Introduction

GUI network constructor

Pathway search for virtual knockout mutants

Automatic layout system

Dynamic simulator

Converter

 

JUMP TO URL SITE

CADLIVE GUI Network Constructor with a Pathway Search Module for Knockout Mutants

CADLIVE Automatic Layout

CADLIVE Dynamic Simulator

CADLIVE Converter

 

References

 

Kentaro Inoue, Sayaka Tomeda, Shinpei Tonami, Yuki Shimokawa, Masayo Ono, Hiroyuki Kurata, CADLIVE Converter for constructing a biochemical network map. Biochem Eng J 54:200–206, 2011.

 

Hiroyuki Kurata, Kentaro Inoue, Kazuhiro Maeda, Koichi Masaki, Yuki Shimokawa, Quanyu Zhao, Extended CADLIVE: a novel graphical notation for designing a biochemical network map that enables computational pathway analysis, Nucleic Acids Res. 35(20):e134, 2007.

 

Hiroyuki Kurata, Kouichi Masaki, Yoshiyuki Sumida, Rei Iwasaki, CADLIVE Dynamic Simulator: Direct Link of Biochemical Networks to Dynamic Models, Genome Res., 15: 590-600, 2005.

 

Weijiang Li and Hiroyuki Kurata, A Grid Layout Algorithm for Automatic Drawing of Biochemical Networks, Bioinformatics, 21: 2036-2042, 2005.

 

Hiroyuki Kurata, Nana Matoba, Natsumi Shimizu, CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle, Nucleic Acids Res.31: 4071-4084, 2003.

 

 

Introduction

 

CADLIVE is a comprehensive computational tool that analyzes and rationally designs large-scale biochemical networks at the molecular interaction level. It consists of a GUI network constructor, database, a pathway search module for knockout mutants, a network layout module, and the dynamic simulator that automatically converts biochemical network maps into mathematical models.

 

Figure The whole image of CADLIVE

 

 

CADLIVE GUI network constructor

 

 

Figure GUI network constructor and SBML based database

Place species symbols by dragging and binds them by reaction arrows in the panel.

Drawing a biochemical network (left) by the GUI constructor automatically generates SBML-based regulator reaction equations (right).

 

Table Fundamental graphical notation based on the regulator-reaction model

Details are described elsewhere.

 

Figure A biochemical map of p53 drawn by CADLIVE

 

 

Pathway search for virtual knockout mutants

 

We developed a pathway search module for virtual knockout mutants as a built-in application of CADLIVE. This module analyzes gene function in the same way as molecular genetics, which simulates a change in mutant phenotypes or confirms the validity of the network map.

 

 

(A)

(B)                                         (C)                                    

 

 

Figure Pathway search for knockout mutants

(A) The window for virtual knockout. The blue-highlighted species are removed by clicking the "KnockOut" button in the bottom part. The deleted species and reactions appear in the middle and bottom tables.

(B) The dotted symbols and lines are the deleted species and reactions on the network constructor.

(C) Pathway viewer for the knockout mutant. When specific pathways are searched in the knockout mutant, the resulting pathways are marked in the red lines on the network constructor.

 

 

 

Automatic layout system

 

CADLIVE automatically layouts a biochemical network map by calculating the coordinates of all the molecular species. This facilitates exploring topological structures such as modularity.

 

Figure An automatically drawn map of the budding yeast cell cycle network

 

 

Dynamic simulator

The dynamic simulator is a client-server model.

It automatically converts a biochemical network map into a dynamic model.

It supports optimization, system analysis, and Gird computation.

 

 

Figure A process flow of CADLIVE

 

 

Figure Two stage and three layer model for converting regulator-reaction equations into a mathematical model.

 

 

 

 

 

 

Figure Input of the biochemical network map created by the CADLIVE GUI network constructor

 

 

 

Figure Mathematical equations that CADLIVE automatically converts the input biochemical network file into.

 

 

 

Figure Windows for setting the values of biochemical parameters

 

 

 

Figure Simulation results calculated by CADLIVE.