{"id":37610884,"url":"https://github.com/brsynth/reservoir","last_synced_at":"2026-01-16T10:20:40.587Z","repository":{"id":290789753,"uuid":"846600987","full_name":"brsynth/reservoir","owner":"brsynth","description":null,"archived":false,"fork":false,"pushed_at":"2025-09-19T11:51:34.000Z","size":5322,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-14T12:59:57.623Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/brsynth.png","metadata":{"files":{"readme":"README.md","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,"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":"2024-08-23T14:51:46.000Z","updated_at":"2025-10-21T13:31:35.000Z","dependencies_parsed_at":"2025-04-30T15:52:26.690Z","dependency_job_id":"5d6901d7-42ad-4da6-8a4f-3532580f1d30","html_url":"https://github.com/brsynth/reservoir","commit_stats":null,"previous_names":["brsynth/reservoir"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/brsynth/reservoir","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Freservoir","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Freservoir/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Freservoir/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Freservoir/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brsynth","download_url":"https://codeload.github.com/brsynth/reservoir/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Freservoir/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478049,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"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":"2026-01-16T10:20:40.021Z","updated_at":"2026-01-16T10:20:40.579Z","avatar_url":"https://github.com/brsynth.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Supporting content for the Reservoir Computing paper with Bacteria paper\n\n[![Github Version](https://img.shields.io/github/v/release/brsynth/molecule-signature-paper?display_name=tag\u0026sort=semver\u0026logo=github)](version)\n[![Github Licence](https://img.shields.io/github/license/brsynth/molecule-signature-paper?logo=github)](LICENSE.md)\n\nThis repository contains code to support the Computing paper with Bacteria publication. See citation for details.\n\n## Table of Contents\n- [1. Repository structure](#1-repository-structure)\n- [2. Installation](#2-installation)\n- [3. Citation](#3-citation)\n\n## 1. Repository structure\n\n```text\n.\n├── Dataset_input       \u003c placeholder for data files \u003e\n│   └── ..\n├── Reservoir       \u003c trained reservoir model\u003e\n│   └── ..\n├── Result     \n│   └── ..\n├── Library       \u003c supporting code for notebook \u003e\n│   └── ..\n├── 1.Dataset-species.ipynb\n├── 2.Fixed-prior.ipynb\n├── 3.ML-covid.ipynb\n├── 4.Reservoir-covid.ipynb\n├── 5.Reservoir-species.ipynb\n├── README.md\n└── requirements.yaml\n\n\n```\n## 2. Installation\n\nThe following steps will set up a `reservoir` conda environment.\n\n0. **Install Conda**\n\n    The conda package manager is required. If you do not have it installed, you\n    can download it from [here](https://docs.conda.io/en/latest/miniconda.html).\n    Follow the instructions on the page to install Conda. For example, on\n    Windows, you would download the installer and run it. On macOS and Linux,\n    you might use a command like:\n\n    ```bash\n    bash ~/Downloads/Miniconda3-latest-Linux-x86_64.sh\n    ```\n\n    Follow the prompts on the installer to complete the installation.\n\n1. **Install dependencies**\n\n    1.1. **Windows \u0026 Linux**\n\n    ```bash\n    conda env create -f requirements.yml\n    conda activate reservoir\n    ```\n\n    1.2. **macOS (Intel processors)**\n\n    ```bash\n    conda env create -f requirements.yml\n    conda activate reservoir\n    pip install tensorflow-macos tensorflow-metal\n    ```\n\n    1.3. **macOS (Apple Silicon Mx processors)**\n\n    ```bash\n    conda env create --platform osx-64 -f requirements.yml\n    conda activate reservoir\n    conda env config vars set CONDA_SUBDIR=osx-64\n    conda deactivate\n    conda activate reservoir\n    pip install tensorflow-macos tensorflow-metal\n    ```\n\n2. **Download data**\n\n    Trained reservoir models and most important datasets are available as a Zenodo archive: \u003chttps://doi.org/10.5281/zenodo.14961167\u003e. Extract the files and place them in the `Dataset-input`, `Reservoir`, `Result` directory.\n   \n## 3. Citation\n\nIf you use this software, please cite it as below.\n\n\u003e *Living Bacterial Reservoir Computers for Information Processing and Sensing*. Paul Ahavi; Thi-Ngoc-An Hoang; Philippe Meyer; Sylvie Berthier; Federica Fiorini; Florence Castelli; Olivier Epaulard; Audrey Le Gouellec; Jean-Loup Faulon. Preprint: \u003chttps://doi.org/10.1101/2024.09.12.612674\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Freservoir","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrsynth%2Freservoir","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Freservoir/lists"}