{"id":20081096,"url":"https://github.com/trangdata/tpot-fss-ms","last_synced_at":"2026-02-07T13:02:40.326Z","repository":{"id":78462888,"uuid":"154879608","full_name":"trangdata/tpot-fss-ms","owner":"trangdata","description":"Manuscript for tpot-fss","archived":false,"fork":false,"pushed_at":"2019-09-13T14:11:40.000Z","size":16864,"stargazers_count":2,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-07-27T12:26:53.980Z","etag":null,"topics":["automl","machine-learning","manubot","manuscript","tpot"],"latest_commit_sha":null,"homepage":"https://trangdata.github.io/tpot-fss-ms/","language":"HTML","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/trangdata.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE-CC0.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null}},"created_at":"2018-10-26T18:41:34.000Z","updated_at":"2022-05-05T20:28:44.000Z","dependencies_parsed_at":null,"dependency_job_id":"c6b174bc-e300-40ec-a415-8ae17c8f13d3","html_url":"https://github.com/trangdata/tpot-fss-ms","commit_stats":{"total_commits":349,"total_committers":16,"mean_commits":21.8125,"dds":0.5587392550143266,"last_synced_commit":"d0de3ece81d493d84e9e26e58f4cd1f62cca6e58"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/trangdata/tpot-fss-ms","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Ftpot-fss-ms","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Ftpot-fss-ms/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Ftpot-fss-ms/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Ftpot-fss-ms/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/trangdata","download_url":"https://codeload.github.com/trangdata/tpot-fss-ms/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Ftpot-fss-ms/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29194423,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-07T12:38:28.597Z","status":"ssl_error","status_checked_at":"2026-02-07T12:38:23.888Z","response_time":63,"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":["automl","machine-learning","manubot","manuscript","tpot"],"created_at":"2024-11-13T15:33:24.331Z","updated_at":"2026-02-07T13:02:40.308Z","avatar_url":"https://github.com/trangdata.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Scaling tree-based automated machine learning to biomedical big data with a dataset selector\n\n\u003c!-- usage note: edit the H1 title above to personalize the manuscript --\u003e\n\n[![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://trang1618.github.io/tpot-fss-ms/)\n[![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://trang1618.github.io/tpot-fss-ms/manuscript.pdf)\n[![Build Status](https://travis-ci.org/trang1618/tpot-fss-ms.svg?branch=master)](https://travis-ci.org/trang1618/tpot-fss-ms)\n\n## Manuscript description\n\n\u003c!-- usage note: edit this section. --\u003e\n\nThis repository is the manuscript for a current development of TPOT with two new features: Dataset Selector and Template. Analysis code is available in the repository https://github.com/trang1618/tpot-fss. The manuscript is collaboratively written on GitHub using [Manubot](https://github.com/greenelab/manubot-rootstock).\n\n## Manubot\n\n\u003c!-- usage note: do not edit this section --\u003e\n\nManubot is a system for writing scholarly manuscripts via GitHub.\nManubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub.\nAn [overview manuscript](https://greenelab.github.io/meta-review/ \"Open collaborative writing with Manubot\") presents the benefits of collaborative writing with Manubot and its unique features.\nThe [rootstock repository](https://git.io/fhQH1) is a general purpose template for creating new Manubot instances, as detailed in [`SETUP.md`](SETUP.md).\nSee [`USAGE.md`](USAGE.md) for documentation how to write a manuscript.\n\nPlease open [an issue](https://git.io/fhQHM) for questions related to Manubot usage, bug reports, or general inquiries.\n\n### Repository directories \u0026 files\n\nThe directories are as follows:\n\n+ [`content`](content) contains the manuscript source, which includes markdown files as well as inputs for citations and references.