GridCell
A Stochastic Particle-Based Biological System Simulator
What is GridCell?
GridCell is a stochastic simulator which divides the simulation space into a 3D cubic grid composed of discrete voxels. The simulation advances through time in discrete time steps. It allows the analysis of biological and chemical networks under multiple spatial influences such as molecular crowding and localization.
Installation Files:
GridCell 1.2 is now available. Check out the changes.
GridCell can be downloaded for the Windows XP/Vista platform.
The downloadable file includes:
The winXP executable
The GridCell User Manual
Example packages
Download GridCellv1.2.
Required Files:
GridCell requires two library files to be installed:
- OpenGL Utility Toolkit: GLUT 3.7.6
Available here. The .dll and the Object File Library files should be placed in the same directory as the executable.
- Systems Biology Markup Language (or SBML) library. You must use libSBML version 2.3.4-Xerces.
Available here.
GridCell User Manual:
GridCell's user interface provides an easy way to interact with the application, through different menus and interactive options. The GridCell User Manual describes in detail the application and how to use it.
Download User Manual: PDF.
Any correspondence regarding the GridCell application should be directed to: Laurier Boulianne.
For more information about the GridCell algorithm:
Boulianne, L., Dumontier, M., Gross, W. J. (2007) A Stochastic Particle-Based Biological System Simulator, Proceedings of the Summer Computer Simulation Conference 2007 (SCSC07), San Diego, California (USA), 794-801.
Boulianne, L., Al Assaad, S., Dumontier, M., Gross, W. J. (2008) GridCell: A stochastic particle-based biologicial system simulator, BMC Systems Biology, 2:66
Disclaimer:
The User shall use the Software for research purposes only. Should the User decide to publish the results of the research, the User will acknowledge the use of the Software and obtain prior written approval from the Author.
Restrictions
The User agrees not to:
sell, lease, loan, encumber or otherwise deal with any portion of the Software;
decompile, disassemble or reverse engineer any portion of the Software;
use the Software for any commercial activity without prior written approval from the Author.
The Software and the Software Documentation and all other technology are provided on an “as is” basis. Without limiting the foregoing, the Author makes no representations, extends no warranties of any kind, either express or implied, (a) concerning the merchantability of the Software and its fitness for any purpose, or (b) concerning the performance, the usefulness, the quality or the operation of the Software or the results stemming from its intended or other use. The User is solely responsible to determine and assure, by any means, the appropriateness of the Software for its needs, its adequate performance and to assure that it will not cause any damages to any persons or property.
The Author makes no representations, extends no warranties of any kind, either express or implied, that the Software is free from error, that they will perform without interruption, that it will be compatible with
the User's equipment, software or operating system configuration, or that it will meet the User's needs. The Author is under no obligation to correct any errors deemed to be internal (“Malfunctions”) that may arise in any version of the Software, the use of the Software or any technology will not infringe any patent, copyright, trademark, service mark, or other proprietary rights of others. The Author shall not be liable to the User with respect to: any claim arising from use of the Software and technical information or any technology.