{"id":18810818,"url":"https://github.com/ecell/epdp_ecell4_impl_temporary","last_synced_at":"2026-01-11T00:30:15.482Z","repository":{"id":14859294,"uuid":"17582574","full_name":"ecell/epdp_ecell4_impl_temporary","owner":"ecell","description":null,"archived":false,"fork":false,"pushed_at":"2014-03-10T07:45:09.000Z","size":7832,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":8,"default_branch":"use-ecell4-namespace","last_synced_at":"2024-12-29T23:44:18.423Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","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}},"created_at":"2014-03-10T05:18:09.000Z","updated_at":"2014-03-10T07:45:10.000Z","dependencies_parsed_at":"2022-08-30T12:10:23.892Z","dependency_job_id":null,"html_url":"https://github.com/ecell/epdp_ecell4_impl_temporary","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fepdp_ecell4_impl_temporary","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fepdp_ecell4_impl_temporary/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fepdp_ecell4_impl_temporary/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fepdp_ecell4_impl_temporary/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ecell","download_url":"https://codeload.github.com/ecell/epdp_ecell4_impl_temporary/tar.gz/refs/heads/use-ecell4-namespace","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239748254,"owners_count":19690232,"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","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":"2024-11-07T23:22:40.226Z","updated_at":"2026-01-11T00:30:15.429Z","avatar_url":"https://github.com/ecell.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n:author: Koichi Takahashi\n\n\nE-Cell Particle Dynamics Prototype\n\nCopyright (C) 2008-2010 RIKEN\nCopyright (C) 2009-2010 AMOLF\nCopyright (C) 2005-2008 The Molecular Sciences Institute\n\n\nAbout this package\n========================\n\nThis package is tentatively named E-Cell Particle Dynamics Prototype\n(EPDP).  It currently implements the enhanced Greens Function Reaction\nDynamics (eGFRD) algorithm and the reaction Brownian Dynamics (BD) simulation\nalgorithm.  Implementation of the original version of GFRD will\npossibly be added in future.  The code is implemented with the hope\nthat it will eventually be part of the E-Cell System Version 4\nmulti-algorithm, multi-space simulation platform.\n\nThe purpose of this prototype code written in mixed Python and C++ is\nto establish a solid and practical implementation of the algorithms,\nand to extend it into a form that is suitable for large-scale\nbiochemical and cell simulations.\n\nThe eGFRD algorithm first appeared and be used in a paper by\nTakahashi, Tanase-Nicola and ten Wolde [1], and will be described more\nin detail in a forthcoming paper[2].\n\nThe reaction Brownian Dynamics algorithm is described in a paper by\nMorrelli and ten Wolde[3].\n\n\nAuthors\n========================\n\n(alphabetical order)\nKazunari Kaizu\nMoriyoshi Koizumi\nThomase Miedema\nKoichi Takahashi\n\n\nLicense\n========================\n\nThis package is distributed under the terms of GNU General Public License\nversion 2.  See COPYING.\n\n\nBuilding this package\n========================\n\nSee INSTALL.\n\n\nHistory of the Code\n========================\n\nKoichi Takahashi initially stated development of the code in 2005 to\nimplement his prototype of Greens Function Reaction Dynamics\nsimulation method invented by Jeroen van Zon and Pieter Rein ten Wolde\nin AMOLF, Amsterdam[4].  He gave a brief invited talk about\nperformance evaluation and applicability of the method to yeast\npheromon response pathway (the Alpha pathway) using the prototype in\nthe Third Annual Alpha Project Research Symposium (June 16-27, 2005, at UC\nBerkeley Art Museum).\n\nLater, in December 2006, ten Wolde, Sorin Tanase-Nicola, and Takahashi\nintroduced the concept called first-passage processes[5][6] to Greens\nFunction Reaction Dynamics by putting protective domains around\nparticles to further boost the performance and accuracy of the method.\nThe new method was named eGFRD (enhanced Greens Function Reaction\nDynamics).\n\n\nPlans\n=========================\n\nSome features planned to be added are; surfaces, interactions between\nmembrane proteins and proteins in solution, optimistic discrete-event\nscheduling for massive parallelization, connections to non-spatial \nsimulation methods such as ODE and Gillespie methods.\n\n\n[1] K. Takahashi, S. Tanase-Nicola and P.R. ten Wolde, PNAS doi:10.1073/pnas.0906885107 (2010).\n[2] K. Takahashi, S. Tanase-Nicola and P.R. ten Wolde, in preparation. \n[3] M.J. Morelli and P.R. ten Wolde, J. Chem. Phys. 7;129(5):054112 (2008).\n[4] van Zon and ten Wolde, Phys. Rev. Lett. 94 (2005).\n[5] T. Opplestrup, V.V. Bulatov, G.H. Gilmer, M.H. Kalos, and B. Sadigh, Phys. Rev. Lett. 97 (2006).\n[6] M.H. Kalos, D. Levesque and L. Verlet, Phys. Rev. A 9 (1974).\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecell%2Fepdp_ecell4_impl_temporary","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fecell%2Fepdp_ecell4_impl_temporary","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecell%2Fepdp_ecell4_impl_temporary/lists"}