Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.
PLoS Comput Biol. 2013;9(9):e1003194. doi: 10.1371/journal.pcbi.1003194. Epub 2013 Sep 19.
A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial connections between cellular processes, identifying significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine. Due to its complexity and fragmented nature, however, working with pathway data is still difficult. We present Paxtools, a Java library that contains algorithms, software components and converters for biological pathways represented in the standard BioPAX language. Paxtools allows scientists to focus on their scientific problem by removing technical barriers to access and analyse pathway information. Paxtools can run on any platform that has a Java Runtime Environment and was tested on most modern operating systems. Paxtools is open source and is available under the Lesser GNU public license (LGPL), which allows users to freely use the code in their software systems with a requirement for attribution. Source code for the current release (4.2.0) can be found in Software S1. A detailed manual for obtaining and using Paxtools can be found in Protocol S1. The latest sources and release bundles can be obtained from biopax.org/paxtools.
不断增长的形式化、可计算的途径信息库可用于回答重要的生物学问题，包括在细胞过程之间找到非平凡的联系、识别疾病状态下细胞网络中显著改变的部分，以及构建可用于精准医学的预测模型。然而，由于其复杂性和碎片化的性质，处理途径数据仍然很困难。我们提出了 Paxtools，这是一个 Java 库，包含了以标准 BioPAX 语言表示的生物途径的算法、软件组件和转换器。Paxtools 通过消除访问和分析途径信息的技术障碍，使科学家能够专注于他们的科学问题。Paxtools 可以在任何具有 Java 运行时环境的平台上运行，并在大多数现代操作系统上进行了测试。Paxtools 是开源的，并根据较宽松的通用公共许可证（LGPL）授权，允许用户在其软件系统中自由使用代码，但需要注明出处。当前版本（4.2.0）的源代码可以在软件 S1 中找到。获取和使用 Paxtools 的详细手册可以在协议 S1 中找到。最新的源文件和发布包可以从 biopax.org/paxtools 获得。
