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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":["deep-learning","genomics","manubot","manuscript","neural-networks","review"],"created_at":"2024-08-02T15:00:44.430Z","updated_at":"2026-01-27T11:03:37.002Z","avatar_url":"https://github.com/greenelab.png","language":"HTML","funding_links":[],"categories":["HTML","Ranked by starred repositories"],"sub_categories":[],"readme":"# The Deep Review\n\n[![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://greenelab.github.io/deep-review/)\n[![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://greenelab.github.io/deep-review/manuscript.pdf)\n[![GitHub Actions Status](https://github.com/greenelab/deep-review/workflows/Manubot/badge.svg)](https://github.com/greenelab/deep-review/actions)\n[![Code Climate](https://codeclimate.com/github/greenelab/deep-review/badges/gpa.svg)](https://codeclimate.com/github/greenelab/deep-review)\n\n## Manuscript description\n\nThis repository is home to the **Deep Review**, a review article on deep learning in precision medicine.\nThe Deep Review is collaboratively written on GitHub using a tool called Manubot (see [below](#manubot)).\nThe project operates on an open contribution model, welcoming contributions from anyone (see [`CONTRIBUTING.md`](CONTRIBUTING.md) or an [existing example](https://github.com/greenelab/deep-review/pull/147 \"Pull request 147: Hardware Limitations and Scaling\") for more info).\nTo see what's incoming, check the open [pull requests](https://github.com/greenelab/deep-review/pulls).\nFor project discussion and planning see the [Issues](https://github.com/greenelab/deep-review/issues).\n\nThe original version of the Deep Review was published in 2018 and should be cited as:\n\u003e Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, and Greene CS. 2018. Opportunities and obstacles for deep learning in biology and medicine. _Journal of The Royal Society Interface_ 15(141):20170387. [doi:10.1098/rsif.2017.0387](https://doi.org/10.1098/rsif.2017.0387)\n\n\n### Current stage: planning Deep Review version 2.0\n\nAs of writing, we are aiming to publish an update of the deep review.\nWe will continue to make project preprints available on bioRxiv or another preprint service and aim to continue publishing the finished reviews in a peer-reviewed venue as well.\nLike the initial release, we are planning for an open and collaborative effort.\nNew contributors are welcome and will be listed as version 2.0 authors.\nPlease see [issue #810](https://github.com/greenelab/deep-review/issues/810) to contribute to the discussion of future plans, and help decide how to best continue this project.\n\n**Manubot updates:**\nWe recently [updated](https://github.com/greenelab/deep-review/pull/681) this repository to use the latest Manubot version.\nCitations must now be semicolon separated like `[@doi:10.1002/minf.201501008; @doi:10.1002/jcc.24764]` and citation tags are required when the identifier contains [forbidden characters](USAGE.md#citation-tags).\nPreviously, multiple citations were just separated by whitespace.\nIn addition, we're switching from wrapping text at a character cutoff to \"one sentence per line\" as described in [`USAGE.md`](USAGE.md).\nPlease make sure you base your pull requests off of the latest version of the `greenelab:master` branch.\nKeep your fork synced by [setting](https://help.github.com/articles/configuring-a-remote-for-a-fork/) its `upstream` remote to `greenelab` and running:\n\n```sh\n# If your branch only has commits from greenelab:master but is outdated\ngit pull --ff-only upstream master\n\n# If your branch is outdated and has diverged from greenelab:master\ngit pull --rebase upstream master\n```\n\n### Headline review format\n\nThe [initial manuscript](https://doi.org/10.1098/rsif.2017.0387) was a headline review for [_Journal of the Royal Society Interface_](http://rsif.royalsocietypublishing.org/) on a topic overlapping the computer and life sciences in the area of systems pharmacology.\nThe headline review solicitation states:\n\n\u003e A Headline Review is one in a short, targeted series of high-level reviews within a particular topic of a burgeoning research area.\nWe encourage authors to write in a style that opens the door to a broad range of readers working at the\nphysical sciences - life sciences interface.\nWe intend the reviews to address critical developments in an area of cross-disciplinary research and, when possible, to place such research in a broader context.\nThis is not a place for comprehensive literature surveys.\n\u003e\n\u003e We do encourage you to speculate in an informed way, and to be topical and provocative about the subject without worrying unduly about space, (the provisional target length is 8-12,000 words).\nPlease think of this as an article which will be a landmark in your area, and will come to be considered as a classic paper of the literature.\n\n### Inspiration\n\nOn August 2, 2016, project maintainer [Casey Greene](https://github.com/cgreene) introduced the project and its motivations:\n\n\u003e I was recently inspired by [Harold Pimentel's](https://github.com/pimentel) crowd-sourced [collection of deep learning papers](https://github.com/pimentel/deep_learning_papers).\nInstead of having one individual write this, I thought that this invitation provided a wonderful opportunity to take advantage of the wisdom of crowds to bring a team together around this topic.\n\u003e\n\u003e This repository provides a home for the paper.\nWe'll operate on a pull request model.\nAnyone whose contributions meet the ICJME standards of authorship will be included as an author on the manuscript.\nI can't guarantee that it will be accepted, but I look forward to trying this approach out.\n\nOn August 5, Deep Review was announced with a [tweet](https://twitter.com/GreeneScientist/status/761606546774163456).\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.\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 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\n### Local execution\n\nThe easiest way to run Manubot is to use [continuous integration](#continuous-integration) to rebuild the manuscript when the content changes.\nIf you want to build a Manubot manuscript 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 from this root directory.\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\nbash 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# This is required to view local images in the HTML output.\n\n# Configure the webpage directory\nmanubot webpage\n\n# You can now open the manuscript webpage/index.html in a web browser.\n# Alternatively, open a local webserver at http://localhost:8000/ with the\n# following commands.\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` script and `manubot webpage` command upon content changes:\n\n```sh\nbash build/autobuild.sh\n```\n\n### Continuous Integration\n\nWhenever a pull request is opened, CI (continuous integration) 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 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), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/greenelab/deep-review/tree/gh-pages) and [`output`](https://github.com/greenelab/deep-review/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://greenelab.github.io/deep-review/\n+ **PDF manuscript** at https://greenelab.github.io/deep-review/manuscript.pdf\n\nFor continuous integration configuration details, see [`.github/workflows/manubot.yaml`](.github/workflows/manubot.yaml) if using GitHub Actions or [`.travis.yml`](.travis.yml) if using Travis CI.\n\n## License\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/greenelab/deep-review.\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/greenelab/deep-review/issues) for any question related to licensing.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fdeep-review","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fdeep-review","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fdeep-review/lists"}