Odefy--from discrete to continuous models.
Odefy--from discrete to continuous models.
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DOI：
10.1186/1471-2105-11-233
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发表时间：
2010-05-07
影响因子：
3
通讯作者：
Theis FJ
中科院分区：
文献类型：
--
作者：
Krumsiek J;Pölsterl S;Wittmann DM;Theis FJ
有关调控相互作用的现象学信息是经常可用的，可以很容易地转换为布尔模型。另一方面，完全定量的模型提供了对基础系统精确动态的详细见解。为了连接离散和连续建模方法，最近开发了将布尔系统转换为常微分方程系统的方法。随着生物相互作用网络的规模和复杂性稳步增长，需要一个完全自动化的转换过程框架。我们提出Ofify，一个MATLAB和Octave兼容的工具箱，用于将布尔模型自动转换为常微分方程系统。模型可以从布尔方程组或布尔网络的图形表示创建。或者，用户可以从CellNetAnalyzer工具箱、GINSim和PBN工具箱导入布尔模型。通过多元多项式插值和S形Hill函数的选择性应用，将布尔模型转化为常微分方程组。我们的工具箱包含布尔模型和连续模型的基本模拟和可视化功能。对于进一步的分析，模型可以导出到SQUAD，GNA，MATLAB脚本文件，SB工具箱，SBML和R脚本文件。Ofify包含一个用户友好的图形用户界面，方便访问模拟和导出功能。我们说明了我们的转换方法的有效性以及Odefy工具箱的使用和好处的两个生物系统：一个相互抑制开关已知的干细胞分化和监管网络引起一个特定的空间表达模式在中后脑边界。Odefy提供了一个易于使用的工具箱，用于将布尔模型自动转换为常微分方程系统。它可以有效地连接到各种输入和输出格式，以进行进一步的分析和调查。该工具箱是开源的，可以在http://cmb.helmholtz-muenchen.de/odefy下载。
Phenomenological information about regulatory interactions is frequently available and can be readily converted to Boolean models. Fully quantitative models, on the other hand, provide detailed insights into the precise dynamics of the underlying system. In order to connect discrete and continuous modeling approaches, methods for the conversion of Boolean systems into systems of ordinary differential equations have been developed recently. As biological interaction networks have steadily grown in size and complexity, a fully automated framework for the conversion process is desirable. We present Odefy, a MATLAB- and Octave-compatible toolbox for the automated transformation of Boolean models into systems of ordinary differential equations. Models can be created from sets of Boolean equations or graph representations of Boolean networks. Alternatively, the user can import Boolean models from the CellNetAnalyzer toolbox, GINSim and the PBN toolbox. The Boolean models are transformed to systems of ordinary differential equations by multivariate polynomial interpolation and optional application of sigmoidal Hill functions. Our toolbox contains basic simulation and visualization functionalities for both, the Boolean as well as the continuous models. For further analyses, models can be exported to SQUAD, GNA, MATLAB script files, the SB toolbox, SBML and R script files. Odefy contains a user-friendly graphical user interface for convenient access to the simulation and exporting functionalities. We illustrate the validity of our transformation approach as well as the usage and benefit of the Odefy toolbox for two biological systems: a mutual inhibitory switch known from stem cell differentiation and a regulatory network giving rise to a specific spatial expression pattern at the mid-hindbrain boundary. Odefy provides an easy-to-use toolbox for the automatic conversion of Boolean models to systems of ordinary differential equations. It can be efficiently connected to a variety of input and output formats for further analysis and investigations. The toolbox is open-source and can be downloaded at http://cmb.helmholtz-muenchen.de/odefy.
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影响因子：
4.3
作者：
Saez-Rodriguez J;Simeoni L;Lindquist JA;Hemenway R;Bommhardt U;Arndt B;Haus UU;Weismantel R;Gilles ED;Klamt S;Schraven B
通讯作者：
Schraven B
影响因子：
1.6
作者：
Gonzalez, A. Gonzalez;Naldi, A.;Chaouiya, C.
通讯作者：
Chaouiya, C.
影响因子：
--
作者：
Wittmann DM;Krumsiek J;Saez-Rodriguez J;Lauffenburger DA;Klamt S;Theis FJ
通讯作者：
Theis FJ
影响因子：
4.3
作者：
Li, Shenghua;Brazhnik, Paul;Tyson, John J.
通讯作者：
Tyson, John J.
表达模式的空间分析可以预测中后脑边界处的遗传相互作用。
影响因子：
4.3
作者：
Wittmann, Dominik M.;Bloechl, Florian;Truembach, Dietrich;Wurst, Wolfgang;Prakash, Nilima;Theis, Fabian J.
通讯作者：
Theis, Fabian J.