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, as produced by many text editor (but not word processors). By default, it is called config.cym.

Cytosim understand a small set of commands and predefined objects with their associated parameters.

One needs to call at least:

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

About the config file:

• Parameters should be specified in units of (s, um, pN)
• Parameter names are predefined in the simulations for each object class
• Parameters are specified with a = sign, and can contain multiple values
• Two parameters can be specified on the same line if they are separated by a semi-column: ;
• Curly brackets { } are used to group the parameters together in logical units
• Parentheses ( ) can be used for subgroups, such as display
• Strings can be encapsulated by double quotes " " or parentheses

Editing

Cytosim’s configuration files *.cym are plain text ASCII file, and should be edited using a PLAIN TEXT editor. Do not use word processors such as Microsoft Word.

Recommended editors:

• TextMate
• Atom
• Gleany
• Sublime text

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

Example

Many examples can be found in the directory cym/.

% 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
	display = ( style=2; )
}

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

	bind_also_end = 1
	hold_growing_end = 1

	display = ( size=7; width=7; )
}

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
}