ABOUT DiSCUS is a simulator for bacterial populations in discrete space/time focused on the study of Horizontal Gene Transfer. [email protected], MIT License
This release is the first developers' version of the code (2012) with an
update (2023) to match pymunk 4 requirements.
Email: [email protected]
Tested under Linux, Windows and MacOS
REQUIREMENTS
* Python (www.python.org. The code has been developed in version 2.7)
* Pygame (www.pygame.org - Python library)
* Scipy (www.scipy.org - Python library)
* NumPy (www.scipy.org - Python library)
* Pymunk (www.pymunk.org - Physics engine. The code has been tested for
versions 2.0 and 4.0 so we recommend to install those ones. In the
pymunk site there is an installation guide)
HOW TO USE
The example files (cross.py, pipe.py and plain.py) make use of the main
program (discus.py) in order to run the simulation. The parameters and
definitions are in files included in the Imports folder
After installing all required tools, type the next line to run example
"cross":
> python cross.py
Without modification, the simulation will show growing cells in a cross-shaped
channel. The donors (left) have an oscillator inside which will be transferred
to recipients (right at the beginning)
Type the next line to run the "pipe" example:
> python pipe.py
Without modification, the simulation will show growing cells in a
longitudinal channel. One strain (recipient strain from cross.py) is simulated
Type the next line to run the "plain" example:
> python plain.py
Without modification, the "plain" example will display an empty space
(no walls) where empy cells (genetic circuit set to NONE) grow.