{"id":46697222,"url":"https://github.com/csiro/emmai","last_synced_at":"2026-03-09T05:33:27.416Z","repository":{"id":339330664,"uuid":"1054629629","full_name":"csiro/emmai","owner":"csiro","description":"Computational pipeline to enhance Genome-Scale Modelling prediction accuracy","archived":false,"fork":false,"pushed_at":"2026-02-19T06:08:40.000Z","size":35120,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-02-19T12:20:23.499Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/csiro.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-09-11T05:46:40.000Z","updated_at":"2026-02-19T06:08:45.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/csiro/emmai","commit_stats":null,"previous_names":["csiro/emmai"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/csiro/emmai","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csiro%2Femmai","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csiro%2Femmai/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csiro%2Femmai/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csiro%2Femmai/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/csiro","download_url":"https://codeload.github.com/csiro/emmai/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csiro%2Femmai/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30283935,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-09T02:57:19.223Z","status":"ssl_error","status_checked_at":"2026-03-09T02:56:26.373Z","response_time":61,"last_error":"SSL_read: 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":[],"created_at":"2026-03-09T05:33:26.135Z","updated_at":"2026-03-09T05:33:27.409Z","avatar_url":"https://github.com/csiro.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# EMMAi pipeline\n\n## Description\n\nThe `EMMAi` repository contains a collection of IPython notebooks,\nPython scripts, and SLURM batch files designed to facilitate the EMMAi\ncomputational workflow.\n\n## Contents\n\n- **IPython Notebooks**: Interactive notebooks for data analysis and visualization.\n- **Python Scripts**: Standalone scripts for various computational tasks. These\nfor the most part duplicate the code in the IPython notebooks.\n- **SLURM Batch Files**: Scripts to manage and execute jobs on SLURM-based\nhigh-performance computing clusters. These execute the Python scripts after\nactivating a CONDA environment.\n\n## Requirements\n\nTo use the contents of this repository, you will need the following:\n\n- Python 3.9\n- Jupyter Notebook\n- SLURM workload manager (for batch files)\n- MAMBA (or CONDA if you prefer)\n\n## Installation\n\n1. Clone the repository:\n\n   ```bash\n   git clone --recurse-submodules git@github.com:csiro-internal/emmai.git\n   ```\n\n2. There are two installation scripts provided in the setup_scripts directory. 1\nOne for HPC systems with GPU and CPU clusters - [see the detailed README](setup_scripts/README_HPC.md) and\none for standalone systems - [see the detailed README](setup_scripts/README_standalone.md)\n\n## Executing the pipeline\n\n1. After following the installation guidelines you can choose to execute the\npipeline in 1 of three ways, or a combination of the three - if you know what\nyou are doing.\n\n    i. By running the Jupyter notebooks sequentially starting with:\n    notebooks/1_data_retrieval.ipynb\n\n    ii. By executing the python scripts sequentially starting with:\n    source env.sh\n    python_scripts/1_data_retrieval.py\n\n    iii. Or by running a combination of the batch scripts in hpc_scripts. See\n    [See the HPC README](hpc_scripts/README.md) for details.\n\n## License\n\nThis software is licensed under the GNU General Public License, version 3 (GPLv3).\n\nCopyright (C) 2025, CSIRO\n\nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or any later version.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcsiro%2Femmai","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcsiro%2Femmai","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcsiro%2Femmai/lists"}