RuleBender: a visual interface for rule-based modeling

被引：21

作者：

Xu, Wen ^{[2
]}

Smith, Adam M. ^{[2
]}

Faeder, James R. ^{[1
]}

Marai, G. Elisabeta ^{[2
]}

机构：

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

[2] Univ Pittsburgh, Dept Comp Sci, Pittsburgh, PA 15260 USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 12期

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

SIMULATION; SYSTEMS;

D O I：

10.1093/bioinformatics/btr197

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling intracellular biochemistry. Current interfaces for RBM are predominantly text-based and command-line driven. Better visual tools are needed to make RBM accessible to a broad range of users, to make specification of models less error prone and to improve workflows. We present RULEBENDER, an open-source visual interface that facilitates interactive debugging, simulation and analysis of RBMs.

引用

页码：1721 / 1722

页数：2

共 6 条

[1] Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations [J].

Collins, Christopher ;

Penn, Gerald ;

Carpendale, Sheelagh .

IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 2009, 15 (06) :1009-1016

[2] RuleMonkey: software for stochastic simulation of rule-based models [J].

Colvin, Joshua ;

Monine, Michael I. ;

Gutenkunst, Ryan N. ;

Hlavacek, William S. ;

Von Hoff, Daniel D. ;

Posner, Richard G. .

BMC BIOINFORMATICS, 2010, 11

[3]

Danos V, 2007, LECT NOTES COMPUT SC, V4807, P139

[4]

Faeder James R., 2009, V500, P113, DOI 10.1007/978-1-59745-525-1_5

[5] Internal coarse-graining of molecular systems [J].

Feret, Jerome ;

Danos, Vincent ;

Krivine, Jean ;

Harmer, Russ ;

Fontana, Walter .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (16) :6453-6458

[6] Efficient modeling, simulation and coarse-graining of biological complexity with NFsim [J].

Sneddon, Michael W. ;

Faeder, James R. ;

Emonet, Thierry .

NATURE METHODS, 2011, 8 (02) :177-U112

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