phpMs: A PHP-Based Mass Spectrometry Utilities Library,Journal of Proteome Research

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phpMs: A PHP-Based Mass Spectrometry Utilities Library
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2018-02-13 00:00:00 , DOI: 10.1021/acs.jproteome.7b00783
Andrew Collins ₁ , Andrew R. Jones ₁

Affiliation

The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs.

中文翻译：

phpMs：一个基于PHP的质谱实用程序库

云计算，高吞吐量网络以及更通用的Web标准和浏览器的最新建立引起了人们对基于Web的应用程序的新兴趣。尽管传统上大数据已成为优化的台式机和服务器应用程序的领域，但现在可以在云存储和计算提供商中存储大量数据并在异地执行必要的计算，并在高质量的跨平台中可视化结果通过网络浏览器的界面。有许多新兴的平台可用于基于云的质谱数据分析。但是，Web开发人员可以访问的现有代码有限，特别是对于那些受限于共享托管环境的代码，在该环境中，托管提供程序通常禁止使用Java和C应用程序。为了解决这个问题，我们为最常用的Web开发语言之一PHP提供了一个开源质谱库。我们的新库phpMs提供了用于存储和操作光谱和识别数据的对象，以及用于文件读取，文件写入，计算，肽片段化和蛋白质消化的实用程序，以及用于控制搜索引擎的软件界面。我们在http://pgb.liv.ac.uk/phpMs上提供了一些功能的工作演示。

更新日期：2018-02-13

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