adam analysis of discrete models of biological systems using computer algebra亚当的分析生物系统使用计算机代数的离散模型.pdfVIP

Hinkelmann et al. BMC Bioinformatics 2011, 12:295 /1471-2105/12/295 RESEARCH ARTICLE Open Access ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra 1,2 3† 4† 5† 1 Franziska Hinkelmann , Madison Brandon , Bonny Guang , Rustin McNeill , Grigoriy Blekherman , Alan Veliz-Cuba1,2 and Reinhard Laubenbacher1,2* Abstract Background: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. Results: We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on exte