CADLIVE Converter for constructing a biochemical network map

Inoue, Kentaro; Tomeda, Sayaka; Tonami, Shinpei; Shimokawa, Yuki; Ono, Masayo; Kurata, Hiroyuki

doi:10.1016/j.bej.2011.02.022

Cited by 3 publications

(2 citation statements)

References 34 publications

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“…To demonstrate the feasibility of the hybrid algorithms, we applied them to 16 metabolic networks in KEGG [72] ( Table 2 ), which are converted into the CADLIVE format by the CADLIVE Converter [73] .…”

Section: Methodsmentioning

confidence: 99%

Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

et al. 2012

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BackgroundFor visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process.ResultsWe propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts.Conclusions Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

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Section: Methodsmentioning

confidence: 99%

Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

et al. 2012

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“…We presented a web-based dynamic simulator, the CADLIVE (Computer-Aided Design of LIVing systEms) Dynamic Simulator that takes a strong advantage in automatic conversion from a biochemical network map to its associated dynamic model [ 8 - 11 ], while it has not implemented any built-in parameter estimator yet. Users are required to manually edit computer programs and to handle complicated procedures on the Linux command line, hampering the optimization in the CADLIVE system.…”

Section: Introductionmentioning

confidence: 99%

CADLIVE optimizer: web-based parameter estimation for dynamic models

Inoue

Maeda

Kato

et al. 2012

Source Code Biol Med

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Computer simulation has been an important technique to capture the dynamics of biochemical networks. In most networks, however, few kinetic parameters have been measured in vivo because of experimental complexity. We develop a kinetic parameter estimation system, named the CADLIVE Optimizer, which comprises genetic algorithms-based solvers with a graphical user interface. This optimizer is integrated into the CADLIVE Dynamic Simulator to attain efficient simulation for dynamic models.

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CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis

Inoue

Maeda

Miyabe

et al. 2014

Bioprocess Biosyst Eng

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Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

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CADLIVE Converter for constructing a biochemical network map

Cited by 3 publications

References 34 publications

Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

CADLIVE optimizer: web-based parameter estimation for dynamic models

CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis

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