{"id":18810825,"url":"https://github.com/ecell/ecell3","last_synced_at":"2025-08-02T03:10:19.171Z","repository":{"id":142035884,"uuid":"1765424","full_name":"ecell/ecell3","owner":"ecell","description":null,"archived":false,"fork":false,"pushed_at":"2016-09-05T01:21:11.000Z","size":23571,"stargazers_count":8,"open_issues_count":5,"forks_count":5,"subscribers_count":9,"default_branch":"master","last_synced_at":"2025-06-17T11:08:27.983Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://www.e-cell.org/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ecell.png","metadata":{"files":{"readme":"README","changelog":"ChangeLog","contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2011-05-18T10:21:32.000Z","updated_at":"2016-09-05T01:21:14.000Z","dependencies_parsed_at":null,"dependency_job_id":"ea3a97f0-ba9d-4f39-86d2-92744284f17f","html_url":"https://github.com/ecell/ecell3","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/ecell/ecell3","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fecell3","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fecell3/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fecell3/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fecell3/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ecell","download_url":"https://codeload.github.com/ecell/ecell3/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fecell3/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268330914,"owners_count":24233152,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-02T02:00:12.353Z","response_time":74,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-07T23:22:44.159Z","updated_at":"2025-08-02T03:10:19.148Z","avatar_url":"https://github.com/ecell.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"=======================================================================\nRelease notes for E-Cell Simulation Environment Version 3 (E-Cell SE 3)\n=======================================================================\n\nKoichi Takahashi \u003cshafi@e-cell.org\u003e\n\nE-Cell dev mailing list \u003cdev@e-cell.org\u003e\n\n|build-status|\n\nWhat is E-Cell System?\n======================\nE-Cell is a generic software package for cellular modeling and simulation.  \n\nFiles and directories\n=====================\nIn the package, files are organized as follows::\n\n  -+- README:    This file\n   |\n   +- INSTALL:   Installation instructions\n   |\n   +- ChangeLog: Automatically generated cvs log \n   |\n   +- NEWS:      Project log\n   |\n   +- COPYING:   License\n   |\n   +- AUTHORS:   List of authors\n   |\n   +- ecell/ --\u003e Core portion of E-Cell SE 3, or Hekkoro\n   |  |\n   |  +- libecs/       --\u003e Koyurugi: Class library for cell modeling and\n   |  |                    simulation (E-Cell SE 3's innermost core)\n   |  +- libemc/       --\u003e E-Cell Micro Core (EMC): C++ Facade API of Koyurugi\n   |  |\n   |  +- pyecs/        --\u003e Python binding of EMC and Koyurugi\n   |  |\n   |  +- pyecell/      --\u003e Python E-Cell library\n   |  |\n   |  +- session-monitor/  --\u003e GUI session monitor (gecell)\n   |  |\n   |  +- model-editor/ --\u003e GUI model editor (ecell3-modeleditor)\n   |  |\n   |  +- toollauncher/ --\u003e GUI tool launcher \n   |\n   +- dmtool/          --\u003e C++ class library for dynamic loading of object\n   |\n   +- doc/             --\u003e Documentations \n   |  |\n   |  +- users-manual/ --\u003e Users manual\n   |  |\n   |  +- samples/      --\u003e Sample models\n   |\n   +- libltdl/         --\u003e Libtool's dynamic module loader library\n\nAnd installed in the following structure::\n\n PREFIX -+- bin/       --\u003e E-Cell system toolsuite\n         |\n         +- include/   --\u003e Header files (for developers)\n         |  |\n         |  +- dmtool/\n         |  |\n         |  +- ecell-3.1/\n         |     |\n         |     +- libecs/\n         |     |\n         |     +- libemc/\n         |\n         +- lib/       --\u003e Shared libraries and python modules\n         |  |\n         |  +- python?.?/  --\u003e Python modules\n         |  |\n         |  +- ecell-3.1/\n         |     |\n         |     +- dms      --\u003e Standard dynamic modules\n         |     |\n         |     +- model-editor     --\u003e Scripts and data for Model Editor\n         |     |\n         |     +- session-monitor  --\u003e Scripts and data for Session Monitor\n         |     |\n         |     +- toollauncher     --\u003e Scripts and data for Tool Launcher\n         |\n         +- share/\n            |\n            +- ecell-3.1/\n            |  |\n            |  +- dms/     --\u003e Sources for the standard dynamic modules.