JCAMP-DX for NMR

Davies, Antony N.; Lampen, Peter

doi:10.1366/0003702934067874

Cited by 81 publications

(65 citation statements)

References 3 publications

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“…The user can also measure the distance between two points of the 2D window. One can add curve by reading a text multiple columns file, JDX format [16][17][18] file, and JMRui 19 text file (Fig. 6).…”

Section: Other Propertiesmentioning

confidence: 99%

Gabedit—A graphical user interface for computational chemistry softwares

2010

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Gabedit is a freeware graphical user interface, offering preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. It includes tools for editing, displaying, analyzing, converting, and animating molecular systems. A conformational search tool is implemented using a molecular mechanics or a semiempirical potential. Input files can be generated for the computational chemistry software supported by Gabedit. Some molecular properties of interest are processed directly from the output of the computational chemistry programs; others are calculated by Gabedit before display. Molecular orbitals, electron density, electrostatic potential, nuclear magnetic resonance shielding density, and any other volumetric data properties can be displayed. It can display electronic circular dichroism, UV-visible, infrared, and Raman-computed spectra after a convolution. Gabedit can generate a Povray file for geometry, surfaces, contours, and color-coded planes. Output can be exported to a selection of popular image and vector graphics file formats; the program can also generate a series of pictures for animation. Quantum mechanical electrostatic potentials can be calculated using the partial charges on atoms, or by solving the Poisson equation using the multigrid method. The atoms in molecule charges can also be calculated. Gabedit is platform independent. The code is distributed under free open source X11 style license and is available at

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Section: Other Propertiesmentioning

confidence: 99%

Gabedit—A graphical user interface for computational chemistry softwares

2010

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“…The reporting requirements specify the required content of FID and spectra based on the JCAMP-DX format for NMR (Davies and Lampen, 1993;Lampen et al, 1999). This format was designed for spectral data transfer without loss of information.…”

Section: Data Setsmentioning

confidence: 99%

“…These databases are mainly built to facilitate deposition of NMR spectra together with various amounts of associated metadata. In addition, data exchange formats for NMR data sets are available from both the CCPN project (Fogh et al, 2002;Vranken et al, 2005), that offers a data model for macromolecular NMR and related areas, and JCAMP-DX (Davies and Lampen, 1993;Lampen et al, 1999). Also, a more general XML (eXtensible Markup Language) (http:// www.w3.org/TR/xml11) format for analytical chemistry, that is currently in pre-release form, has been developed by the AnIML (Analytical Information Markup Language) (http://www.animl.sourceforge.net/) initiative.…”

Section: Introductionmentioning

confidence: 99%

Proposed reporting requirements for the description of NMR-based metabolomics experiments

et al. 2007

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The amount of data generated by NMR-based metabolomic experiments is increasing rapidly. Furthermore, diverse techniques increase the need for informative and comprehensive meta-data. These factors present a challenge in the dissemination, interpretation, reviewing and comparison of experimental results using this technology. Thus, there is a strong case for unification and standardisation of the data representation for both academia and industry. Here, a systems analysis of an NMR-based metabolomics experiment is presented in order to reveal the reporting requirements. An in-depth analysis of the NMR component of a metabolomics experiment has been produced, and a first round of data standard development completed. This has focussed on both one-and two-dimensional 1 H NMR experiments, but is also applicable to higher dimensions and other nuclei. We also report the modelling of this schema using Unified Modelling Language (UML), and have extended this to a proof-of-concept implementation of the standard as an XML schema.

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“…This will happen in two phases: The techniques chosen for Phase 1 all have agreed upon ontologies, documented data dictionaries, and existing standardized file formats for their result data. [1][2][3][4][5][6][7][8][9][10][11][12] Domain expertise for many of these techniques exists within the other subcommittees of ASTM E-13 and within the IUPAC Subcommittee on Electronic Data Standards. However, we are seeking collaborations with other groups of domain experts to augment this list.…”

Section: Standards Development Processmentioning

confidence: 99%

Documenting Laboratory Workflows Using the Analytical Information Markup Language

Schäfer

Poetz

Kramer

2004

JALA: Journal of the Association for Laboratory Automation

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T he Analytical Information Markup Language (AnIML) is a standardization effort of ASTM (formerly American Society for Testing and Materials) Subcommittee E13.15 on Analytical Data. AnIML provides an XML-based format for analytical data. It is designed specifically for spectroscopy and chromatography data, but is suitable for use with many different analytical measurement techniques. AnIML consists of a generic core structure that permits the storage of arbitrary analytical data. These include multi-dimensional data, name-value pairs, and hierarchies. The concept of technique definitions permits the formal specification of constraints for usage of the core. This way, a definition can prescribe how the data for specific measurement techniques should be captured in the data file. To address changing requirements, AnIML supports an extension concept that allows vendors or end users to specify additional data that should be stored for a technique. These extensions can also be formally documented so that they do not break compatibility with existing software. This article presents an overview of AnIML and demonstrates how AnIML can be used to record data from everyday experimental workflows in a laboratory environment. Issues related to the usage of AnIML in regulated environments are also discussed, including the use of digital signatures and audit trail functionality to ensure data integrity. ( JALA 2004;9:375-81) This project is funded (in part) by NIST's Systems Integration for Manufacturing Applications (SIMA) Program.

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JCAMP-DX for NMR

Cited by 81 publications

References 3 publications

Gabedit—A graphical user interface for computational chemistry softwares

Gabedit—A graphical user interface for computational chemistry softwares

Proposed reporting requirements for the description of NMR-based metabolomics experiments

Documenting Laboratory Workflows Using the Analytical Information Markup Language

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