Cytosim PI Cytoskeleton Simulator

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Executables

See also Filename extensions

The cytosim platform has two main executables:

- `sim` executes the instructions contained in a config file,
- `play` generates a graphical representation of a simulation state.

## Sim

`sim` performs the instructions specified in a config file, and it should generate 3 output files:

File | Type | Content
--- | --- | ---
`properties.cmo` | text | the properties of all objects
`objects.cmo` | binary | positions of the objects at different time points
`messages.cmo` | text | informations such as the execution time

The trajectory file `properties.cmo` is by default a binary file, but it can be written in to a text-based format (see command `write`).

By default the config file is `config.cym` in the current working directory, but another file can be specified on the command line, if its name ends with a .cym extension, for example:

sim spindle.cym

For more instructions on how to use `sim`, check Running simulations.

## Play

`play` generates a graphical representation of the system, and it is sometimes named `cytosim`. While `sim` can run on any computer, `play` requires OpenGL capabilities, and some of its functionality (eg. GIF support) depends on external libraries.

The Display parameters that control the graphical output can be embedded in the config file. The properties of most object have a `display` parameter that `play` will read. These parameters are ignored by `sim`, but they are copied verbatim to `properties.cmo`, where they are read by `play`. The display parameters can also be included in a separate file with extension ".cms", as in `play 3d.cms`.

`play` can be used to:

Purpose | Command
--- | ---
Display the simulation in the current folder | `play`
Perform a live simulation | `play live`
Generate images offscreen | `play image`

### Display Mode

Use `play` to display a simulation calculated by `sim`. By default, play reads `properties.cmo` and `objects.cmo`, in the current directory.

A different trajectory file can be specified:

play final.cmo

### Live Mode

Use `play live` to start a simulation and display it online:

play live
play live spindle.cym

This should open a window. This simulation is calculated on the fly, and nothing is saved.

### Offscreen Mode

Play can generate images without opening a window, as for example:

Command | Result
--- | ---
`play image frame=10` | An image representing frame 10
`play image frame=10,20,30` | Three images representing the specified frames
`play image frame=10 image_format=png` | a PNG image representing frame 10
`play image magnification=3 frame=10` | an image for frame 10 at 3x magnified resolution
`play movie` | an image for each frame in the trajectory file

Cytosim is always able to generate PPM images, that can be open with ImageJ. Cytosim may be able to generate images in the GIF or PNG formats, if the required libraries were included during compilation.

### Keyboard controls

Play is controlled by the keyboard and a pull-down menu. Here are the most useful controls:

Key | Action
--- | ---
`h` | show online help (press again to hide)
`p` `s` | play, stop
`<` `>` | previous, next frame
`+` `=` | zoom in, zoom out
arrow-keys | move around
`R` | write display parameters to terminal
`CTRL-Q` | quit (mac osx)

A list of keyboard commands is given by 'play keys'.

## Accessory Programs

Cytosim has a number of other tools:

Program | Typical usage
--- | ---
`report` | generate analysis data from trajectory files
`frametool` | extract frames from trajectory files

See how they are used on Running simulations.

## Clickable Icons

On MacOS or Linux, it is possible to use a script to start cytosim with a double-click. See for example `bash/play_live.command` and `bash/play0000.command`.