\n            |\n            +- doc/\n               |\n               +- ecell/   --\u003e E-Cell Documents\n                  |\n                  +- samples/      --\u003e Sample models\n                  |\n                  +- users-manual* --\u003e Users manual\n                  |\n                  +- api           --\u003e API reference\n                  |\n                  +- model-editor  --\u003e Model Editor documentation\n\n\nAbout the code names\n--------------------\nHekkoro\n    Code name for E-Cell SE Version 3 (libecs, libemc and pyecs)\nKoyurugi\n    Code name for the libecs class library\nOsogo\n    Code name for the GUI Session monitor (gecell)\n\nDocumentation\n=============\nE-Cell 3 users manual is hosted on Read the Docs.\nhttp://ecell3.readthedocs.org/en/latest/\n\nBasic Usage\n===========\n\n1. Using E-Cell from python interpreter\n---------------------------------------\nBy default a python binding (pyecs) is built.\n\nTo 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. \n(If you have not specified it, it falls back to ``/usr/local``.)\n\nA typical command-line session is as follows::\n\n   $ ecell3-session\n   ecell3-session [ E-Cell SE Version 3.1.106, on Python Version 2.3.4 ]\n   Copyright (C) 1996-2014 Keio University\n   Copyright (C) 2008-2014 RIKEN\n   Copyright (C) 2005-2009 The Molecular Sciences Institute\n   Send feedback to Koichi Takahashi \u003cshafi@e-cell.org\u003e\n   ecell3-session\u003e\u003e\u003e\n\nIn the above output, ``ecell3-session\u003e\u003e\u003e`` is the prompt of ecell3-session. That accepts almost everything of interactive Python.\n\nThe below example first loads a model that is stored in simple.eml, and then run it for 10 seconds in simulation time::\n\n   ecell3-session\u003e\u003e\u003e loadModel( 'simple.eml' )\n   \u003csimple.eml, t=0\u003e\u003e\u003e run( 10 )\n   \u003csimple.eml, t=10.001\u003e\u003e\u003e\n\n2. Using E-Cell from Session Monitor GUI\n----------------------------------------\nIf you have python, and pygtk2 installed, a GUI session monitor, is built.\n\nTo use Session Monitor, type::\n\n   $ ecell3-session-monitor\n\nSample Models\n=============\n\nSample models are installed under {PREFIX}/share/doc/samples.  Each model is\nstored as a EM script, while ecell toolsuite only accept XML-based EML files.\n\nEM scripts can be converted to EML files through the program ``ecell3-em2eml``::\n\n   $ ecell3-em2eml Drosophila.em\n\nThis will create Drosophila.eml in the current working directory.\n\nSome samples require that the accompanying dynamic modules (DM's) be\nbuilt before running simulation.  These modules are provided as C++ sources\nwhich can be compiled using ``ecell3-dmc``::\n\n   $ ecell3-dmc SomeModule.cpp\n\nFor more information about the dynamic module, refer to the users manual.\n\n\nCopyright Notice\n================\nE-Cell System is distributed under the GNU General Public License\nversion 2.\n\n  Copyright (C) 1996-2014 Keio University\n  Copyright (C) 2008-2014 RIKEN\n  Copyright (C) 2005-2009 The Molecular Sciences Institute\n\n  E-Cell System is free software; you can redistribute it and/or\n  modify it under the terms of the GNU General Public\n  License as published by the Free Software Foundation; either\n  version 2 of the License, or (at your option) any later version.\n  \n  E-Cell System is distributed in the hope that it will be useful,\n  but WITHOUT ANY WARRANTY; without even the implied warranty of\n  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n  See the GNU General Public License for more details.\n  \n  You should have received a copy of the GNU General Public\n  License along with E-Cell System -- see the file COPYING.\n  If not, write to the Free Software Foundation, Inc.,\n  59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\n \nIt should be mentioned this package contains the following softwares\nfor convenience.  Please note that these are not covered by the license\nunder which a copy of E-Cell System is licensed to you, while neither\ncomposition nor distribution of any derivative work of E-Cell System with\nthese software violates the terms of each license, provided that it meets\nevery condition of the respective licenses.\n\n* PLY\n\n  PLY is written by David M. Beazley and distributed under the GNU\n  Lesser General Public License.  See COPYING.LGPLv2 or COPYING.LGPLv3 for the\n  full license terms of the LGPL(s).\n\n    Author: David M. Beazley (beazley@cs.uchicago.edu)\n            Department of Computer Science\n            University of Chicago\n            Chicago, IL  60637\n    \n    Copyright (C) 2001, David M. Beazley\n    \n    This library is free software; you can redistribute it and/or\n    modify it under the terms of the GNU Lesser General Public\n    License as published by the Free Software Foundation; either\n    version 2.1 of the License, or (at your option) any later version.\n    \n    This library is distributed in the hope that it will be useful,\n    but WITHOUT ANY WARRANTY; without even the implied warranty of\n    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU\n    Lesser General Public License for more details.