The bioperl toolkit:: Perl modules for the life sciences
The bioperl toolkit:: Perl modules for the life sciences
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DOI：
10.1101/gr.361602
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发表时间：
2002-10-01
期刊：
影响因子：
7
通讯作者：
Birney, E
中科院分区：
文献类型：
--
作者：
Stajich, JE;Block, D;Birney, E
Bioperl项目是一个由生物学家、生物信息学家和计算机科学家组成的国际开源合作项目，在过去的7年里，它已经发展成为管理和操纵生命科学信息的最全面的Perl模块库。Bioperl为生物信息学应用程序员提供了一个易于使用，稳定和一致的编程接口。Bioperl模块已成功地反复用于将复杂的任务减少到只有几行代码。Bioperl对象模型已被证明足够灵活，可以支持企业级应用程序，如EnsEMBL，同时为Perl程序员新手保持简单的学习曲线。Bioperl能够执行分析和处理来自BLAST、ClustalW或BLOSS套件等程序的结果。通过不断发展的BioCORBA桥，支持与Python和lava编写的模块的互操作。Bioperl通过一系列灵活的序列输入/输出模块提供对数据存储（如GenBank和SwissProt）的访问，以及对开放生物信息学数据库访问项目的新兴通用序列数据存储格式的访问。这项研究描述了工具包的整体架构，它解决的问题域，并给出了具体的例子，该工具包可以用来解决常见的生命科学问题。最后，我们讨论了该项目的开源性质如何有助于开发工作。
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and lava is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.