Titlebook: Computational Methods in Systems Biology; 12th International C Pedro Mendes,Joseph O. Dada,Kieran Smallbone Conference proceedings 2014 Spr

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Dynamic Modeling and Simulation of Leukocyte Integrin Activation through an Electronic Design Automaico simulations of a biochemical model allows one to test different experimental conditions, helping in the discovery of the dynamics that regulate the system. Several characteristics and issues of biological system modeling are common to the electronics system modeling, such as concurrency, reactiv

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A Rule-Based Model of Base Excision Repairtions or whether substrate specificity is sufficient to explain how DNA intermediates are channeled from one repair enzyme to the other. In order to address these questions we designed a model of the Base Excision Repair pathway in Kappa, a rule based formalism for modeling protein-protein and prote

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Exploring the Cellular Objective in Flux Balance Constraint-Based Models analysis (FBA). FBA requires not only the stoichiometry of the network, but also an appropriate cellular objective function and possible additional physico-chemical constraints to predict the set of resulting flux distributions of an organism..To compute the metabolic flux distributions in microbes

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Optimization Based Design of Synthetic Oscillators from Standard Biological Partsfied performance requirements, to automatically find the circuit configuration and its tuning so that self-sustained oscillations meeting the requirements are produced. To solve this design problem, we present a methodology based on mixed-integer nonlinear optimization. This method also takes into a

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Conference proceedings 2014er submissions. The papers are organized in topical sections on formalisms for modeling biological processes, model inference from experimental data, frameworks for model verification, validation, and analysis of biological systems, models and their biological applications, computational approaches for synthetic biology, and flash posters.

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