{"id":13559195,"url":"https://github.com/genular/pandora","last_synced_at":"2025-04-03T14:31:40.869Z","repository":{"id":39557283,"uuid":"139613266","full_name":"genular/pandora","owner":"genular","description":"PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:","archived":false,"fork":false,"pushed_at":"2024-04-22T14:29:21.000Z","size":16817,"stargazers_count":134,"open_issues_count":10,"forks_count":21,"subscribers_count":11,"default_branch":"master","last_synced_at":"2024-09-01T14:02:49.884Z","etag":null,"topics":["bioinformatics","biomarkers","clinical-data","clustering","data-integration","data-mining","data-science","data-visualization","drug-discovery","genomic-data-analysis","machine-learning","microbiome","pandora","predictive-analytics","systems-biology","transcriptomics","tsne","umap","unsupervised-machine-learning"],"latest_commit_sha":null,"homepage":"https://atomic-lab.org","language":"Vue","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/genular.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-07-03T16:58:25.000Z","updated_at":"2024-07-04T14:21:53.000Z","dependencies_parsed_at":"2023-02-13T03:31:48.720Z","dependency_job_id":"0c7fb4f5-4733-4c0f-b35f-f1ad0b3d4fea","html_url":"https://github.com/genular/pandora","commit_stats":null,"previous_names":["genular/simon-frontend"],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/genular%2Fpandora","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/genular%2Fpandora/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/genular%2Fpandora/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/genular%2Fpandora/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/genular","download_url":"https://codeload.github.com/genular/pandora/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":222978349,"owners_count":17067508,"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","biomarkers","clinical-data","clustering","data-integration","data-mining","data-science","data-visualization","drug-discovery","genomic-data-analysis","machine-learning","microbiome","pandora","predictive-analytics","systems-biology","transcriptomics","tsne","umap","unsupervised-machine-learning"],"created_at":"2024-08-01T12:05:25.340Z","updated_at":"2025-04-03T14:31:40.859Z","avatar_url":"https://github.com/genular.png","language":"Vue","readme":"\u003cdiv align=\"center\"\u003e\n    \u003c!-- \n    \u003cp align=\"center\"\u003e\n        \u003ca href=\"https://genular.org\" target=\"_blank\"\u003e\n            \u003cimg width=\"200\" src=\"https://github.com/genular/pandora/raw/master/.github/static/favicon.png\"\u003e\u003c/a\u003e\n    \u003c/p\u003e\n    --\u003e\n    \u003ch1\u003ePANDORA\u003c/h1\u003e\n    \u003cp align=\"center\"\u003e\n        \u003ca href=\"https://crowdin.com/project/genular\" alt=\"Help us translate\"\u003e\n            \u003cimg src=\"https://d322cqt584bo4o.cloudfront.net/genular/localized.svg\" /\u003e\u003c/a\u003e\n        \u003ca href=\"#reposize\"\u003e\n            \u003cimg src=\"https://img.shields.io/github/repo-size/genular/pandora.svg\" /\u003e\u003c/a\u003e\n        \u003ca href=\"http://webchat.freenode.net/?randomnick=1\u0026channels=genular\u0026uio=d4\" alt=\"chat on freenode\"\u003e\n            \u003cimg src=\"https://img.shields.io/badge/chat-on%20freenode-brightgreen.svg\" alt=\"chat on freenode\"\u003e\u003c/a\u003e\n    \u003c/p\u003e\n\u003c/div\u003e\n\n`PANDORA` is a research platform developed and maintained by [aTomic Lab](https://atomic-lab.org/). It leverages advanced statistical methodologies, many uniquely designed for high-dimensional data in biomedical research. `PANDORA` supports predictive modeling, biomarker discovery, and comprehensive OMICS data analysis, contributing to new insights in systems biology.\n\n## Installation\n\n`PANDORA` can be installed using Docker, a pre-built version of the platform can be pulled from [DockerHub](https://hub.docker.com/). In order to run `PANDORA`, users will first need to install [Docker](https://www.docker.com/).