Matsuno Hiroshi, Tanaka Yukiko, Aoshima Hitoshi, Doi Atsushi, Matsui Mika, Miyano Satoru
Faculty of Science, Yamaguchi University, Japan.
In Silico Biol. 2003;3(3):389-404.
The following two matters should be resolved in order for biosimulation tools to be accepted by users in biology/medicine: (1) remove issues which are irrelevant to biological importance, and (2) allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism. From these criteria, we firstly define a novel notion of Petri net called Hybrid Functional Petri Net (HFPN). Then, we introduce a software tool, Genomic Object Net, for representing and simulating biopathways, which we have developed by employing the architecture of HFPN. In order to show the usefulness of Genomic Object Net for representing and simulating biopathways, we show two HFPN representations of gene regulation mechanisms of Drosophila melanogaster (fruit fly) circadian rhythm and apoptosis induced by Fas ligand. The simulation results of these biopathways are also correlated with biological observations. The software is available to academic users from http://www.GenomicObject.Net/.
为了使生物模拟工具被生物学/医学领域的用户所接受，需要解决以下两个问题：（1）消除与生物学重要性无关的问题，（2）允许用户直观地表示生物途径，并轻松理解/管理表示和模拟机制的细节。基于这些标准，我们首先定义了一种名为混合功能Petri网（HFPN）的新型Petri网概念。然后，我们介绍了一种用于表示和模拟生物途径的软件工具——基因组对象网（Genomic Object Net），它是我们采用HFPN架构开发的。为了展示基因组对象网在表示和模拟生物途径方面的有用性，我们展示了黑腹果蝇（果蝇）昼夜节律和Fas配体诱导的细胞凋亡的基因调控机制的两种HFPN表示。这些生物途径的模拟结果也与生物学观察结果相关。该软件可供学术用户从http://www.GenomicObject.Net/获取。
