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cytosim-0.0.1
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مشاهده بیشترتوضیحات
Cytosim: Langevin dynamics of active polymer networks
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | cytosim-0.0.1 |
| نام | cytosim |
| نسخه کتابخانه | 0.0.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | - |
| ایمیل نویسنده | - |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/cytosim/ |
| مجوز | - |
# 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.
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-
* Maud Formanek 2020-
# Contact
Email: cytosim@cytosim.org
نحوه نصب
نصب پکیج whl cytosim-0.0.1:
pip install cytosim-0.0.1.whl
نصب پکیج tar.gz cytosim-0.0.1:
pip install cytosim-0.0.1.tar.gz