| Name | cytosim JSON |
| Version |
1.0.0
JSON |
| download |
| home_page | None |
| Summary | Cytosim: Langevin dynamics of active polymer networks |
| upload_time | 2025-10-08 08:20:09 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | None |
| license | None |
| keywords |
simulation
actin
microtubule
polymer
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Cytosim
Cytosim is an [Open Source](LICENSE.txt) cytoskeleton simulation suite designed to model large systems of flexible filaments and their associated proteins, such as molecular motors. It has been extensively used to study actin and microtubule dynamics in 1D, 2D, and 3D.
Built around an optimized C++ core engine, Cytosim runs on UNIX, macOS, GNU/Linux, and within the Windows Subsystem for Linux (WSL). The modular and extensible design makes it highly adaptable, allowing customization for specific research needs. Additionally, a versatile set of Python programs streamlines the standard simulation workflow. It is also available as a python module.
Cytosim has been used in approximately 100 research articles from [our](doc/publications/index.md) and [other research groups](doc/publications/biblio.md).
Cytosim offers command-line tools with simulation and display capabilities. Simulations are defined using a [configuration file](doc/sim/config.md) which specifies objects, their parameters, and a sequence of operations such as advancing time, saving frames, or [generating reports](doc/sim/report.md). Below is a basic example, where parameters are expressed in [seconds, micrometers and pico-Newtons](doc/sim/units.md).
set simul system
{
time_step = 0.005
viscosity = 0.02
}
set space cell
{
shape = sphere
}
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
confine = inside, 200, cell
}
new cell
{
radius = 5
}
new 5 microtubule
{
length = 11
}
run 5000 system
{
nb_frames = 10
}
# Installation
Cytosim uses the CPU and does not require any specific hardware. It can be installed via Anaconda, or [can be compiled](doc/compile/index.md) from source code before use.
To install it using Anaconda (requires no library installation) :
conda install -c conda-forge cytosim
To compile cytosim from source code :
* On Mac OS X: install [Xcode](https://developer.apple.com/xcode), free on the App Store.
* Linux: install [the GNU compiler](https://gcc.gnu.org) or another standard compiler.
* Compiling natively on Windows would require changes to the code. For Windows 10 and later, please use the [Windows Subsystem for Linux](doc/compile/wsl.md), and for older Windows versions, [use Cygwin](doc/compile/cygwin.md).
## Required Libraries
* [BLAS](http://netlib.org/blas)
* [LAPACK](http://netlib.org/lapack)
* [Ncurses](https://invisible-island.net/ncurses)
- [pthreads](http://en.wikipedia.org/wiki/POSIX_Threads)
- [OpenGL](http://www.opengl.org)
- [GLUT](http://www.opengl.org/resources/libraries/glut) or [freeGLUT](http://freeglut.sourceforge.net).
There are [different ways](doc/compile/index.md) to install these libraries.
## Instructions
To download the source code, enter these commands in a terminal window:
git clone https://gitlab.com/f-nedelec/cytosim
cd cytosim
To compile using [make](https://www.gnu.org/software/make), try:
make
If this fails, parameters of `makefile.inc` need to be updated.
Altermatively, it is possible to use [cmake](https://cmake.org) to configure `make` automatically in a separate folder `build`:
mkdir build
cd build
cmake ..
make
Compilation will take a few minutes and should produce two executables: `sim` and `play`.
For troubleshooting, please check [the compile instructions](doc/compile/index.md).
# Testing
A batch simulation is started from [the command line](https://en.wikipedia.org/wiki/Command-line_interface) preferably in a separate folder, for example `run0`:
mkdir run0
cp cym/self.cym run0/config.cym
cd run0
../bin/sim
Within less than a minute, this should produce output files (`objects.cmo` and `properties.cmp`) in the subdirectory. These binary files can be read by `play` to produce a graphical display:
../bin/play
Alternatively, a live graphical simulation can be started also from [the command line](https://en.wikipedia.org/wiki/Command-line_interface) by specifying the path of a configuration file, for example:
bin/play cym/self.cym
This will open a window and display the simulated cytoskeleton directly, without writing any file.
