We recognized that deep learning in precision medicine is a rapidly developing area. Hence, diverse expertise was required to provide a forward-looking perspective. Accordingly, we collaboratively wrote this review in the open, enabling anyone with expertise to contribute. We wrote the manuscript in markdown and tracked changes using git. Contributions were handled through GitHub, with individuals submitting "pull requests" to suggest additions to the manuscript. This collaborative writing approach was later generalized into Manubot [@doi:10.1371/journal.pcbi.1007128].

Manubot supports citations of persistent identifiers, such as DOIs, PubMed Central IDs, PubMed IDs, arXiv IDs, and URLs. This reduces one major barrier to writing collaboratively, which is syncing reference managers between participants. In addition, Manubot uses continuous integration to build and deploy manuscripts. This allows for automated error checking of proposed changes to catch malformated citations and invalid syntax. Originally, the Deep Review used Travis CI for continuous integration, but in 2020 switched to GitHub Actions, which became the default for Manubot manuscripts.

For version 1.0 of the Deep Review, author order was randomized as described in [version 1.0] [@tag:techblog-perkel]. However, this was a one-time manual process. Starting with version 2.0, we began shuffling authors for every manuscript version. Manubot allowed us to automate this process, using the Git commit hash as a random seed to ensure reproducible ordering.

We continued using the open repository on the GitHub version control platform (greenelab/deep-review) [@url:https://github.com/greenelab/deep-review], which was established to write the version 1.0 manuscript. {% for v2, authors in manubot.authors|groupby('v2') %} {% if v2|length %}{{ v2 }}: {% for author in authors %}{{author.name }}{% if not loop.last %}, {% endif %}{% endfor %}. {% endif %} {% endfor %}

|Author|Competing Interests|Last Reviewed| |---|---|---|{% for author in manubot.authors %} |{{author.name}}|{{author.coi.string}}|{{author.coi.lastapproved}}|{% endfor %}

We acknowledge funding from the Gordon and Betty Moore Foundation award GBMF4552 (C.S.G. and D.S.H.); the National Institutes of Health awards R01HG010067 (C.S.G. and D.S.H.), R01CA237170 (C.S.G), T32LM012204 (A.J.T.), R01CA216265 (B.C.C.); the Burroughs Wellcome Fund Big Data in the Life Sciences training grant at Dartmouth (J.L.L,); and the Dartmouth College Neukom Institute for Computational Science CompX award (B.C.C.).

We created an open repository on the GitHub version control platform (greenelab/deep-review) [@url:https://github.com/greenelab/deep-review]. Here, we engaged with numerous authors from papers within and outside of the area. The manuscript was drafted via GitHub commits by individuals who met the ICMJE standards of authorship. These were individuals who contributed to the review of the literature; drafted the manuscript or provided substantial critical revisions; approved the final manuscript draft; and agreed to be accountable in all aspects of the work. Individuals who did not contribute in all of these ways, but who did participate, are acknowledged below. We grouped authors into the following four classes of approximately equal contributions and randomly ordered authors within each contribution class. Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion: Travers Ching, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M. Hoffman. Edited the manuscript, reviewed pull requests, and developed Manubot: Daniel S. Himmelstein. Drafted one or more sub-sections: Wei Xie, Gail L. Rosen, Benjamin J. Lengerich, Johnny Israeli, Jack Lanchantin, Stephen Woloszynek, Anne E. Carpenter, Avanti Shrikumar, Jinbo Xu, Evan M. Cofer, Christopher A. Lavender, Srinivas C. Turaga, Amr M. Alexandari, Zhiyong Lu. Drafted sub-sections, edited the manuscript, reviewed pull requests, and coordinated co-authors: Anthony Gitter, Casey S. Greene. Revised specific sub-sections or supervised drafting one or more sub-sections: David J. Harris, Dave DeCaprio, Yanjun Qi, Anshul Kundaje, Yifan Peng, Laura K. Wiley, Marwin H.S. Segler, Simina M. Boca, S. Joshua Swamidass, Austin Huang.

We acknowledge funding from the Gordon and Betty Moore Foundation awards GBMF4552 (C.S.G. and D.S.H.) and GBMF4563 (D.J.H.); the Howard Hughes Medical Institute (S.C.T.); the National Institutes of Health awards DP2GM123485 (A.K.), P30CA051008 (S.M.B.), R01AI116794 (B.K.B.), R01GM089652 (A.E.C.), R01GM089753 (J.X.), R01LM012222 (S.J.S.), R01LM012482 (S.J.S.), R21CA220398 (S.M.B.), T32GM007753 (B.T.D.), T32HG000046 (G.P.W.), and U54AI117924 (A.G.); the National Institutes of Health Intramural Research Program and National Library of Medicine (Y.P. and Z.L.); the National Science Foundation awards 1245632 (G.L.R.), 1531594 (E.M.C.), and 1564955 (J.X.); the Natural Sciences and Engineering Research Council of Canada award RGPIN-2015-3948 (M.M.H.); and the Roy and Diana Vagelos Scholars Program in the Molecular Life Sciences (M.Z.).

We gratefully acknowledge Christof Angermueller, Kumardeep Chaudhary, Gökcen Eraslan, Mikael Huss, Bharath Ramsundar and Xun Zhu for their discussion of the manuscript and reviewed papers on GitHub. We would like to thank Aaron Sheldon, who contributed text but did not formally approve the manuscript. We would like to thank Anna Greene for a careful proofreading of the manuscript in advance of the first submission. We would like to thank Sebastian Raschka for clarifying edits to the abstract and introduction. We would like to thank Robert Gieseke, Ruibang Luo, Stephen Ra, Sourav Singh, and GitHub user snikumbh for correcting typos, formatting, and references.