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93
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APLAS
2007
ACM
15 years 1 months ago
Scalable Simulation of Cellular Signaling Networks
Abstract. Given the combinatorial nature of cellular signalling pathways, where biological agents can bind and modify each other in a large number of ways, concurrent or agent-base...
Vincent Danos, Jérôme Feret, Walter F...
AB
2007
Springer
15 years 3 months ago
A Stochastic Pi Calculus for Concurrent Objects
We present SpiCO, a new modeling and simulation language for systems biology. SpiCO is based on the stochastic π-calculus. It supports higher level modeling via multi-profile con...
Céline Kuttler, Cédric Lhoussaine, J...
BMCBI
2007
147views more  BMCBI 2007»
14 years 9 months ago
Modeling biochemical transformation processes and information processing with Narrator
Background: Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated gr...
Johannes J. Mandel, Hendrik Fuß, Niall M. Pa...
108
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CSB
2005
IEEE
128views Bioinformatics» more  CSB 2005»
14 years 11 months ago
Application of a Generalized MWC Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes
In our effort to elucidate the systems biology of the model organism, Escherichia coli, we have developed a mathematical model that simulates the allosteric regulation for threoni...
Tarek S. Najdi, Chin-Rang Yang, Bruce E. Shapiro, ...
LCPC
2004
Springer
15 years 3 months ago
Trimaran: An Infrastructure for Research in Instruction-Level Parallelism
Trimaran is an integrated compilation and performance monitoring infrastructure. The architecture space that Trimaran covers is characterized by HPL-PD, a parameterized processor a...
Lakshmi N. Chakrapani, John C. Gyllenhaal, Wen-mei...