{"id":29016273,"url":"https://github.com/karrlab/wc_utils","last_synced_at":"2025-06-25T22:07:54.529Z","repository":{"id":62588356,"uuid":"69289809","full_name":"KarrLab/wc_utils","owner":"KarrLab","description":"Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and others","archived":false,"fork":false,"pushed_at":"2022-04-29T03:07:52.000Z","size":1072,"stargazers_count":1,"open_issues_count":5,"forks_count":1,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-05-29T19:49:51.033Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KarrLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2016-09-26T20:26:02.000Z","updated_at":"2020-09-28T22:39:44.000Z","dependencies_parsed_at":"2022-11-03T23:31:09.148Z","dependency_job_id":null,"html_url":"https://github.com/KarrLab/wc_utils","commit_stats":null,"previous_names":[],"tags_count":23,"template":false,"template_full_name":null,"purl":"pkg:github/KarrLab/wc_utils","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fwc_utils","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fwc_utils/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fwc_utils/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fwc_utils/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KarrLab","download_url":"https://codeload.github.com/KarrLab/wc_utils/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fwc_utils/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261960463,"owners_count":23236575,"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":"2025-06-25T22:07:53.795Z","updated_at":"2025-06-25T22:07:54.521Z","avatar_url":"https://github.com/KarrLab.png","language":"Python","readme":"[![PyPI package](https://img.shields.io/pypi/v/wc_utils.svg)](https://pypi.python.org/pypi/wc_utils)\n[![Documentation](https://readthedocs.org/projects/wc-utils/badge/?version=latest)](http://docs.karrlab.org/wc_utils)\n[![Test results](https://circleci.com/gh/KarrLab/wc_utils.svg?style=shield)](https://circleci.com/gh/KarrLab/wc_utils)\n[![Test coverage](https://coveralls.io/repos/github/KarrLab/wc_utils/badge.svg)](https://coveralls.io/github/KarrLab/wc_utils)\n[![Code analysis](https://api.codeclimate.com/v1/badges/8139298cdbc1e32dcde4/maintainability)](https://codeclimate.com/github/KarrLab/wc_utils)\n[![License](https://img.shields.io/github/license/KarrLab/wc_utils.svg)](LICENSE)\n![Analytics](https://ga-beacon.appspot.com/UA-86759801-1/wc_utils/README.md?pixel)\n\n# Whole-cell modeling utilities\n\nThis package contains utilities that are useful to multiple whole-cell (WC) software components.\n\n## Installation\n\n1. Install the third-party dependencies listed below. Detailed installation instructions are available in [An Introduction to Whole-Cell Modeling](http://docs.karrlab.org/intro_to_wc_modeling/master/0.0.1/installation.html).\n        \n    * [ChemAxon Marvin](https://chemaxon.com/products/marvin): optional to calculate major protonation states\n      * [Java](https://www.java.com) \u003e= 1.8\n    * [Git](https://git-scm.com/)\n    * [OpenBabel](http://openbabel.org): optional to calculate chemical formulae\n    * [Pip](https://pip.pypa.io) \u003e= 18.0\n    * [Python](https://www.python.org) \u003e= 3.6\n\n2. To use Marvin to calculate major protonation states, set ``JAVA_HOME`` to the path to your Java virtual machine (JVM)\n   ```\n   export JAVA_HOME=/usr/lib/jvm/default-java\n   ```\n\n3. To use Marvin to calculate major protonation states, add Marvin to the Java class path\n   ```\n   export CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar\n   ```\n\n4. Install this package \n\n    * Install the latest release from PyPI\n      ```\n      pip install wc_utils[all]\n      ```\n\n    * Install the latest revision from GitHub\n      ```\n      pip install git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils[all]\n      pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[all]\n      ```\n\n## Example usage\n\n## Documentation\nPlease see the [API documentation](http://docs.karrlab.org/wc_utils).\n\n## License\nThe build utilities are released under the [MIT license](LICENSE).\n\n## Development team\nThis package was developed by the [Karr Lab](http://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York, USA.\n\n* Arthur Goldberg\n* Jonathan Karr\n\n## Questions and comments\nPlease contact the [Karr Lab](http://www.karrlab.org) with any questions or comments.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarrlab%2Fwc_utils","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkarrlab%2Fwc_utils","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarrlab%2Fwc_utils/lists"}