Using Petri net tools to study properties and dynamics of biological systems
Using Petri net tools to study properties and dynamics of biological systems
复制标题
DOI：
10.1197/jamia.m1637
复制
发表时间：
2005-03-01
影响因子：
6.4
通讯作者：
Altman, RB
中科院分区：
文献类型：
--
作者：
Peleg, M;Rubin, D;Altman, RB
Petri网(PNS)及其扩展是一种很有前途的生物系统建模和仿真方法。我们考察了PN的形式和工具，并根据它们的数学能力以及它们是否适合表示典型的生物过程进行了比较。我们衡量了这些工具对生物系统的特定特征进行建模的能力，并回答了我们定义的一组生物学问题。我们发现需要不同的工具来提供我们评估的所有功能。我们创建了软件，将通用的PN模型转换为所讨论的大多数形式化和工具。我们还提供了三个模型，并建议这样一个模型库将通过PNS促进定性建模的进展。开发和广泛采用通用格式将使研究人员能够共享模型并使用不同的工具对其进行分析，而无需转换为专有格式。
Petri Nets (PNs) and their extensions are promising methods for modeling and simulating biological systems. We surveyed PN formalisms and tools and compared them based on their mathematical capabilities as well as by their appropriateness to represent typical biological processes. We measured the ability of these tools to model specific features of biological systems and answer a set of biological questions that we defined. We found that different tools are required to provide all capabilities that we assessed. We created software to translate a generic PN model into most of the formalisms and tools discussed. We have also made available three models and suggest that a library of such models would catalyze progress in qualitative modeling via PNs. Development and wide adoption of common formats would enable researchers to share models and use different tools to analyze them without the need to convert to proprietary formats.