Commit 2a66b470 authored by nedelec's avatar nedelec

reviewed README

parent f81db429
# Cytosim
Cytosim is a cytoskeleton simulation designed to handle large systems of flexible filaments with associated proteins such as molecular motors. It is a versatile base that has been used to study actin and microtubule systems in 1D, 2D and 3D. It is built around a core cross-platform C++ engine. It runs on UNIX, Mac OSX, GNU/Linux and within Cygwin on Windows. The code is modular and extensible, making Cytosim a convenient base that can be customized to meet particular tasks.
Cytosim is a cytoskeleton simulation suite designed to handle large systems of flexible filaments with associated proteins such as molecular motors. It is a versatile base that has been used to study actin and microtubule systems in 1D, 2D and 3D. It is built around a cross-platform C++ core engine that runs on UNIX, Mac OSX, GNU/Linux and within Cygwin on Windows. The code is modular and extensible, making Cytosim a convenient base that can be customized to meet particular tasks. Some of the most upstream operations are implemented in Python.
![Cytosim](doc/data/cytosim.png)
Cytosim is a suite of command-line tools with simulation and display capabilities. The simulation is specified in a [configuration file](doc/sim/config.md), defining objects, their parameters and a suite of operations, such as advancing time, saving frames or [generating reports](doc/sim/report.md). Here is a basic example:
Cytosim is a suite of command-line tools with simulation and display capabilities. The simulation is specified in a [configuration file](doc/sim/config.md), defining objects, their parameters and a suite of operations, such as advancing time, saving frames or [generating reports](doc/sim/report.md). Here is a basic example, with parameters specified in [units of second, micrometers and pico-Newtons](doc/sim/units.md).
set simul system
{
......@@ -39,20 +40,18 @@ Cytosim is a suite of command-line tools with simulation and display capabilitie
nb_frames = 10
}
The parameters are specified in [units of second, micrometers and pico-Newtons](doc/sim/units.md).
# Documentation
The documentation is formatted with [Markdown](https://en.wikipedia.org/wiki/Markdown).
You can view the files with [MacDown (Mac OSX only)](https://macdown.uranusjr.com) or [Typora (Cross platform)](https://typora.io)
[Link to documentation](doc/index.md)
[Link to cytosim documentation](doc/index.md)
The Brownian dynamics approach was described in:
[Collective Langevin Dynamics of Flexible Cytoskeletal Fibers](http://iopscience.iop.org/article/10.1088/1367-2630/9/11/427/meta)
The Brownian dynamics approach was described in: [Collective Langevin Dynamics of Flexible Cytoskeletal Fibers (New Journal of Physics)](http://iopscience.iop.org/article/10.1088/1367-2630/9/11/427/meta).
The documentation source files use [Markdown](https://en.wikipedia.org/wiki/Markdown) and are best viewed with [MacDown (Mac OSX only)](https://macdown.uranusjr.com) or [Typora (Cross platform)](https://typora.io)
# Installation
Cytosim is distributed as source code and [must be compiled](doc/compile/index.md) before use. On Mac OS X and Linux this should be uncomplicated if you are familiar with compilation in general. On Windows, this is more challenging, and we suggest to [compile within Cygwin](doc/compile/cygwin.md).
Cytosim is distributed as source code and [must be compiled](doc/compile/index.md) before use. On Mac OS X and Linux this should be uncomplicated even if you are not familiar with compilation in general. On Windows, this is more challenging, and we suggest to [compile within Cygwin](doc/compile/cygwin.md).
To compile, enter these commands in a terminal window:
......@@ -61,7 +60,7 @@ To compile, enter these commands in a terminal window:
make
For more information, please check [the compile instructions](doc/compile/index.md).
Once cytosim is running on your machine, check the tutorials, the page on [running simulations](doc/main/runs.md), and the examples contained in the folder `cym`. Inspect in particular the short configuration files (e.g. fiber.cym, self.cym).
Once *cytosim* is running on your machine, check the tutorials, the page on [running simulations](doc/main/runs.md), and the examples contained in the folder `cym`. Inspect in particular the short configuration files (e.g. fiber.cym, self.cym).
# Contributors
......
# Cytosim's Documentation
*work in progress*
*This is work in progress*
* [**Overview**](main/overview.md)
* [The configuration file](sim/config.md)
......
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