Introduction

CeCe is a simulation environment capturing in one setting the key processes that influence cell-cell signal transmission.The underlying scene is a simple 2D world. Cells enter and exit this world through predefined channels of arbitrary shape. Each cell executes its own stochastic biochemical reactions and based on its state interacts with the rest of the population. As such, CeCe is easy to setup, intuitive to interpret, and fast to run.

Motivation

Until now, intercellular interactions has been difficult to model. And because we also use microfluidics as a tool to confirm our designs, we made a decision to create an instrument which allows easy and completely boundless simulation of cell communication in any microfluidic environment. We decided to name the instrument CeCe, as abbreviation of Cell-Cell interaction.

Architecture

The simulator is designed to be highly modular. The core contains almost no functionality and missing functionality is provided by plugins. This design allows to extend simulator functionality by adding plugins written by someone else. Plugins are loaded on demand by simulation file so unnecessary functionality is not used.

Simulation is computed by stepping over independent iterations. Each iteration is defined by time step and all modules and objects (provided by plugins) are updated. Module is unit that is updated in each iteration and provides some global functionality (e.g. diffusion). Only one of same type is allowed to be in simulation. Objects are simulation entities that provides some local functionality (e.g. Yeast cells).

Visualization

The CeCe simulator has ability to visualize given simulation (by OpenGL on GPU). Final scene visualization is done by combination of modules and objects visualization (if they provide it).

Demo

Modeling

Default simulator package contains several plugins that offer some additional functionality.

Diffusion

Streamlines - Lattice-Boltzman method

Stochastic reactions - Gillespie algorithm

Read more...

Download

Simulator binaries are available to download for following platforms:

• Windows 64bit
• Mac OS X
• Ubuntu/Mint x64

Package contains simulator binary, examples, manual and tutorial (HTML).

Source code

The CeCe simulator source code is available on [http://github.com/GeorgievLab/CeCe GitHub].