\n  See [`USAGE.md`](USAGE.md) for more information.\n+ [`output`](output) contains the outputs (generated files) from the manubot including the resulting manuscripts.\n  You should not edit these files manually, because they will get overwritten.\n+ [`webpage`](webpage) is a directory meant to be rendered as a static webpage for viewing the HTML manuscript.\n+ [`build`](build) contains commands and tools for building the manuscript.\n+ [`ci`](ci) contains files necessary for deployment via continuous integration.\n  For the CI configuration, see [`.travis.yml`](.travis.yml).\n\n### Local execution\n\nTo run the Manubot locally, install the [conda](https://conda.io) environment as described in [`build`](build).\nThen, you can build the manuscript on POSIX systems by running the following commands.\n\n```sh\n# Activate the manubot conda environment (assumes conda version \u003e= 4.4)\nconda activate manubot\n\n# Build the manuscript, saving outputs to the output directory\nsh build/build.sh\n\n# At this point, the HTML \u0026 PDF outputs will have been created. The remaining\n# commands are for serving the webpage to view the HTML manuscript locally.\n\n# Configure the webpage directory\npython build/webpage.py\n\n# View the manuscript locally at http://localhost:8000/\ncd webpage\npython -m http.server\n```\n\nSometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is detected.\nThe following command, while running, will trigger both the `build.sh` and `webpage.py` scripts upon content changes:\n\n```sh\nsh build/autobuild.sh\n```\n\n### Continuous Integration\n\n[![Build Status](https://travis-ci.org/trang1618/tpot-fss-ms.svg?branch=master)](https://travis-ci.org/trang1618/tpot-fss-ms)\n\nWhenever a pull request is opened, Travis CI will test whether the changes break the build process to generate a formatted manuscript.\nThe build process aims to detect common errors, such as invalid citations.\nIf your pull request build fails, see the Travis CI logs for the cause of failure and revise your pull request accordingly.\n\nWhen a commit to the `master` branch occurs (for example, when a pull request is merged), Travis CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/trang1618/tpot-fss-ms/tree/gh-pages) and [`output`](https://github.com/trang1618/tpot-fss-ms/tree/output) branches.\nThe `gh-pages` branch uses [GitHub Pages](https://pages.github.com/) to host the following URLs:\n\n+ **HTML manuscript** at https://trang1618.github.io/tpot-fss-ms/\n+ **PDF manuscript** at https://trang1618.github.io/tpot-fss-ms/manuscript.pdf\n\nFor continuous integration configuration details, see [`.travis.yml`](.travis.yml).\n\n## License\n\n\u003c!--\nusage note: edit this section to change the license of your manuscript or source code changes to this repository.\nWe encourage users to openly license their manuscripts, which is the default as specified below.\n--\u003e\n\n[![License: CC BY 4.0](https://img.shields.io/badge/License%20All-CC%20BY%204.0-lightgrey.svg)](http://creativecommons.org/licenses/by/4.0/)\n[![License: CC0 1.0](https://img.shields.io/badge/License%20Parts-CC0%201.0-lightgrey.svg)](https://creativecommons.org/publicdomain/zero/1.0/)\n\nExcept when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License ([`LICENSE.md`](LICENSE.md)), which allows reuse with attribution.\nPlease attribute by linking to https://github.com/trang1618/tpot-fss-ms.\n\nSince CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication ([`LICENSE-CC0.md`](LICENSE-CC0.md)).\nAll files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:\n\n+ `*.sh`\n+ `*.py`\n+ `*.yml` / `*.yaml`\n+ `*.json`\n+ `*.bib`\n+ `*.tsv`\n+ `.gitignore`\n\nAll other files are only available under CC BY 4.0, including:\n\n+ `*.md`\n+ `*.html`\n+ `*.pdf`\n+ `*.docx`\n\nPlease open [an issue](https://github.com/trang1618/tpot-fss-ms/issues) for any question related to licensing.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftrangdata%2Ftpot-fss-ms","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftrangdata%2Ftpot-fss-ms","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftrangdata%2Ftpot-fss-ms/lists"}