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HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
Journal of Cheminformatics ( IF 8.6 ) Pub Date : 2019-12-05 , DOI: 10.1186/s13321-019-0399-7
Julien Wist

Metabolic profiling has been shown to be useful to improve our understanding of complex metabolic processes. Shared data are key to the analysis and validation of metabolic profiling and untargeted spectral analysis and may increase the pace of new discovery. Improving the existing portfolio of open software may increase the fraction of shared data by decreasing the amount of effort required to publish them in a manner that is useful to others. However, a weakness of open software, when compared to commercial ones, is the lack of user-friendly graphical interface that may discourage inexperienced researchers. Here, a web-browser-oriented solution is presented and demonstrated for metabolic profiling analysis that combines the power of R for back-end statistical analyses and of JavaScript for front-end visualisations and user interactivity. This unique combination of statistical programming and web-browser visualisation brings enhanced data interoperability and interactivity into the open source realm. It is exemplified by characterizing the extent to which bariatric surgery perturbs the metabolisms of rats, showing the value of the approach in iterative analysis by the end-user to establish a deeper understanding of the system perturbation. HastaLaVista is available at: (https://github.com/jwist/hastaLaVista, https://doi.org/10.5281/zenodo.3544800) under MIT license. The approach described in this manuscript can be extended to connect the interface to other scripting languages such as Python, and to create interfaces for other types of data analysis.

中文翻译:

HastaLaVista,基于Web的用户界面,用于生物医学科学中基于NMR的非目标代谢谱分析:迈向新的出版标准

代谢谱分析已被证明有助于增进我们对复杂代谢过程的理解。共享数据是代谢谱分析和非目标光谱分析的分析和验证的关键,并且可能会加快新发现的步伐。改进现有开放软件组合可能会减少共享数据的发布量,从而减少以对他人有用的方式发布共享数据所需的工作量。但是,与商业软件相比,开放软件的一个缺点是缺乏用户友好的图形界面,这可能会使经验不足的研究人员望而却步。在此,针对代谢谱分析提出并演示了面向Web浏览器的解决方案,该解决方案结合了R的功能(用于后端统计分析)和JavaScript的功能(用于前端可视化和用户交互)。统计编程和Web浏览器可视化的这种独特结合将增强的数据互操作性和交互性带入了开源领域。通过表征减肥手术对大鼠新陈代谢的影响程度来举例说明,表明最终用户在进行迭代分析以建立对系统扰动的更深入理解方面该方法的价值。在麻省理工学院(MIT)许可下,可在(https://github.com/jwist/hastaLaVista,https://doi.org/10.5281/zenodo.3544800)上获取HastaLaVista。可以扩展本手稿中描述的方法,以将接口连接到其他脚本语言(例如Python),并创建用于其他类型的数据分析的接口。
更新日期:2019-12-05
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