CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis.

Simon P Skinner,Timothy J Ragan,Geerten W Vuister,Rasmus H Fogh,Luca G Mureddu,Wayne Boucher

doi:10.1007/s10858-016-0060-y

Simon P Skinner, Timothy J Ragan + Show 4 more

Open Access

https://doi.org/10.1007/s10858-016-0060-y

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Abstract

NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations.

Highlights

NMR spectroscopy is an incredibly powerful, non-invasive, analytical technique used in many areas of research, including materials science, medical diagnosis, industrial process control and chemistry
We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow
According to BMRB statistics, the five most cited packages for NMR analysis are Sparky (Goddard and Kneller), Cara (Keller 2005), CcpNmr Analysis (Vranken et al 2005), NmrView (Johnson and Blevins 1994) and XEASY (Bartels et al 1995), such analysis is somewhat flawed as the depositors are not required to specify the software used for their studies

Summary

Introduction

NMR spectroscopy is an incredibly powerful, non-invasive, analytical technique used in many areas of research, including materials science, medical diagnosis, industrial process control and chemistry (ur-Rahman and Choudhary 2015). AnalysisAssign has been written using modern software engineering principles, including the complete and clean separation of graphical and data code This separation ensures that graphical developers need only interact with graphical code and do not need a deep understanding of data handling routines and vice versa. Data routines and graphical interfaces can be developed independently and fused together when needed This ensures a greater level of maintainability and testability of the code base, leading to highly robust and stable software. We have created a so-called ‘‘wrapper layer’’ around the main CCPN data API (Fogh et al 2010) to enable access to the data via a simple, Python-based, command interface Using this wrapper layer, a user can create their own macros in a language that spectroscopists understand. This transparency of both graphical components and data access make the CcpNmr version-3 software platform very easy to extend without having to learn an entire software framework first, as is currently the case with Sparky, for example

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