基于SAT的同步布尔网络吸引子计算算法

BoolSi: a tool for distributed simulations and analysis of Boolean networks

We present BoolSi, an open-source cross-platform command line tool for distributed simulations of deterministic Boolean networks with synchronous update. It uses MPI standard to support execution on computational clusters, as well as parallel processing on a single computer. BoolSi can be used to model the behavior of complex dynamic networks, such as gene regulatory networks. In particular, it allows for identification and statistical analysis of network attractors. We perform a case study of the activity of a cambium cell to demonstrate the capabilities of the tool.

网络拓扑结构对遗传控制离散状态模型稳定性的影响

The effect of network topology on the stability of discrete state models of genetic control

布尔网络已被提出作为遗传控制的潜在有用的模型。这些网络的一个重要方面是其动态响应小扰动的稳定性。以前的稳定性方法假设不相关的随机网络结构。真实基因网络通常具有与随机网络范式显著不同的非平凡拓扑结构。为了解决这种情况下，我们提出了一个通用的方法来确定任何指定的网络拓扑结构的大型布尔网络的稳定性，并预测其稳态行为响应于小扰动。此外，我们概括的情况下，个别基因有一个分布的“表达偏见”，我们认为非同步更新，以及我们的方法扩展到非布尔模型，其中有两个以上的可能的基因状态。我们发现，稳定性是由修改后的邻接矩阵的最大特征值，我们测试这个结果与数值模拟比较。我们还讨论了我们的工作可能的应用实验推断的基因网络。

Synchrony in a Boolean network model of the L-arabinose operon in Escherichia coli

The lactose operon in Escherichia coli was the first known gene regulatory network, and it is frequently used as a prototype for new modeling paradigms. Historically, many of these modeling frameworks use differential equations. More recently, Stigler and Veliz-Cuba proposed a Boolean network model that captures the bistability of the system and all of the biological steady states. In this paper, we model the well-known arabinose operon in E. coli with a Boolean network. This has several complex features not found in the lac operon, such as a protein that is both an activator and repressor, a …

Boolean constraint satisfaction problems for reaction networks

This Thesis presents research at the boundary between Statistical Physics and Biology. First, we have devised a class of Boolean constraint satisfaction problems (CSP) whose solutions describe the feasible operational states of a chemical reaction network. After developing statistical mechanics techniques to generate solutions and studying the properties of the solution space for both ensembles and individual instances of random reaction networks, we have applied this framework to the metabolic network of the bacterium E.Coli. Results highlight, on one hand, a complex organization of operation…

Boolean constraint satisfaction problems for reaction networks

We define and study a class of (random) Boolean constraint satisfaction problems representing minimal feasibility constraints for networks of chemical reactions. The constraints we consider encode, respectively, for hard mass-balance conditions (where the consumption and production fluxes of each chemical species are matched) and for soft mass-balance conditions (where a net production of compounds is in principle allowed). We solve these constraint satisfaction problems under the Bethe approximation and derive the corresponding Belief Propagation equations, that involve 8 different messages. …

Searching for feasible stationary states in reaction networks by solving a Boolean constraint satisfaction problem

We analyze the solutions, on single network instances, of a recently introduced class of constraint-satisfaction problems (CSPs), describing feasible steady states of chemical reaction networks. First, we show that the CSPs generalize the scheme known as Network Expansion, which is recovered in a specific limit. Next, a full statistical mechanics characterization (including the phase diagram and a discussion of physical origin of the phase transitions) for Network Expansion is obtained. Finally, we provide a message-passing algorithm to solve the original CSPs in the most general form.

一种基于满足度的新型抗脆弱性度量及其在随机和生物布尔网络中的应用

A Novel Antifragility Measure Based on Satisfaction and Its Application to Random and Biological Boolean Networks

本文提出一种基于满足度的抗脆弱性度量，应用于随机和生物布尔网络，发现有序网络最抗脆弱，并展示七个生物系统具有抗脆弱性。