## ABSTRACT APPROACHES TO COMPLEXITY REDUCTION IN A SYSTEMS BIOLOGY

### BibTeX

@MISC{Perrone_abstractapproaches,

author = {L. F. Perrone and F. P. Wiel and J. Liu and B. G. Lawson and D. M. Nicol and R. M. Fujimoto},

title = {ABSTRACT APPROACHES TO COMPLEXITY REDUCTION IN A SYSTEMS BIOLOGY},

year = {}

}

### OpenURL

### Abstract

Due to the complexity of biochemical reaction networks, socalled complexity reduction algorithms play a crucial role for making simulations efficient and for dissecting biochemical networks into meaningful subnetworks for analysis. Here, different approaches are presented, which we are developing in the context of a computational research environment for systems biology (SYCAMORE). These approaches are based on time-scale decomposition, sensitivity analysis, and hybrid simulation methods. 1

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Citation Context ... Intrinsic Low-Dimensional Manifolds (ILDM) (Maas and Pope 1992). Several variants of these two methods have been successfully used, e.g., in atmospheric and combustion chemistry modeling (see, e.g., =-=Schmidt et al. 1998-=-). We describe here the adaptation of an ILDM method for the use in the computational decomposition and analysis of biochemical systems with respect to time-scales. In comparison to the ILDM methods f... |

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Citation Context ...this can aid in network dissection. 2 TIME SCALE DECOMPOSITION In this section, we describe the adaptation of the method of Intrinsic Low-Dimensional Manifolds (ILDM) to biochemical systems (see also =-=Zobeley et al. 2005-=-). Originally, the ILDM techniques were introduced by Maas and Pope (1992) for the mathematical equations of combustion problems. In contrast, our method has an additional focus on reducing Surovtsova... |

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Citation Context ...mples building on the concept of time-scale decomposition are the Computational Singular Perturbation (CSP) method (Lam and Goussis 1994) and the so-called Intrinsic Low-Dimensional Manifolds (ILDM) (=-=Maas and Pope 1992-=-). Several variants of these two methods have been successfully used, e.g., in atmospheric and combustion chemistry modeling (see, e.g., Schmidt et al. 1998). We describe here the adaptation of an ILD... |

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Citation Context ... disturbances or tosdetermine the robustness of parameter estimation. In addition, principal component analysis can be used to understand the interaction between reactions and their grouped behavior (=-=Tomlin et al. 1995-=-). For SYCAMORE, we are following another strategy, that we believe to be quite promising for investigating biochemical networks — an approach based on parameter scans and second order sensitivities. ... |

1 | IRINA SUROVTSOVA is a Research Associate at EML Research gGmbH. She received the Ph.D. degree in 1997 at the St. Petersburg State University. Her fields of interests are system biology, complexity reduction, fluid–structure interaction, blood flow and ela - BIOGRAPHIES |

1 | is a research associate at EML Research gGmbH. Being trained as a physicist, he received a Ph.D. in 2005 from Tübingen University. He works on methods and tools for simulations in systems biology, with a focus on nonlinear dynamics. He is one of the main - SAHLE |