pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library
pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library
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DOI：
10.1002/pmic.201300246
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发表时间：
2014-01-01
期刊：
影响因子：
3.4
通讯作者：
Malmstroem, Lars
中科院分区：
文献类型：
--
作者：
Roest, Hannes L.;Schmitt, Uwe;Malmstroem, Lars
pyOpenMS 是一个基于 Python 的开源 C++ OpenMS 库接口，可轻松访问功能丰富的开源算法库，以进行基于 MS 的蛋白质组学分析。它包含 Python 绑定，允许对 OpenMS 中实现的数据结构和算法进行原始访问，特别是文件访问（mzXML、mzML、TraML、mzIdentML 等）、基本信号处理（平滑、过滤、去同位素和峰值选取）和复杂数据分析（包括无标签、SILAC、iTRAQ 和 SWATH 分析工具）。因此，pyOpenMS 允许以完全交互的方式（使用交互式 Python 解释器）进行快速原型设计和高效工作流程开发，并且非常适合不精通 C++ 的研究人员。此外，我们包装复杂 C++ 库的代码是完全开源的，允许其他项目轻松创建类似的绑定。 pyOpenMS 框架可在 https://pypi.python.org/pypi/pyopenms 上免费获取，而自动创建 Cython 代码的 autowrap 工具可在 https://pypi.python.org/pypi/autowrap 上获取（两者均根据 3 条款 BSD 许可证发布）。
pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence).