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BIBE
2007
IEEE
149views Bioinformatics» more  BIBE 2007»
13 years 10 months ago
XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes
Multi-state molecules and multi-component complexes are commonly involved in cellular signaling. Accounting for molecules that have multiple potential states, such as a protein tha...
Michael L. Blinov, Ion I. Moraru
ICNC
2005
Springer
13 years 12 months ago
Reaction-Driven Membrane Systems
Abstract. Membrane systems are gaining a prominent role in the modeling of biochemical processes and cellular dynamics. We associate specific reactivity values to the production r...
Luca Bianco, Federico Fontana, Vincenzo Manca
BMCBI
2010
149views more  BMCBI 2010»
13 years 6 months ago
RuleMonkey: software for stochastic simulation of rule-based models
Background: The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be...
Joshua Colvin, Michael I. Monine, Ryan N. Gutenkun...
SYNASC
2007
IEEE
119views Algorithms» more  SYNASC 2007»
14 years 19 days ago
Graph Rewriting and Strategies for Modeling Biochemical Networks
In this paper, we present a rewriting framework for modeling molecular complexes, biochemical reaction rules, and generation of biochemical networks based on the representation of...
Oana Andrei, Hélène Kirchner
BMCBI
2010
131views more  BMCBI 2010»
13 years 6 months ago
A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems
Background: Sensitivity analysis is an indispensable tool for the analysis of complex systems. In a recent paper, we have introduced a thermodynamically consistent variance-based ...
Hong-Xuan Zhang, John Goutsias