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, modeling of microfluidic channels has been difficult. And because we 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 any microfluidic scene. We decided to name the instrument MOSBI.

MOSBI

The MOSBI is modular tool for simulation of biological systems inside microfludic channels.

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).

Demo

Modeling

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

Download

Simulator binaries are available to download for following platforms:

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

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

Source code

The CeCe simulator is open-source and it's source is available on [http://github.com GitHub].