config.md

Cytosim's Configuration File

The virtual system and the sequence of actions to be performed is specified in a configuration file. This config file must be a plain (ASCII) text file. By default cytosim will look for config.cym, but any file ending with .cym should work.

Many examples can be found in the directory cym/.

Cytosim understands a small set of commands and has a set of predefined objects with associated parameters.

The fundamental commands are:

• set to define a new object category, and set its parameter values,
• new to create objects,
• run to perform simulation steps.

Curly brackets { } after each command are used to group the parameters associated with the command.

About the config file:

• Parameter names are predefined in the simulations for each object class
• Parameters are specified with a = sign, and can contain multiple values
• Parameter values should be specified in units of (seconds, micrometers, picoNewtons)
• A parameter assignment is terminated by the end of a line, or by a semi-column: ;
• Parentheses ( ) can be used for subgroups, such as display
• Strings can be encapsulated by double quotes " " or parentheses if they include spaces
• A line of comment should start with %, and longer comments should be enclosed by %{ }.

Editing

Cytosim's configuration files *.cym are plain text ASCII file. Avoid word processors such as Microsoft Word, and prefer PLAIN TEXT editors, for example:

• TextMate
• Atom
• Gleany
• Sublime text

Manuel Lera-Ramirez made a syntax highlighting configuration for TextMate.

Example

% Self organization of Microtubules driven by bivalent Motors
% Adapted from Nedelec et al. Nature, 1998

set simul system
{
	time_step = 0.01
	viscosity = 0.05
}

set space cell
{
	shape = circle
}

new cell
{   
	radius = 10
}

set fiber microtubule
{
	rigidity = 20
	segmentation = 0.5
	confine = inside, 100
	display = ( line_width=1; color=white; )
}

set hand kinesin
{
	binding = 10, 0.01   % rate, range
	unbinding = 0.1, 3   % rate, force
	
	activity = move
	unloaded_speed = 0.8
	stall_force = 5
	
	display = ( size=7; color=green; )
}

set couple complex
{
	hand1 = kinesin
	hand2 = kinesin
	stiffness = 100
	diffusion = 10
}

new 100 microtubule
{
	length = 9
}

new 2000 complex

run 5000 system
{
	nb_frames = 50
}