| Name | cytosim JSON |
| Version |
0.0.11
JSON |
| download |
| home_page | |
| Summary | Cytosim: Langevin dynamics of active polymer networks |
| upload_time | 2023-09-08 07:58:11 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | |
| license | |
| 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 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 running 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 common tasks encountered during a simulation project are implemented in Python.
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 with 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 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
}
# 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)
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 even if you are not familiar with program development. Compiling natively on Windows would require changes to the code, but Cytosim should [compile within Cygwin](doc/compile/cygwin.md).
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 manually.
Altermatively, it is possible to use [cmake](https://cmake.org) to configure `make` automatically:
mkdir build
cd build
cmake ..
make
For troubleshooting, please check [the compile instructions](doc/compile/index.md).
Once *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`.
Inspect in particular the short configuration files (e.g. fiber.cym, self.cym).
# 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
* Serge Dmitrieff 2013-
* Julio Belmonte 2014-
* Gaelle Letort 2014-
* Manuel Lera-Ramirez 2017-2022
* Maud Formanek 2020-2021
# Contact
Email: cytosim@cytosim.org
Raw data
{
"_id": null,
"home_page": "",
"name": "cytosim",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "simulation actin microtubule polymer",
"author": "",
"author_email": "",
"download_url": "https://files.pythonhosted.org/packages/af/80/66b9851d64bf0460b8b5308e0e57e5d92d6dc39a8ee6a8edac3f398b373b/cytosim-0.0.11.tar.gz",
"platform": "Windows",
"description": "# Cytosim\n\nCytosim 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 running 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 common tasks encountered during a simulation project are implemented in Python.\n\n\n\nCytosim 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 with 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 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# 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\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# Installation\n\nCytosim 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 program development. Compiling natively on Windows would require changes to the code, but Cytosim should [compile within Cygwin](doc/compile/cygwin.md).\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 manually.\nAltermatively, it is possible to use [cmake](https://cmake.org) to configure `make` automatically:\n\n\tmkdir build\n\tcd build\n\tcmake ..\n\tmake\n\nFor troubleshooting, please check [the compile instructions](doc/compile/index.md).\nOnce *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`. \nInspect in particular the short configuration files (e.g. fiber.cym, self.cym). \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* Serge Dmitrieff 2013-\n* Julio Belmonte 2014-\n* Gaelle Letort 2014-\n* Manuel Lera-Ramirez 2017-2022\n* Maud Formanek 2020-2021\n\n# Contact\n\nEmail: cytosim@cytosim.org\n\n\n",
"bugtrack_url": null,
"license": "",
"summary": "Cytosim: Langevin dynamics of active polymer networks",
"version": "0.0.11",
"project_urls": null,
"split_keywords": [
"simulation",
"actin",
"microtubule",
"polymer"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "af8066b9851d64bf0460b8b5308e0e57e5d92d6dc39a8ee6a8edac3f398b373b",
"md5": "8a1b439273af567b6f32b5204a651b40",
"sha256": "30dd71ffa02c280dba8f3fd50400ec785e52f1e4df28c0cfda665681d5519007"
},
"downloads": -1,
"filename": "cytosim-0.0.11.tar.gz",
"has_sig": false,
"md5_digest": "8a1b439273af567b6f32b5204a651b40",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 982299,
"upload_time": "2023-09-08T07:58:11",
"upload_time_iso_8601": "2023-09-08T07:58:11.259549Z",
"url": "https://files.pythonhosted.org/packages/af/80/66b9851d64bf0460b8b5308e0e57e5d92d6dc39a8ee6a8edac3f398b373b/cytosim-0.0.11.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-09-08 07:58:11",
"github": false,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"lcname": "cytosim"
}