\n\n#### Requirements\n\n##### Software:\n\n-   Windows, Linux or MacOS\n-   [Docker](https://docs.docker.com/engine/installation/) (`version 17.05` or later is required)\n\n##### Minimum suggested hardware:\n\n-   64GB RAM\n-   8 CPU Cores / 16 threads with 3 GHz base frequency\n\n#### Installing PANDORA\n\n-   Please **open** your favorite **Terminal** and **run** the **command below**. On Windows - open `Windows Power Shell` =\u003e _Click Start, type PowerShell, and then click Windows PowerShel_\n\n```bash\ndocker run --rm --detach --name genular --tty --interactive --env IS_DOCKER='true' --env TZ=Europe/London --oom-kill-disable --volume genular_frontend_latest:/var/www/genular/pandora --volume genular_backend_latest:/var/www/genular/pandora-backend --volume genular_data_latest:/mnt/usrdata --publish 3010:3010 --publish 3011:3011 --publish 3012:3012 --publish 3013:3013 genular/pandora:latest\n```\n\n`PANDORA` will be downloaded and started, and it can be accessed via a web browser at [http://localhost:3010](http://localhost:3010)\n\n-   If you get asked, please _allow connections_ through your _Windows Firewall_.\n\n#### Reinstalling PANDORA\n\nTo ensure a clean re-installation of PANDORA, follow these steps to remove the existing Docker container, images, and volumes associated with PANDORA. This process will remove all data and settings related to the previous PANDORA installation.\n\nIdentify the names or IDs of your PANDORA container(s), volume(s), and image(s). \nUse these commands to list entities:\n\n-   Containers: `docker ps` (for running) or `docker ps -a` (for all)\n-   Images: `docker images`\n-   Volumes: `docker volume ls`\n\n(Or use Docker GUI)\n\n```bash\n##############################################\n#### 1) Stop and Remove Docker Containers ####\n##############################################\n# List all Docker container\ndocker ps\n# Stop the Docker container\ndocker stop \u003cCONTAINER_ID \u003e\n\n# Remove the Docker container if needed\n# docker rm \u003cCONTAINER_ID\u003e\n\n#################################\n#### 2) Remove Docker Images ####\n#################################\n# List all Docker images\ndocker images\n# Remove the Docker image\ndocker rmi \u003cIMAGE_ID\u003e\n\n##################################\n#### 3) Remove Docker Volumes ####\n##################################\n# List all Docker volumes\ndocker volume ls\n# Remove all 3 specific Docker volumes\ndocker volume rm genular_frontend_latest genular_backend_latest genular_data_latest\n\n## Now you can proceed with clean installation\n```\n\n### Contributing, writing code\n\nContributions are very much welcome!\n\n1. Check out our [public issues board][0]. If your issue isn't on the board, [open a new one][1].\n2. Pick an issue that nobody has claimed and start working on it.\n3. Fork the project ([Need help forking a project?][3]). You'll do all of your work on your forked copy.\n4. Create a branch specific to the issue or feature you are working on. Push your work on that branch ([Need help with branching?][4]).\n5. Name the branch something like `fixes-xxx-issue` or `add-xxx-feature` where `xxx` is a short description of the changes or feature you are adding.\n6. Once your code is ready, submit a pull request from your branch to `PANDORA` `master` branch. We'll do a quick review and give you feedback.\n\n[0]: https://github.com/genular/pandora/issues\n[1]: https://github.com/genular/pandora/issues/new/choose\n[3]: https://help.github.com/articles/fork-a-repo/\n[4]: https://github.com/Kunena/Kunena-Forum/wiki/Create-a-new-branch-with-git-and-manage-branches\n\n### Reaching Out\n\nIf you'd like to start a conversation feel free to [e-mail us](mailto:atomic.research.lab@gmail.com).\nI would also like to hear from you if you find this project useful and helpful!\n\n-   Find us [on Twitter](https://x.com/tomicadriana) under @tomicadriana\n\n## License\n\nFor more information please check `LICENCE` file.\n\n## Citation\n\n`PANDORA` can be used for research purposes, you should cite\nthe aforementioned papers in any resulting publication.\n\n```bash\n    Adriana Tomic, Ivan Tomic, Yael Rosenberg-Hasson, Cornelia L. Dekker, Holden T. Maecker, Mark M. Davis.\n    SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses\n    http://www.jimmunol.org/content/early/2019/06/13/jimmunol.1900033.abstract\n    doi: 10.4049/jimmunol.1900033\n```\n\n```bash\n    Adriana Tomic, Ivan Tomic, Levi Waldron, Ludwig Geistlinger, Max Kuhn, Rachel L. Spreng, Lindsay C. Dahora, Kelly E. Seaton, Georgia Tomaras, Jennifer Hill, Niharika A. Duggal, Ross D. Pollock, Norman R. Lazarus, Stephen D.R. Harridge, Janet M. Lord, Purvesh Khatri, Andrew J. Pollard, Mark M. Davis.\n    SIMON: Open-Source Knowledge Discovery Platform\n    https://www.cell.com/patterns/fulltext/S2666-3899(20)30242-7\n    doi:10.1016/j.patter.2020.100178\n```\n","funding_links":[],"categories":["Vue","data-visualization"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenular%2Fpandora","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenular%2Fpandora","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenular%2Fpandora/lists"}