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ICTAI
2003
IEEE
13 years 10 months ago
Adaptive Modeling of Biochemical Pathways
In bioinformatics, biochemical pathways can be modeled by many differential equations. It is still an open problem how to fit the huge amount of parameters of the equations to the...
Rüdiger W. Brause
CMSB
2007
Springer
13 years 11 months ago
A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets
We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms. Each per...
David Gilbert, Monika Heiner, Sebastian Lehrack
BMCBI
2010
191views more  BMCBI 2010»
13 years 5 months ago
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
Background: Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabili...
Jan Schellenberger, Junyoung O. Park, Tom M. Conra...
ECAI
2004
Springer
13 years 10 months ago
Towards a Logical Analysis of Biochemical Reactions
We provide a logical model of biochemical reactions and show how hypothesis generation using weakest sufficient and strongest necessary conditions may be used to provide addition...
Patrick Doherty, Steve Kertes, Martin Magnusson, A...
CMSB
2008
Springer
13 years 6 months ago
Automatic Complexity Analysis and Model Reduction of Nonlinear Biochemical Systems
Kinetic models for biochemical systems often comprise a large amount of coupled differential equations with species concentrations varying on different time scales. In this paper w...
Dirk Lebiedz, Dominik Skanda, Marc Fein