{"id":18810799,"url":"https://github.com/ecell/reaction_reader","last_synced_at":"2025-10-04T00:10:46.113Z","repository":{"id":145041287,"uuid":"1859171","full_name":"ecell/reaction_reader","owner":"ecell","description":null,"archived":false,"fork":false,"pushed_at":"2012-10-10T06:58:35.000Z","size":792,"stargazers_count":1,"open_issues_count":17,"forks_count":0,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-05-22T03:09:21.207Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ecell.png","metadata":{"files":{"readme":"README","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2011-06-07T09:49:49.000Z","updated_at":"2017-06-03T17:38:02.000Z","dependencies_parsed_at":"2023-03-22T14:44:04.394Z","dependency_job_id":null,"html_url":"https://github.com/ecell/reaction_reader","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ecell/reaction_reader","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Freaction_reader","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Freaction_reader/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Freaction_reader/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Freaction_reader/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ecell","download_url":"https://codeload.github.com/ecell/reaction_reader/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Freaction_reader/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278245459,"owners_count":25955029,"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":"2025-10-03T02:00:06.070Z","response_time":53,"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":"2024-11-07T23:22:28.797Z","updated_at":"2025-10-04T00:10:46.078Z","avatar_url":"https://github.com/ecell.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"---------------------\nHow to use pybngl.py\n---------------------\n\nHow to run\n\n  - $ python pybngl.py [options] [simfile]\n    -- options : options, see below.\n    -- simfile : simulation model file name.\n\n\nOptions (inside [] is default value, allow arbitrary order)\n\n  -r FILENAME : output generated reactions to FILENAME\n  -s STEP_NUM : run a simulation with STEP_NUM step [120]\n  -i ITR_NUM  : loop reaction genaration with ITR_NUM times [10]\n  -d          : allow duplicated rule\n  -t END_TIME : run a simulation by END_TIME(sec)[run a simulation with 120 steps, END_TIME is not defined]\n  -v          : print out generated reactions to stdout\n  -l          : allow loc[cation] notation (You have to use this option, if you use location info in model.)\n\n When both option \"-s\" and \"-t\" are defined, pybngl.py use \"-t\" option only.\n\n\nExamples\n\n  - $ python pybngl.py -s 10 -v test/testToy.py\n    -- run a simulation with the model written in test/testToy.py\n    -- (-s 10) : Number of the ODE step is 10\n    -- (-v)    : print out generated reactions to stdout\n\n  - $ python pybngl.py -s 0 -i 20 -v test/testLabel.py\n    -- run a simulation with the model written in test/testLabel.py\n    -- (-s 0)  : Number of the ODE step is 0 (generate reactions without simulation)\n    -- (-i 20) : loop reaction generation 20 times (it takes long long time...)\n    -- (-v)    : print out generated reactions to stdout\n\n  - $ python pybngl.py -l test/testLoc.py\n    -- run a simulation with the model written in test/testLoc.py\n    -- (-l)    : allow loc notation(testLoc.py use loc natation)\n\n\n-------------------\nModel samples\n-------------------\n\n  - test/testConc.py\n    -- a model with user defined function\n\n  - test/testEgfr.py\n    -- a model with EGF receptor signaling pathway\n\n  - test/testFunc.py\n    -- a model with user defined function\n    -- definition and usage of functions are written in head of the file\n\n  - test/testLabel.py\n    -- a model with label(%) notation\n    -- It takes a long time to generate reactions\n\n  - test/testLoc.py\n    -- a model with loc notation\n    -- needs \"-l\" option in use\n\n  - test/testToy.py\n    -- a model with label(%) notation\n\n  - working/testDuplicatedLabel.py\n    -- a model with optical isomer notatio(_)\n    -- currently not supported\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecell%2Freaction_reader","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fecell%2Freaction_reader","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecell%2Freaction_reader/lists"}