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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bioinformatics","neo4j","sbml"],"created_at":"2026-01-16T10:20:42.735Z","updated_at":"2026-01-16T10:20:43.503Z","avatar_url":"https://github.com/brsynth.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Neo4jSbml\n\n[![Github Version](https://img.shields.io/github/v/release/brsynth/neo4jsbml?display_name=tag\u0026sort=semver)](version) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)  \n[![Documentation Status](https://readthedocs.org/projects/neo4jsbml/badge/?version=latest)](https://neo4jsbml.readthedocs.io/en/latest/?badge=latest) [![GitHub Super-Linter](https://github.com/brsynth/neo4jsbml/workflows/Tests/badge.svg)](https://github.com/marketplace/actions/super-linter)  \n[![DOI](https://zenodo.org/badge/585859244.svg)](https://zenodo.org/badge/latestdoi/585859244)  \n\n## Install\n\n```sh\nconda install -c conda-forge neo4jsbml\n```\n\n## Usage\n\n### Step 1\n\nCreate a schema with [arrows](https://arrows.app) like:  \n![schema](docs/_static/usage/PathwayModelisation-1.0.0.png \"Schema SBML\")  \nRules:\n* Nodes are labelled based on SBML object name as defined in the [SBML specification](https://sbml.org)\n* Properties are labelled based on SBML object properties as defined the [SBML specification](https://sbml.org)\n\n### Step 2\n\nExport your schema at the JSON format.  \n![schema](docs/_static/usage/arrows.dwl.png \"Download JSON\")\n\n### Step 3\n\nImport your data with `neo4jsbml` into Neo4j.  \n* Use either a configuration file `ini` or individual parameters\n* Password needs to be store in a file for safety security\n* If you have multiple model in the database, pass a `tag` to identify the model loaded into the database if you want to avoid collision\n\n```sh\nneo4jsbml sbml-to-neo4j \\\n    # Database parameters\n    --input-protocol-str [\"neo4j\", \"neo4j+s\", \"neo4j+ssc\", \"bolt\", \"bolt+s\", \"bolt+ssc\"] \\\n    --input-url-str \"localhost\" \\\n    --input-user-str \"neo4j\" \\\n    --input-port-int \u003cport\u003e \\\n    --input-password-file \u003cfile\u003e \\\n    --input-database-str \u003cstr\u003e \\\n    # Config file\n    --input-config-file \u003cfile\u003e \\\n    # AuraDB file\n    --input-auradb-file \u003cfile\u003e \\\n\n    # Input\n    --input-file-sbml \u003cfile\u003e \\\n    --input-modelisation-json \u003cfile\u003e \\\n\n    # Parameter\n    --input-tag-str \"\"\n```\n\n## Config file\n\n### Neo4jsbml\n\nA config file is expected `.ini`\n```ini\n[connection]\nprotocol = neo4j\nurl = localhost\nport = 7687\n\n[database]\nuser = neo4j\npassword = abc\nname = neo4j\n```\n\n### AuraDB\n\nA file provided by AuraDB\n```bash\n# one comment\nNEO4J_URI=neo4j+s://test.neo4j.io\nNEO4J_USERNAME=neo4j\nNEO4J_PASSWORD=thepassword\n# second comment\nAURA_INSTANCEID=422DEf4\nAURA_INSTANCENAME=Instance01\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Fneo4jsbml","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrsynth%2Fneo4jsbml","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Fneo4jsbml/lists"}