This is work in progress
- Overview
- The configuration file
- Units in Cytosim
(s, um, pN) - Set of standard config files
- Introduction to the command line
- Tutorials
- Simulation engine
- Running simulations on your computer
- Running cytosim on a cluster
- Getting numbers out of Cytosim with
report - Frequently asked questions
- The different executables
- Graphical rendering
- Making movies
- Prior work
- Syntax highlighting for config file
- File types
Cytosim is distributed as source code and must be compiled before use. On Mac OS X and Linux this should be straightforward if you are familiar with compilation in general. On Windows, we suggest to compile within Cygwin.
To compile, enter these commands in a terminal window:
git clone https://gitlab.com/f.nedelec/cytosim
cd cytosim
make
Once cytosim is running on your machine, check the tutorials, the page on running simulations, and the examples contained in the folder cym. Inspect in particular the short configuration files (e.g. fiber.cym, self.cym).
For more information, please check the compilation guideline.
cytosimATcytosimDOTorg