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BMCBI
2010
149views more  BMCBI 2010»
13 years 7 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...
CEC
2005
IEEE
14 years 1 months ago
An empirical analysis of the grouping genetic algorithm: the timetabling case
A grouping genetic algorithm (GGA) for the university course timetabling problem is outlined. We propose six different fitness functions, all sharing the same common goal, and look...
Rhydian Lewis, Ben Paechter
BMCBI
2010
150views more  BMCBI 2010»
13 years 7 months ago
Systematic calibration of a cell signaling network model
Background: Mathematical modeling is being applied to increasingly complex biological systems and datasets; however, the process of analyzing and calibrating against experimental ...
Kyoung Ae Kim, Sabrina L. Spencer, John G. Albeck,...
BMCBI
2011
13 years 2 months ago
Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars
Background: The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity and low levels of accuracy of state...
Zsuzsanna Sukosd, Bjarne Knudsen, Morten Vaerum, J...
PE
2011
Springer
167views Optimization» more  PE 2011»
13 years 2 months ago
Passage-time computation and aggregation strategies for large semi-Markov processes
High-level semi-Markov modelling paradigms such as semi-Markov stochastic Petri nets and process algebras are used to capture realistic performance models of computer and communic...
Marcel C. Guenther, Nicholas J. Dingle, Jeremy T. ...