CONNJUR spectrum translator: an open source application for reformatting NMR spectral data

Abstract

NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, instead of writing a separate converter to each existing format. Secondly, the use of layout descriptors allows a single fid data translation engine to be used for all formats. For the end user, sophisticated metadata readers allow conversion of the majority of files with minimum user configuration. The open source code is freely available at http://connjur.sourceforge.net for inspection and extension.Electronic supplementary materialThe online version of this article (doi:10.1007/s10858-011-9497-1) contains supplementary material, which is available to authorized users.

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction

“…This same library, when coupled with a command line interface, is released separately as CONNJUR ST (Nowling et al 2011). …”

“…We had previously released a Java application for translating binary spectral data between the various software specific file formats (Nowling, et al, 2011). In this paper we describe a larger-scope software integration application – CONNJUR Workflow Builder (WB).…”

An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities

“…We have previously deployed applications [6] which leverage the CONNJUR framework [7] for data integration, the BioJava library [8] for analyzing proteins sequences and structures, as well as the Jmol tool [9] for molecular visualization. One of the concerns that small laboratories face in designing large, data driven applications is the maintenance of their code base, which can grow quite rapidly.…”

A Pipeline Software Architecture for NMR Spectrum Data Translation

“…Our vision is to develop a comprehensive application that integrates a variety of data analysis tools with data management to support the process of protein structure determination using NMR [4, 5]. One main component of this integrated environment is a spectrum converter, the CONNJUR Spectrum Translator (CONNJUR-ST) tool.…”

“…CONNJUR-ST supports the translation of data between the formats used by both different spectrometers as well as the variety of tools used to process the data. The application of CONNJUR-ST to processing NMR data for an NMR audience as well as initial development efforts is described in [4]. In this paper, we provide a comprehensive description of the CONNJUR-ST architecture, how it works, and its possible application to other domains, as well as a detailed discussion of the difficulties of data translation in the NMR domain.…”