Modeling for (physical) biologists: an introduction to the rule-based approach

被引：34

作者：

Chylek, Lily A. ^{[1
,2
,3
]}

Harris, Leonard A. ^{[4
]}

Faeder, James R. ^{[5
]}

Hlavacek, William S. ^{[2
,3
,6
]}

机构：

[1] Cornell Univ, Dept Chem & Chem Biol, Ithaca, NY 14853 USA

[2] Los Alamos Natl Lab, Div Theoret, Theoret Biol & Biophys Grp, Los Alamos, NM 87545 USA

[3] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA

[4] Vanderbilt Univ, Sch Med, Dept Canc Biol, Nashville, TN 37212 USA

[5] Univ Pittsburgh, Sch Med, Dept Computat & Syst Biol, Pittsburgh, PA 15260 USA

[6] New Mexico Consortium, Los Alamos, NM 87544 USA

来源：

PHYSICAL BIOLOGY | 2015年 / 12卷 / 04期

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

rule-based modeling; systems biology; cell signaling; BIOMOLECULAR SITE DYNAMICS; GROWTH-FACTOR RECEPTOR; FC-EPSILON-RI; CELL-SURFACE; STOCHASTIC SIMULATION; SIGNALING PATHWAYS; REACTION NETWORKS; DETAILED BALANCE; VISUAL INTERFACE; EARLY EVENTS;

D O I：

10.1088/1478-3975/12/4/045007

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Models that capture the chemical kinetics of cellular regulatory networks can be specified in terms of rules for biomolecular interactions. A rule defines a generalized reaction, meaning a reaction that permits multiple reactants, each capable of participating in a characteristic transformation and each possessing certain, specified properties, which may be local, such as the state of a particular site or domain of a protein. In other words, a rule defines a transformation and the properties that reactants must possess to participate in the transformation. A rule also provides a rate law. A rule-based approach to modeling enables consideration of mechanistic details at the level of functional sites of biomolecules and provides a facile and visual means for constructing computational models, which can be analyzed to study how system-level behaviors emerge from component interactions.

引用

页数：24

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