Boolean network simulations for life scientists.
Boolean network simulations for life scientists.
复制标题
DOI：
10.1186/1751-0473-3-16
复制
发表时间：
2008-11-14
影响因子：
--
通讯作者：
Albert, Reka
中科院分区：
文献类型：
--
作者：
Albert, Istvan;Thakar, Juilee;Li, Song;Zhang, Ranran;Albert, Reka
现代生命科学研究越来越依赖于计算解决方案，从大规模的数据分析到理论建模。在理论模型中，布尔网络扮演着越来越重要的角色，因为它们非常适合将生物学观察和假设映射成数学形式。即使没有量化科学的背景，布尔建模的概念基础也非常容易理解，但它允许生命科学家描述和探索广泛的令人惊讶的复杂现象。在本文中，我们对布尔模拟中使用的概念进行了清晰的概述，提出了一个可以基于简单文本输入执行这些模拟的软件库，并给出了三个案例研究。这些案例研究中的大规模模拟展示了布尔范例及其适用性，以及我们的软件包允许的高级功能和复杂的用例。我们的软件通过自由开放源码许可证分发，并可从
Modern life sciences research increasingly relies on computational solutions, from large scale data analyses to theoretical modeling. Within the theoretical models Boolean networks occupy an increasing role as they are eminently suited at mapping biological observations and hypotheses into a mathematical formalism. The conceptual underpinnings of Boolean modeling are very accessible even without a background in quantitative sciences, yet it allows life scientists to describe and explore a wide range of surprisingly complex phenomena. In this paper we provide a clear overview of the concepts used in Boolean simulations, present a software library that can perform these simulations based on simple text inputs and give three case studies. The large scale simulations in these case studies demonstrate the Boolean paradigms and their applicability as well as the advanced features and complex use cases that our software package allows. Our software is distributed via a liberal Open Source license and is freely accessible from