Using biological pathway data with paxtools.
Using biological pathway data with paxtools.
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DOI：
10.1371/journal.pcbi.1003194
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发表时间：
2013
影响因子：
4.3
通讯作者：
Sander C
中科院分区：
文献类型：
--
作者：
Demir E;Babur O;Rodchenkov I;Aksoy BA;Fukuda KI;Gross B;Sümer OS;Bader GD;Sander C
一个快速增长的正式的、可计算的途径信息库可以用来回答重要的生物学问题，包括发现细胞过程之间的重要联系，识别疾病状态下细胞网络的显著改变部分，以及建立可用于精准医学的预测模型。然而，由于其复杂性和分散性，使用路径数据仍然很困难。我们提出Paxtools，一个Java库，包含算法，软件组件和转换器的生物途径表示在标准的BioPAX语言。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可以运行在任何具有Java Runtime Environment的平台上，并在大多数现代操作系统上进行了测试。Paxtools是开源的，并在LGPL（Lesser GNU public license）下提供，该许可证允许用户在其软件系统中自由使用代码，但需要署名。当前版本（4.2.0）的源代码可在软件S1中找到。获取和使用Paxtools的详细手册可以在Protocol S1中找到。最新的源代码和发行包可以从biopax.org/paxtools获得。
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.
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影响因子：
14.9
作者：
Babur O;Demir E;Gönen M;Sander C;Dogrusoz U
通讯作者：
Dogrusoz U
影响因子：
14.9
作者：
Schaefer, Carl F.;Anthony, Kira;Buetow, Kenneth H.
通讯作者：
Buetow, Kenneth H.
影响因子：
14.9
作者：
Caspi R;Altman T;Dale JM;Dreher K;Fulcher CA;Gilham F;Kaipa P;Karthikeyan AS;Kothari A;Krummenacker M;Latendresse M;Mueller LA;Paley S;Popescu L;Pujar A;Shearer AG;Zhang P;Karp PD
通讯作者：
Karp PD
影响因子：
14.9
作者：
Hornbeck PV;Kornhauser JM;Tkachev S;Zhang B;Skrzypek E;Murray B;Latham V;Sullivan M
通讯作者：
Sullivan M
影响因子：
3
作者：
Dogrusoz, Ugur;Cetintas, Ahmet;Babur, Ozgun
通讯作者：
Babur, Ozgun