{"id":18260381,"url":"https://github.com/carrascomj/rust_sbml","last_synced_at":"2025-08-06T16:22:05.881Z","repository":{"id":46289598,"uuid":"303336259","full_name":"carrascomj/rust_sbml","owner":"carrascomj","description":"SBML parser + bindings to python","archived":false,"fork":false,"pushed_at":"2024-09-20T09:07:20.000Z","size":178,"stargazers_count":8,"open_issues_count":6,"forks_count":4,"subscribers_count":1,"default_branch":"trunk","last_synced_at":"2024-10-31T11:40:18.439Z","etag":null,"topics":["bioinformatics","parser","sbml"],"latest_commit_sha":null,"homepage":"https://docs.rs/rust_sbml","language":"Rust","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/carrascomj.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE-APACHE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-10-12T09:04:59.000Z","updated_at":"2024-10-30T00:22:01.000Z","dependencies_parsed_at":"2022-09-18T06:53:57.961Z","dependency_job_id":null,"html_url":"https://github.com/carrascomj/rust_sbml","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carrascomj%2Frust_sbml","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carrascomj%2Frust_sbml/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carrascomj%2Frust_sbml/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carrascomj%2Frust_sbml/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/carrascomj","download_url":"https://codeload.github.com/carrascomj/rust_sbml/tar.gz/refs/heads/trunk","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223157390,"owners_count":17097362,"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":["bioinformatics","parser","sbml"],"created_at":"2024-11-05T10:45:05.674Z","updated_at":"2024-11-05T10:45:06.300Z","avatar_url":"https://github.com/carrascomj.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Crates.io](https://img.shields.io/crates/v/rust_sbml.svg)](https://crates.io/crates/rust_sbml)\n[![pypi](https://img.shields.io/pypi/v/rust_sbml.svg)](https://pypi.org/project/rust_sbml/)\n[![Documentation](https://docs.rs/rust_sbml/badge.svg)](https://docs.rs/rust_sbml/)\n[![Build](https://github.com/carrascomj/rust_sbml/workflows/build/badge.svg)](https://github.com/carrascomj/rust_sbml)\n[![Codecov](https://codecov.io/github/carrascomj/rust_sbml/coverage.svg?branch=trunk)](https://codecov.io/gh/carrascomj/rust_sbml)\n\n# rust_sbml\n\nParser for the [Systems Biology Markup Language (SBML)](http://sbml.org/Special/specifications/sbml-level-3/version-2/core/release-2/sbml-level-3-version-2-release-2-core.pdf):\n  * [Standalone Rust library](#rust)\n  * [Python API](#python)\n\n## Getting started\n\n### Rust\nAdd it to your Cargo.toml with no default features to avoid all\n[PyO3](https://github.com/PyO3/pyo3) nuisances.\n\n```toml\n[dependencies.rust_sbml]\nversion = \"0.7.0\"\ndefault_features=false\n```\n\nFor example,\n\n```rust\nuse rust_sbml::Model;\n\nlet example=r#\"\u003c?xml version=\"1.0\" encoding=\"UTF-8\"?\u003e\n\u003csbml xmlns=\"http://www.sbml.org/sbml/level3/version2/core\" level=\"3\" version=\"2\"\u003e\n     \u003cmodel timeUnits=\"second\" extentUnits=\"mole\" substanceUnits=\"mole\"\u003e\n     \u003c/model\u003e\n\u003c/sbml\u003e\"#;\nlet result = Model::parse(example);\nprintln!(\"{:?}\", result.unwrap());\n```\n\nSee [write_to_file.rs](https://github.com/carrascomj/rust_sbml/blob/trunk/examples/write_to_file.rs)\nfor an example on serializing to a file.\n\n### Python\nIt has only been tested on Linux.\n#### Using pip\n\n```shell\npip install rust_sbml\n```\n\n#### From source\nClone the repository.\n```shell\ngit clone https://github.com/carrascomj/rust_sbml.git\n```\nYou need [maturin](https://github.com/PyO3/maturin) for building it.\n```shell\npython -m pip install maturin\n```\n* Build locally\n  ```shell\n  maturin build --release\n  pip install .\n  ```\n* Build on virtualenv (no pip install required)\n  ```shell\n  # --release can be omitted to speed up compilation time\n  maturin develop --release\n  ```\n\nHaving it installed, you can use it as a normal Python package.\n\n```python\nfrom rust_sbml import Model\n\nsbml = Model(\"examples/EcoliCore.xml\")\nreaction = sbml.getListOfReactions()[0]\nprint(reaction.getListOfReactants())\n```\n\n### Milestones\n* `getListOfSpecies()` (id, name)\n* `getListOfCompartments()` (id, name)\n* `getListOfReactions()` (id, name)\n  * `.getListOfReactants()` (id, name)\n  * .`getListOfProducts()` (id, name)\n* Capable of retrieving FBC bounds.\n* Published to pypi\n* Kinetic Laws, with naive mathml tailored for SBML.\n* Metadata, with naive rdf tailored for SBML.\n* Test suite with python calls.\n* Test suite with libsbml comparison trough cobrapy.\n\n## License\n\nLicensed under either of\n\n- Apache License, Version 2.0, ([LICENSE-APACHE](LICENSE-APACHE) or http://www.apache.org/licenses/LICENSE-2.0)\n- MIT license ([LICENSE-MIT](LICENSE-MIT) or http://opensource.org/licenses/MIT)\n\nat your option.\n\n### Contribution\n\nUnless you explicitly state otherwise, any contribution intentionally submitted\nfor inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any\nadditional terms or conditions.\n\n\u003e README.md is automatically generated on CI using [cargo-readme](https://github.com/livioribeiro/cargo-readme). Please, modify README.tpl or lib.rs instead (check [the github worflow](https://github.com/carrascomj/rust_sbml/blob/trunk/.github/workflows/readme.yml) for more details).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcarrascomj%2Frust_sbml","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcarrascomj%2Frust_sbml","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcarrascomj%2Frust_sbml/lists"}