\n    \n    You should have received a copy of the GNU Lesser General Public\n    License along with this library; if not, write to the Free Software\n    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA\n\n  The website for this software is located at:\n\n    http://www.dabeaz.com/ply/\n\n* EmPy \n\n  EmPy is written by Erik Max Francis and distributed under the GNU Lesser\n  General Public License.  See COPYING.LGPLv2 or COPYING.LGPLv3 for the full\n  license terms of the LGPL(s).\n\n    Copyright (C) 2002-2003 Erik Max Francis \u003cmax@alcyone.com\u003e\n\n    This library is free software; you can redistribute it and/or\n    modify it under the terms of the GNU Lesser General Public\n    License as published by the Free Software Foundation; either\n    version 2.1 of the License, or (at your option) any later version.\n    \n    This library is distributed in the hope that it will be useful,\n    but WITHOUT ANY WARRANTY; without even the implied warranty of\n    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU\n    Lesser General Public License for more details.\n    \n    You should have received a copy of the GNU Lesser General Public\n    License along with this library; if not, write to the Free Software\n    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA\n\n  The website for this software is located at:\n\n    http://www.alcyone.com/software/empy/\n\n* libltdl\n\n  libltdl is part of libtool, whose copyright is held by Free Software\n  Foundation.  See COPYING.LGPLv2 or COPYING.LGPLv3 for the full license terms\n  of the LGPL(s).\n\n    Copyright (C) 1998, 1999, 2000 Free Software Foundation, Inc.\n    Originally by Thomas Tanner \u003ctanner@ffii.org\u003e\n\n    This library is free software; you can redistribute it and/or\n    modify it under the terms of the GNU Lesser General Public\n    License as published by the Free Software Foundation; either\n    version 2 of the License, or (at your option) any later version.\n     \n    As a special exception to the GNU Lesser General Public License,\n    if you distribute this file as part of a program or library that\n    is built using GNU libtool, you may include it under the same\n    distribution terms that you use for the rest of that program.\n       \n    This library is distributed in the hope that it will be useful,\n    but WITHOUT ANY WARRANTY; without even the implied warranty of\n    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU\n    Lesser General Public License for more details.\n\n  The website for this software is located at:\n\n    http://www.gnu.org/software/libtool/\n\n* The Loki Library\n\n  Libecs contains part of The Loki Library, which is writen by Andrei \n  Alexandrescu and the contributors.\n\n    Copyright (c) 2001 by Andrei Alexandrescu\n\n    This code accompanies the book:\n    Alexandrescu, Andrei. \"Modern C++ Design: Generic Programming and Design \n    Patterns Applied\". Copyright (c) 2001. Addison-Wesley.\n\n    Permission to use, copy, modify, distribute and sell this software for any \n    purpose is hereby granted without fee, provided that the above copyright \n    notice appear in all copies and that both that copyright notice and this \n    permission notice appear in supporting documentation.\n\n    The author or Addison-Wesley Longman make no representations about the \n    suitability of this software for any purpose. It is provided \"as is\" \n    without express or implied warranty.\n\n  The website for this software is located at:\n\n    http://loki-lib.sourceforge.net/\n\n* TableIO\n\n   Table IO is a module for reading ASCII tables from files to Python lists\n   written by Michael A. Miller and distributed under the GNU General Public\n   License.  See COPYING.GPLv2 or COPYING.GPLv3 for the full license terms of\n   the GPL(s).\n\n     Copyright (C) 2000 Michael A. Miller \u003cmmiller@debian.org\u003e\n\n     This program is free software; you can redistribute it and/or\n     modify it under the terms of the GNU General Public License as\n     published by the Free Software Foundation; either version 2 of the\n     License, or (at your option) any later version.\n     \n     This program is distributed in the hope that it will be useful, but\n     WITHOUT ANY WARRANTY; without even the implied warranty of\n     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU\n     General Public License for more details.\n     \n     You should have received a copy of the GNU General Public License\n     along with this program; if not, write to the Free Software\n     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307\n     USA. \n\n  The website for this software is located at:\n\n     http://php.iupui.edu/~mmiller3/python/\n\n.. Build status badge\n.. |build-status|\n   image:: https://secure.travis-ci.org/ecell/ecell3.png\n   :target: http://travis-ci.org/ecell/ecell3\n   :alt: Build Status\n\n$Id$\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecell%2Fecell3","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fecell%2Fecell3","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecell%2Fecell3/lists"}