GINsim:: A software suite for the qualitative modelling, simulation and analysis of regulatory networks
GINsim:: A software suite for the qualitative modelling, simulation and analysis of regulatory networks
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DOI：
10.1016/j.biosystems.2005.10.003
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发表时间：
2006-05-01
期刊：
影响因子：
1.6
通讯作者：
Chaouiya, C.
中科院分区：
文献类型：
--
作者：
Gonzalez, A. Gonzalez;Naldi, A.;Chaouiya, C.
本文介绍了GINsim，（1）一个用于基因调控网络定性建模、分析和模拟的Java软件包。形式上，我们的方法依赖于离散的数学和图论概念。GINsim包含一个直观的图形编辑器，可以定义和参数化监管图，以及一个模拟引擎来计算相应的定性动态行为。我们的计算方法说明了一个初步的模型分析的细胞间调节网络激活Notch在背腹边界的果蝇翼成虫盘。我们专注于五个基因（内和两个细胞之间）之间的交叉调节，这实现了背腹侧的边界在发展中的成虫盘。我们的模拟定性地再现了野生型发育途径，以及各种类型的实验扰动的结果，如功能丧失突变或异位诱导的基因表达。(c)2005爱思唯尔爱尔兰有限公司保留所有权利。
This paper presents GINsim,(1) a Java software suite devoted to the qualitative modelling, analysis and simulation of genetic regulatory networks. Formally, our approach leans on discrete mathematical and graph-theoretical concepts. GINsim encompasses an intuitive graph editor, enabling the definition and the parameterisation of a regulatory graph, as well as a simulation engine to compute the corresponding qualitative dynamical behaviour. Our computational approach is illustrated by a preliminary model analysis of the inter-cellular regulatory network activating Notch at the dorsal-ventral boundary in the wing imaginal disc of Drosophila. We focus on the cross-regulations between five genes (within and between two cells), which implements the dorsal-ventral border in the developing imaginal disc. Our simulations qualitatively reproduce the wild-type developmental pathway, as well as the outcome of various types of experimental perturbations, such as loss-of-function mutations or ectopically induced gene expression. (c) 2005 Elsevier Ireland Ltd. All rights reserved.