Books etc

This paper describes the fabrication and the evaluation of a reusable Cell Culturing Device, designed for a single cell and cellular networks analysis. This is the first success of combination of Microcontact Printing (mCP) and Vacuum Device. This combination has following advantages; (1) cells stay within the micropatterns for long enough duration to achieve local activation of cells or cellular networks (more than 24 h), (2) the displacement distance of laminar flow from the interface of two fluids in Cell Culturing Device keeps smaller than the diameter of a cell, (3) all components of our device except micropatterned substrate are reusable for further analyses. The success of the combination of above techniques provides a controllable environment for the local activation of a single cell and cellular networks. Our device allows to exhibit the different responses induced with the various conditions in a single observation sight at exactly the same time point.

Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks, using solidly defined and comprehensive graphical representation (SBGN, systems biology graphical notation). CellDesigner is systems biology markup language (SBML) compliant, and has Systems Biology Workbench(SBW)-enabled software so that it can import/export SBML-described documents and integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ordinary differential equation (ODE) Solver, enabling us to simulate through our sophisticated graphical user interface. We can also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java; thus, it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available from our Web site at http://celldesigner.org/. © 2007 Humana Press I

In silico modeling and simulation are effective means to understand how the regulatory systems function in life. In this chapter, we explain how to build a model and run the simulation using CellDesigner, adopting the standards such as SBML and SBGN.