Once these tests passed and *cytosim* is running on your machine, proceed with the [tutorials](doc/tutorials/index.md), the page on [running simulations](doc/main/runs.md), and the examples contained in the folder `cym`.
# Documentation
[Link to 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)
A recent protocol demonstrating the use of Cytosim is:
[A Typical Workflow to Simulate Cytoskeletal Systems](https://dx.doi.org/10.3791/64125)
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)
# Contributors
The project was started in 1995, and received its name in 1999.
We hope cytosim can be useful for your research.
Sincerely yours, The Developers of Cytosim:
* Francois J. Nedelec 1995-
* Dietrich Foethke 2003-2007
* Cleopatra Kozlowski 2003-2007
* Elizabeth Loughlin 2006-2010
* Ludovic Brun 2008-2010
* Beat Rupp 2008-2011
* Jonathan Ward 2008-2014
* Antonio Politi 2010-2012
* Andre-Claude Clapson 2011-2013
* Jamie-Li Rickman 2014-2019
* Gaelle Letort 2014-2022
* Maud Formanek 2020-2023
* Manuel Lera-Ramirez 2017-2024
* Serge Dmitrieff 2013-
* Julio Belmonte 2014-
# History
Older versions of the project:
* [Cytosim-2017](https://github.com/nedelec/cytosim-2017)
* [Cytosim-2023](https://gitlab.com/f-nedelec/cytosim-2023)
# Contact
F.J. Nedelec
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"description": "# Cytosim\n\nCytosim is an [Open Source](LICENSE.txt) cytoskeleton simulation suite designed to model large systems of flexible filaments and their associated proteins, such as molecular motors. It has been extensively used to study actin and microtubule dynamics in 1D, 2D, and 3D.\n\nBuilt around an optimized C++ core engine, Cytosim runs on UNIX, macOS, GNU/Linux, and within the Windows Subsystem for Linux (WSL). The modular and extensible design makes it highly adaptable, allowing customization for specific research needs. Additionally, a versatile set of Python programs streamlines the standard simulation workflow. It is also available as a python module.\n\nCytosim has been used in approximately 100 research articles from [our](doc/publications/index.md) and [other research groups](doc/publications/biblio.md).\n\n\n\nCytosim offers command-line tools with simulation and display capabilities. Simulations are defined using a [configuration file](doc/sim/config.md) which specifies objects, their parameters, and a sequence of operations such as advancing time, saving frames, or [generating reports](doc/sim/report.md). Below is a basic example, where parameters are expressed in [seconds, micrometers and pico-Newtons](doc/sim/units.md).\n\n\tset simul system\n\t{\n\t time_step = 0.005\n\t viscosity = 0.02\n\t}\n\t\n\tset space cell\n\t{\n\t shape = sphere\n\t}\n\t\n\tset fiber microtubule\n\t{\n\t rigidity = 20\n\t segmentation = 0.5\n\t confine = inside, 200, cell\n\t}\n\t \n\tnew cell\n\t{\n\t radius = 5\n\t}\n\t\n\tnew 5 microtubule\n\t{\n\t length = 11\n\t}\n\t\n\trun 5000 system\n\t{\n\t nb_frames = 10\n\t}\n\n# Installation\n\nCytosim uses the CPU and does not require any specific hardware. It can be installed via Anaconda, or [can be compiled](doc/compile/index.md) from source code before use. \n\nTo install it using Anaconda (requires no library installation) : \n\n\tconda install -c conda-forge cytosim\n\n\nTo compile cytosim from source code : \n* On Mac OS X: install [Xcode](https://developer.apple.com/xcode), free on the App Store.\n* Linux: install [the GNU compiler](https://gcc.gnu.org) or another standard compiler. \n* Compiling natively on Windows would require changes to the code. For Windows 10 and later, please use the [Windows Subsystem for Linux](doc/compile/wsl.md), and for older Windows versions, [use Cygwin](doc/compile/cygwin.md).