NeXus: A common format for the exchange of neutron and synchroton data

Klosowski, P.; Koennecke, Mark; Tischler, J. Z.; Osborn, R.

doi:10.1016/s0921-4526(97)00865-x

Cited by 30 publications

(23 citation statements)

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“…Together, these formats provide platform-independent binary data storage with the option of tagged metadata, yet the use of these tags is uneven at best (in fact, we have found that many light source TIFF files are not strictly compliant with the TIFF standard). Scientific data standards, on the other hand, provide an agreed-upon set of required, consistently named tags for recording crucial experimental metadata; this has long been a part of standards such as CIF and NeXus [1,2], and it is part of an APS-developed standard called DataExchange. DataExchange uses HDF5 files, and while NeXus also supports HDF4 and XML (with numerical data represented in character strings), most usage of NeXus now also centers on HDF5.…”

Section: Data File Standardsmentioning

confidence: 99%

“…NeXus is a standard for the storage of raw data acquired at neutron and X-ray user beamlines [2,5,6], which is coordinated by a committee representing 14 major facilities. Although it was initially adopted mainly at neutron facilities, X-ray facilities have played an increasing role in its development; e.g., with the project to become fully interoperable with imgCIF (see sites.google.com/site/nexuscbf and [6]) and with the decision of a leading X-ray detector manufacturer, DECTRIS, to use NeXus for their raw data format.…”

Section: Nexusmentioning

confidence: 99%

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Practices and Standards for Data and Processing at the APS

Toby

Gürsoy

Carlo

et al. 2015

Synchrotron Radiation News

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Section: Data File Standardsmentioning

confidence: 99%

Section: Nexusmentioning

confidence: 99%

Practices and Standards for Data and Processing at the APS

Toby

Gürsoy

Carlo

et al. 2015

Synchrotron Radiation News

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“…The other two experiments aim to determine the structure of atoms of matters (e.g. liquids or solids) using neutron techniques: one uses the neutron diffraction 6 provided by the GEM instrument 7 and the other small angle neutron scattering 8 offered by the Sandals instrument 9 . Both instruments are located at the ISIS neutron spallation source.…”

Section: A Backgroundmentioning

confidence: 99%

Enhancing the Core Scientific Metadata Model to Incorporate Derived Data

Yang

Matthews

Wilson

2010

2010 IEEE Sixth International Conference on E-Science

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The Core Scientific MetaData model (CSMD) is used by large scientific facilities to catalogue scientific data. The current version provides support to experimental scientists to access their raw data, facility managers for accounting for facility usage and other scientists who wish to re-use raw experimental data. Much of the value in scientific data is provided not only in the raw data but through the analysis of that data to derive published results. An analysis of the raw data analysis process for structural science has shown that various data sets derived from the raw data are of use to scientists and should be stored with the raw data. Extensions to the CSMD are presented to describe the analysis process so that the provenance of the derived data can be captured. A pilot implementation incorporating derived data through this extended CSMD model has been trialled with experimental scientists. Remaining challenges to the adoption of CSMD and tools it supports are considered.

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“…• CIF -crystallographic information file 13 • mmCIF -macromolecular crystallographic information file 14 • CML -chemical markup language 15 • PDB -original Protein Data Bank format for macromolecular structures 16 • MDL MOL -file format created by MDL for molecular structures 17 • CBF -crystallographic binary file 18 • NeXus -a common data format for neutron and X-ray data 19 The different online databases provide tools to support the preparation, validation, and deposition of different sets of file formats.…”

Section: Background and Objectivesmentioning

confidence: 99%

Collaborative Annotation of 3D Crystallographic Models

Hunter

Henderson

Khan

2007

J. Chem. Inf. Model.

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This paper describes the AnnoCryst systema tool that was designed to enable authenticated collaborators to share online discussions about 3D crystallographic structures through the asynchronous attachment, storage, and retrieval of annotations. Annotations are personal comments, interpretations, questions, assessments, or references that can be attached to files, data, digital objects, or Web pages. The AnnoCryst system enables annotations to be attached to 3D crystallographic models retrieved from either private local repositories (e.g., Fedora) or public online databases (e.g., Protein Data Bank or Inorganic Crystal Structure Database) via a Web browser. The system uses the Jmol plugin for viewing and manipulating the 3D crystal structures but extends Jmol by providing an additional interface through which annotations can be created, attached, stored, searched, browsed, and retrieved. The annotations are stored on a standardized Web annotation server (Annotea), which has been extended to support 3D macromolecular structures. Finally, the system is embedded within a security framework that is capable of authenticating users and restricting access only to trusted colleagues.

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NeXus: A common format for the exchange of neutron and synchroton data

Cited by 30 publications

References 0 publications

Practices and Standards for Data and Processing at the APS

Practices and Standards for Data and Processing at the APS

Enhancing the Core Scientific Metadata Model to Incorporate Derived Data

Collaborative Annotation of 3D Crystallographic Models

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