共查询到20条相似文献,搜索用时 7 毫秒
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Allan C Burel JM Moore J Blackburn C Linkert M Loynton S Macdonald D Moore WJ Neves C Patterson A Porter M Tarkowska A Loranger B Avondo J Lagerstedt I Lianas L Leo S Hands K Hay RT Patwardhan A Best C Kleywegt GJ Zanetti G Swedlow JR 《Nature methods》2012,9(3):245-253
Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/. 相似文献
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Catherine S. Jarnevich James J. Graham Gregory J. Newman Alycia W. Crall Thomas J. Stohlgren 《Biological invasions》2007,9(5):597-599
Data sensitivity can pose a formidable barrier to data sharing. Knowledge of species current distributions from data sharing
is critical for the creation of watch lists and an early warning/rapid response system and for model generation for the spread
of invasive species. We have created an on-line system to synthesize disparate datasets of non-native species locations that
includes a mechanism to account for data sensitivity. Data contributors are able to mark their data as sensitive. This data
is then ‘fuzzed’ in mapping applications and downloaded files to quarter-quadrangle grid cells, but the actual locations are
available for analyses. We propose that this system overcomes the hurdles to data sharing posed by sensitive data. 相似文献
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Martin Latterich 《Proteome science》2006,4(1):8-3
Scientific publications should provide sufficient detail in terms of methodology and presented data to enable the community
to reproduce the methodology to generate similar data and arrive at the same conclusion, if an identical sample is provided
for analysis. The advent of high-throughput methods in biological experimentation impose some unique challenges both in data
presentation in classical print format, as well as in describing methodology and data analysis in sufficient detail to conform
to good publication practice. To facilitate this process, Proteome Science is adopting a set of methodology and data presentation
guidelines to enable both peer reviewers, as well as the scientific community, to better evaluate high-throughput proteomic
studies. 相似文献
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Peter Güntert Volker Dötsch Gerhard Wider Kurt Wüthrich 《Journal of biomolecular NMR》1992,2(6):619-629
Summary The new program PROSA is an efficient implementation of the common data-processing steps for multi-dimensional NMR spectra. PROSA performs linear prediction, digital filtering, Fourier transformation, automatic phase correction, and baseline correction. High efficiency is achieved by avoiding disk storage of intermediate data and by the absence of any graphics display, which enables calculation in the batch mode and facilitates porting PROSA on a variety of different computer systems; including supercomputers. Furthermore, all time-consuming routines are completely vectorized. The elimination of a graphics display was made possible by the use of a new, reliable automatic phase-correction routine. CPU times for complete processing of a typical heteronuclear three-dimensional NMR data set of a protein vary between less than 1 min on a NEC SX3 supercomputer and 40 min on a Sun-4 computer system. 相似文献
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Sabine Gradmann Christian Ader Ines Heinrich Deepak Nand Marc Dittmann Abhishek Cukkemane Marc van Dijk Alexandre M. J. J. Bonvin Martin Engelhard Marc Baldus 《Journal of biomolecular NMR》2012,54(4):377-387
We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such ??in silico?? data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of sample labeling in light of spectral resolution and structural content, using standard NMR software such as Sparky. In addition, direct comparison to experimental data sets can be used to validate NMR assignments, distinguish different molecular components, refine structural models or other parameters derived from NMR data. The method is demonstrated in the context of solid-state NMR data obtained for the cyclic nucleotide binding domain of a bacterial cyclic nucleotide-gated channel and on membrane-embedded sensory rhodopsin II. FANDAS is freely available as web portal under WeNMR (http://www.wenmr.eu/services/FANDAS). 相似文献
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J M Carazo E H Stelzer A Engel I Fita C Henn J Machtynger P McNeil D M Shotton M Chagoyen P A de Alarcn R Fritsch J B Heymann S Kalko J J Pittet P Rodriguez-Tom T Boudier 《Nucleic acids research》1999,27(1):280-283
Nowadays it is possible to unravel complex information at all levels of cellular organization by obtaining multi-dimensional image information. At the macromolecular level, three-dimensional (3D) electron microscopy, together with other techniques, is able to reach resolutions at the nanometer or subnanometer level. The information is delivered in the form of 3D volumes containing samples of a given function, for example, the electron density distribution within a given macromolecule. The same situation happens at the cellular level with the new forms of light microscopy, particularly confocal microscopy, all of which produce biological 3D volume information. Furthermore, it is possible to record sequences of images over time (videos), as well as sequences of volumes, bringing key information on the dynamics of living biological systems. It is in this context that work on BioImage started two years ago, and that its first version is now presented here. In essence, BioImage is a database specifically designed to contain multi-dimensional images, perform queries and interactively work with the resulting multi-dimensional information on the World Wide Web, as well as accomplish the required cross-database links. Two sister home pages of BioImage can be accessed at http://www. bioimage.org and http://www-embl.bioimage.org 相似文献
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We use the quasilikelihood concept to propose an estimatingequation for spatial data with correlation across the studyregion in a multi-dimensional space. With appropriate mixingconditions, we develop a central limit theorem for a randomfield under various Lp metrics. The consistency and asymptoticnormality of quasilikelihood estimators can then be derived.We also conduct simulations to evaluate the performance of theproposed estimating equation, and a dataset from East LansingWoods is used to illustrate the method. 相似文献
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Becker KG 《Nature reviews. Neuroscience》2001,2(6):438-440
During the initial development of microarrays, much discussion revolved around the technology itself. The discussion has now shifted to data analysis and data sharing. There is great interest in the sharing of cDNA microarray data, but several issues related to format, quality and validation will need to be resolved before microarray data can be meaningfully integrated into other molecular databases. 相似文献
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Ipek Demir 《New genetics and society》2013,32(4):350-365
Despite the centrality of epistemic issues in biobank knowledge generation, there is currently a lacuna in research addressing the epistemic assumptions of biobank science and data sharing. The article addresses this lacuna. Using the insights of philosophical and sociological analysis, we examine standardization and harmonization and central challenges biobank data-sharing faces. We defend two central epistemic values, namely “spatial and temporal translatability” and “epistemic adequacy” which foster effective biobank knowledge generation. The first refers to the way in which biobank data need to be re-usable and re-purposable by bioscience researchers who did not create them. Given the perennial issues of data mutability and incommensurability, we also propose “epistemic adequacy.” In uncovering the social and epistemic foundations of biobank science, we emphasize issues essential for achieving effective and transparent biobank practice and productive communication and engagement with the public about the nature, potential and limits of biobanks. 相似文献
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