https://github.com/ecell/ecell3
https://github.com/ecell/ecell3
Last synced: 11 months ago
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- Host: GitHub
- URL: https://github.com/ecell/ecell3
- Owner: ecell
- License: other
- Created: 2011-05-18T10:21:32.000Z (about 15 years ago)
- Default Branch: master
- Last Pushed: 2016-09-05T01:21:11.000Z (almost 10 years ago)
- Last Synced: 2025-06-17T11:08:27.983Z (about 1 year ago)
- Language: Python
- Homepage: http://www.e-cell.org/
- Size: 22.5 MB
- Stars: 8
- Watchers: 9
- Forks: 5
- Open Issues: 5
-
Metadata Files:
- Readme: README
- Changelog: ChangeLog
- License: COPYING
- Authors: AUTHORS
Awesome Lists containing this project
README
=======================================================================
Release notes for E-Cell Simulation Environment Version 3 (E-Cell SE 3)
=======================================================================
Koichi Takahashi
E-Cell dev mailing list
|build-status|
What is E-Cell System?
======================
E-Cell is a generic software package for cellular modeling and simulation.
Files and directories
=====================
In the package, files are organized as follows::
-+- README: This file
|
+- INSTALL: Installation instructions
|
+- ChangeLog: Automatically generated cvs log
|
+- NEWS: Project log
|
+- COPYING: License
|
+- AUTHORS: List of authors
|
+- ecell/ --> Core portion of E-Cell SE 3, or Hekkoro
| |
| +- libecs/ --> Koyurugi: Class library for cell modeling and
| | simulation (E-Cell SE 3's innermost core)
| +- libemc/ --> E-Cell Micro Core (EMC): C++ Facade API of Koyurugi
| |
| +- pyecs/ --> Python binding of EMC and Koyurugi
| |
| +- pyecell/ --> Python E-Cell library
| |
| +- session-monitor/ --> GUI session monitor (gecell)
| |
| +- model-editor/ --> GUI model editor (ecell3-modeleditor)
| |
| +- toollauncher/ --> GUI tool launcher
|
+- dmtool/ --> C++ class library for dynamic loading of object
|
+- doc/ --> Documentations
| |
| +- users-manual/ --> Users manual
| |
| +- samples/ --> Sample models
|
+- libltdl/ --> Libtool's dynamic module loader library
And installed in the following structure::
PREFIX -+- bin/ --> E-Cell system toolsuite
|
+- include/ --> Header files (for developers)
| |
| +- dmtool/
| |
| +- ecell-3.1/
| |
| +- libecs/
| |
| +- libemc/
|
+- lib/ --> Shared libraries and python modules
| |
| +- python?.?/ --> Python modules
| |
| +- ecell-3.1/
| |
| +- dms --> Standard dynamic modules
| |
| +- model-editor --> Scripts and data for Model Editor
| |
| +- session-monitor --> Scripts and data for Session Monitor
| |
| +- toollauncher --> Scripts and data for Tool Launcher
|
+- share/
|
+- ecell-3.1/
| |
| +- dms/ --> Sources for the standard dynamic modules.
|
+- doc/
|
+- ecell/ --> E-Cell Documents
|
+- samples/ --> Sample models
|
+- users-manual* --> Users manual
|
+- api --> API reference
|
+- model-editor --> Model Editor documentation
About the code names
--------------------
Hekkoro
Code name for E-Cell SE Version 3 (libecs, libemc and pyecs)
Koyurugi
Code name for the libecs class library
Osogo
Code name for the GUI Session monitor (gecell)
Documentation
=============
E-Cell 3 users manual is hosted on Read the Docs.
http://ecell3.readthedocs.org/en/latest/
Basic Usage
===========
1. Using E-Cell from python interpreter
---------------------------------------
By default a python binding (pyecs) is built.
To invoke a E-Cell Session Script interpreter in interactive mode, use ``ecell3-sesion`` script. Note that the script expects {PREFIX}/bin is included in PATH environment, where {PREFIX} is the directory path that was specified to configure.
(If you have not specified it, it falls back to ``/usr/local``.)
A typical command-line session is as follows::
$ ecell3-session
ecell3-session [ E-Cell SE Version 3.1.106, on Python Version 2.3.4 ]
Copyright (C) 1996-2014 Keio University
Copyright (C) 2008-2014 RIKEN
Copyright (C) 2005-2009 The Molecular Sciences Institute
Send feedback to Koichi Takahashi
ecell3-session>>>
In the above output, ``ecell3-session>>>`` is the prompt of ecell3-session. That accepts almost everything of interactive Python.
