Tag: Cell Simulation

E-Cell4 v1.2.0b1 – Whole Cell Simulation

E-Cell4 v1.2.0b1

:: DESCRIPTION

E-Cell Simulation Environment is a software environment for simulation of various cellular phenomena.The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell.

::DEVELOPER

E-Cell Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • Python

:: DOWNLOAD

E-Cell

:: MORE INFORMATION

Citation

E-Cell 2: multi-platform E-Cell simulation system.
Takahashi K, Ishikawa N, Sadamoto Y, Sasamoto H, Ohta S, Shiozawa A, Miyoshi F, Naito Y, Nakayama Y, Tomita M.
Bioinformatics. 2003 Sep 1;19(13):1727-9.

E-Cell 3D demo – 3D Cell Simulation

E-Cell 3D demo

:: DESCRIPTION

E-Cell 3D introduces a whole new dimension for the understanding of dynamic behaviors of complex cellular systems, with dazzling visualization using cutting-edge 3D graphics. This visualization approach allows the user to capture the entire system at a glance, and aids the heuristics of system biologists in the process of modeling.

E-Cell 3D accelerates the understanding of the whole cell with sophisticated 3D graphics.With E-Cell 3D, scientists can easily capture the dynamism in the cellular system, including the molecular concentrations of each of the components, flux and enzymatic activities, and compounds that are controlling the system that change their coordinates. Central process in systems biology is the modeling process, and this type of visualization aids the heuristics of experienced research scientists while modeling.

::DEVELOPER

Dr. Kazuharu Arakawa and Mr. Nozomu Yachie, working under the direction of Dr. Masaru Tomita, Institute for Advanced Biosciences, Keio University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

E-Cell 3D

:: MORE INFORMATION

This demo is a fully functional E-Cell 3D software equipped with the circadian oscillation model of Drosophila by Ueda et al. (2001, Journal of Theoretical Biology), but currently the model cannot be changed.