of geographically distributed networked infra structure, with lab and field instrumentation; site-based experimental infrastructure; natural history archive facilities; and computational, analytical, and modeling capabilities. NEON is intended to transform ecological research by enabling studies on major environmental challenges at regional to continental scales.
From page 232...
... in processing capability would enable great progress in problem domains such as protein folding (ab initio prediction of three-dimensional structure from one-dimensional sequence information) , simulation methods based on quantum mechanics that can provide more accurate predictions of the detailed behavior of interesting biomolecules in solution,4 simulations of large numbers of interacting macromolecules for times of biological interest (i.e., for microseconds and involving millions of atoms)
From page 233...
... Binding of the receptor initiates a cascade of protein conformational changes through the cell membrane, involving a com plex rearrangement of many different proteins, including the Ras enzyme. The Ras enzyme is a molecular switch that can initiate a cascade of protein kinases that in turn transfer the external signal to the cell nucleus where it controls cell proliferation and differentiation.
From page 234...
... Three types of computational problem in biology must be distinguished.5 Problems such as protein folding and the simulation of biological systems are similar to other simulation problems that involve substantial amounts of "number crunching." A second type of problem entails large-scale comparisons or searches in which a very large corpus of data -- for example, a genomic sequence or a protein database -- is compared against another corpus, such as another genome or a large set of unclassified protein sequences. In this kind of problem, the difficult technical issues involve the lack of good software for broadcast and parallel access disk storage subsystems.
From page 235...
... -supported research sites to merge data grid and computer grid cyberinfrastructure into the workflows of biomedical research. The Brain Morphometry BIRN, one of the testbeds driving the development of BIRN, has undertaken a project that uses the new technology by integrating data and analysis methodology drawn from the participating sites.
From page 236...
... and the goal of the MIRIAD project is to measure the changes in brain images, specifically volume changes in cortical and subcortical gray matter, that correlate with clinical outcome. Of particular significance from the standpoint of cyberinfrastructure, the MIRIAD project is distributed among four separate sites: Duke University Neuropsychiatric Imaging Research Laboratory, Brigham and Women's Hospital Surgical Planning Laboratory, University of California, Los Angeles Laboratory of Neuro Imaging, and University of California, San Diego BIRN.
From page 237...
... In addition, protein databases were doubling in size every 12 months. Since 1999, more advanced models of automated DNA sequencer have come into widespread use.13 Today, a state-of-the-art automated sequencer can produce on the order of a million base pairs of raw DNA sequence data per day.
From page 238...
... While microarray experiments provide information on average levels of mRNA or protein within a cell population, the reality is that these levels vary from cell to cell. Knowing the distribution of expression levels across cell types provides important information about the underlying control mechanisms and regulatory network structure.
From page 239...
... Finally, a specialized type of data acquisition technology is the hybrid measurement device that interacts directly with a biological sample to record data from it or to interact with it. As one illustration, contemporary tools for studying neuronal signaling and information processing include implantable probe arrays that record extracellularly or intracellularly from multiple neurons simultaneously.
From page 240...
... This application illustrated that the dynamic clamp effectively introduces a conductance into the target neuron. Demonstration of an artificial voltage-dependent conductance resulted from simulation of the action of a voltage-dependent proctolin response on a neuron in the intact stomatogastric ganglion, which showed that shifts in the activation curve and the maximal conduc tance of the response produced different effects on the target neuron.
From page 241...
... Heiner, et al., "Fluorescence Detection in Automated DNA Sequence Analysis," Nature 321(6071)
From page 242...
... classifies emerging ultralow-cost sequencing technologies into one of five groups: microelectrophoretic methods (which extend and incrementally improve today's mainstream sequencing technologies first developed by Frederick Sanger) ; sequencing by hybridization; cyclic array sequencing on amplified molecules; cyclic array sequencing on single molecules; and noncyclical, single-molecule, real-time methods.
From page 243...
... Mishra, Genomics via Optical Mapping (I) : 0-1 Laws for Single Molecules, S
From page 244...
... By contrast, pharmaceutical firms invested heavily in robotic laboratory automation, and automated facilities to synthesize candidate drugs and to screen their biological effects provided three- to fivefold increases in the number of new compounds screened per unit time. In recent years, manufacturers have marketed "modular" laboratory automation products, including modules for specimen centrifugation and aliquoting, specimen analysis, and postanalytical storage and retrieval.
From page 245...
... While for many types of experiments this is an appropriate approach, there are current and future biological research issues for which this does not provide sufficient resolution. For example, cells within a population may be in different stages of their life cycle, may be experiencing local variations of environmental conditions, or may be of entirely different types.
From page 246...
... Detection and analysis at such low levels must work even in the face of wide statistical fluctuation, transient modifications, and a wide range of physical and chemical properties.33 At the finest grain, detection and analysis of single molecules could provide further understanding of cellular mechanisms. Again, although there are current techniques to analyze molecular structure (such as nuclear magnetic resonance and X-ray crystallography)


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