The below example first loads a model that is stored in simple.eml, and then run it for 10 seconds in simulation time::
ecell3-session>>> loadModel( 'simple.eml' )
>> run( 10 )
>>
2. Using E-Cell from Session Monitor GUI
----------------------------------------
If you have python, and pygtk2 installed, a GUI session monitor, is built.
To use Session Monitor, type::
$ ecell3-session-monitor
Sample Models
=============
Sample models are installed under {PREFIX}/share/doc/samples. Each model is
stored as a EM script, while ecell toolsuite only accept XML-based EML files.
EM scripts can be converted to EML files through the program ``ecell3-em2eml``::
$ ecell3-em2eml Drosophila.em
This will create Drosophila.eml in the current working directory.
Some samples require that the accompanying dynamic modules (DM's) be
built before running simulation. These modules are provided as C++ sources
which can be compiled using ``ecell3-dmc``::
$ ecell3-dmc SomeModule.cpp
For more information about the dynamic module, refer to the users manual.
Copyright Notice
================
E-Cell System is distributed under the GNU General Public License
version 2.
Copyright (C) 1996-2014 Keio University
Copyright (C) 2008-2014 RIKEN
Copyright (C) 2005-2009 The Molecular Sciences Institute
E-Cell System is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
E-Cell System is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU General Public
License along with E-Cell System -- see the file COPYING.
If not, write to the Free Software Foundation, Inc.,
59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
It should be mentioned this package contains the following softwares
for convenience. Please note that these are not covered by the license
under which a copy of E-Cell System is licensed to you, while neither
composition nor distribution of any derivative work of E-Cell System with
these software violates the terms of each license, provided that it meets
every condition of the respective licenses.
* PLY
PLY is written by David M. Beazley and distributed under the GNU
Lesser General Public License. See COPYING.LGPLv2 or COPYING.LGPLv3 for the
full license terms of the LGPL(s).
Author: David M. Beazley (beazley@cs.uchicago.edu)
Department of Computer Science
University of Chicago
Chicago, IL 60637
Copyright (C) 2001, David M. Beazley
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
The website for this software is located at:
http://www.dabeaz.com/ply/
* EmPy
EmPy is written by Erik Max Francis and distributed under the GNU Lesser
General Public License. See COPYING.LGPLv2 or COPYING.LGPLv3 for the full
license terms of the LGPL(s).
Copyright (C) 2002-2003 Erik Max Francis
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
The website for this software is located at:
http://www.alcyone.com/software/empy/
* libltdl
libltdl is part of libtool, whose copyright is held by Free Software
Foundation. See COPYING.LGPLv2 or COPYING.LGPLv3 for the full license terms
of the LGPL(s).
Copyright (C) 1998, 1999, 2000 Free Software Foundation, Inc.
Originally by Thomas Tanner
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
As a special exception to the GNU Lesser General Public License,
if you distribute this file as part of a program or library that
is built using GNU libtool, you may include it under the same
distribution terms that you use for the rest of that program.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
The website for this software is located at:
http://www.gnu.org/software/libtool/
* The Loki Library
Libecs contains part of The Loki Library, which is writen by Andrei
Alexandrescu and the contributors.
Copyright (c) 2001 by Andrei Alexandrescu
This code accompanies the book:
Alexandrescu, Andrei. "Modern C++ Design: Generic Programming and Design
Patterns Applied". Copyright (c) 2001. Addison-Wesley.
Permission to use, copy, modify, distribute and sell this software for any
purpose is hereby granted without fee, provided that the above copyright
notice appear in all copies and that both that copyright notice and this
permission notice appear in supporting documentation.
The author or Addison-Wesley Longman make no representations about the
suitability of this software for any purpose. It is provided "as is"
without express or implied warranty.
The website for this software is located at:
http://loki-lib.sourceforge.net/
* TableIO
Table IO is a module for reading ASCII tables from files to Python lists
written by Michael A. Miller and distributed under the GNU General Public
License. See COPYING.GPLv2 or COPYING.GPLv3 for the full license terms of
the GPL(s).
Copyright (C) 2000 Michael A. Miller
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
USA.
The website for this software is located at:
http://php.iupui.edu/~mmiller3/python/
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