\n\n## Required Libraries\n\n* [BLAS](http://netlib.org/blas)\n* [LAPACK](http://netlib.org/lapack)\n* [Ncurses](https://invisible-island.net/ncurses)\n- [pthreads](http://en.wikipedia.org/wiki/POSIX_Threads)\n- [OpenGL](http://www.opengl.org) \n- [GLUT](http://www.opengl.org/resources/libraries/glut) or [freeGLUT](http://freeglut.sourceforge.net).\n\nThere are [different ways](doc/compile/index.md) to install these libraries.\n\n## Instructions\n\nTo download the source code, enter these commands in a terminal window:\n\n\tgit clone https://gitlab.com/f-nedelec/cytosim\n\tcd cytosim\n\t\nTo compile using [make](https://www.gnu.org/software/make), try:\n\t\n\tmake\n\nIf this fails, parameters of `makefile.inc` need to be updated.\nAltermatively, it is possible to use [cmake](https://cmake.org) to configure `make` automatically in a separate folder `build`:\n\n\tmkdir build\n\tcd build\n\tcmake ..\n\tmake\n\nCompilation will take a few minutes and should produce two executables: `sim` and `play`. \nFor troubleshooting, please check [the compile instructions](doc/compile/index.md).\n\n# Testing\n\nA batch simulation is started from [the command line](https://en.wikipedia.org/wiki/Command-line_interface) preferably in a separate folder, for example `run0`:\n\n\tmkdir run0\n\tcp cym/self.cym run0/config.cym\n\tcd run0\n\t../bin/sim\n\t\nWithin less than a minute, this should produce output files (`objects.cmo` and `properties.cmp`) in the subdirectory. These binary files can be read by `play` to produce a graphical display:\n\n\t../bin/play\n\nAlternatively, a live graphical simulation can be started also from [the command line](https://en.wikipedia.org/wiki/Command-line_interface) by specifying the path of a configuration file, for example:\n\n\tbin/play cym/self.cym\n\nThis will open a window and display the simulated cytoskeleton directly, without writing any file.\nOnce these tests passed and *cytosim* is running on your machine, proceed with the [tutorials](doc/tutorials/index.md), the page on [running simulations](doc/main/runs.md), and the examples contained in the folder `cym`. \n\n# Documentation\n\n[Link to documentation](doc/index.md)\n\nThe Brownian dynamics approach was described in: \n[Collective Langevin Dynamics of Flexible Cytoskeletal Fibers](http://iopscience.iop.org/article/10.1088/1367-2630/9/11/427/meta)\n\nA recent protocol demonstrating the use of Cytosim is:\n[A Typical Workflow to Simulate Cytoskeletal Systems](https://dx.doi.org/10.3791/64125)\n\nThe 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) \n\n\n# Contributors\n\n The project was started in 1995, and received its name in 1999.\n We hope cytosim can be useful for your research. \n Sincerely yours, The Developers of Cytosim:\n\n* Francois J. Nedelec 1995-\n* Dietrich Foethke 2003-2007\n* Cleopatra Kozlowski 2003-2007\n* Elizabeth Loughlin 2006-2010\n* Ludovic Brun 2008-2010\n* Beat Rupp 2008-2011\n* Jonathan Ward 2008-2014\n* Antonio Politi 2010-2012\n* Andre-Claude Clapson 2011-2013\n* Jamie-Li Rickman 2014-2019\n* Gaelle Letort 2014-2022\n* Maud Formanek 2020-2023\n* Manuel Lera-Ramirez 2017-2024\n* Serge Dmitrieff 2013-\n* Julio Belmonte 2014-\n\n# History\n\nOlder versions of the project:\n\n* [Cytosim-2017](https://github.com/nedelec/cytosim-2017)\n* [Cytosim-2023](https://gitlab.com/f-nedelec/cytosim-2023)\n\n# Contact\n\nF.J. Nedelec\n\n\n",
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