content/00.front-matter.md
{## This file contains a Jinja2 front-matter template that adds version and authorship information. Changing the Jinja2 templates in this file may cause incompatibility with Manubot updates. Pandoc automatically inserts title from metadata.yaml, so it is not included in this template.Headers should be surrounded by blank lines##} <!-- include the Font Awesome library, per: https://fontawesome.com/start -->Inline HTML<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.7.2/css/all.css">[Inline HTML[]{.fas .fa-info-circle .fa-lg} **Updated Content**<br>A published version of this manuscript from 04 April 2018, termed version 1.0, is available at <https://doi.org/10.1098/rsif.2017.0387>.New content added after that publication date is being collected in a version 2.0.[GitHub issue #959](https://github.com/greenelab/deep-review/issues/959) lists the new version 2.0 authors and sections.]{.banner .lightred} {## Template to insert build date and source ##}Inline HTML<small><em>This manuscript{% if manubot.ci_source is defined and manubot.ci_source.provider == "appveyor" -%}([permalink]({{manubot.ci_source.artifact_url}})){% elif manubot.html_url_versioned is defined -%}([permalink]({{manubot.html_url_versioned}})){% endif -%}was automatically generated{% if manubot.ci_source is defined -%}from [{{manubot.ci_source.repo_slug}}@{{manubot.ci_source.commit | truncate(length=7, end='', leeway=0)}}](https://github.com/{{manubot.ci_source.repo_slug}}/tree/{{manubot.ci_source.commit}}){% endif -%}on {{manubot.date}}.</em></small> First header should be a top level header## Authors ### Version 2.0 authors {% for author in manubot.authors %} {% if author.v2 -%} {% if author.orcid is defined -%} [{height="11px" width="11px"}](https://orcid.org/{{author.orcid}}) {%- endif %}Inline HTML {{author.name}}<sup>{% for number in author.affiliation_numbers %}2.{{number}}{%- if not loop.last -%},{%- endif -%}{% endfor %}⚄{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}</sup> {%- if not loop.last -%}, {%- endif -%} {%- endif -%}{% endfor %},[The Version 1.0 Deep Review Authors](#version-1.0-authors) Inline HTML<sup>⚄</sup> --- Author order for version 2.0 is currently randomized [with each new build](https://github.com/greenelab/deep-review/pull/997).<br>Inline HTML<sup>†</sup> --- To whom correspondence should be addressed: gitter@biostat.wisc.edu (A.G.) and greenescientist@gmail.com (C.S.G.) Inline HTML<small> {% for affiliation in manubot.affiliations %}Inline HTML2.{{affiliation.affiliation_number}}. {{affiliation.affiliation}}<br>{%- endfor %} </small> ### Version 1.0 authors [{height="11px" width="11px"}](https://orcid.org/0000-0002-5577-3516)Inline HTML Travers Ching<sup>1.1,☯</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-3012-7446)Inline HTML Daniel S. Himmelstein<sup>1.2</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-6700-1468)Inline HTML Brett K. Beaulieu-Jones<sup>1.3</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-4563-3226)Inline HTML Alexandr A. Kalinin<sup>1.4</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-4992-2623)Inline HTML Brian T. Do<sup>1.5</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-0503-9348)Inline HTML Gregory P. Way<sup>1.2</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-8362-100X)Inline HTML Enrico Ferrero<sup>1.8</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-1126-1479)Inline HTML Paul-Michael Agapow<sup>1.9</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-0539-630X)Inline HTML Michael Zietz<sup>1.2</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-4517-1562)Inline HTML Michael M. Hoffman<sup>1.10,1.11,1.12</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-1871-6846)Inline HTML Wei Xie<sup>1.13</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-1763-5750)Inline HTML Gail L. Rosen<sup>1.14</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0001-8690-9554)Inline HTML Benjamin J. Lengerich<sup>1.15</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-1633-5780)Inline HTML Johnny Israeli<sup>1.16</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-0811-0944)Inline HTML Jack Lanchantin<sup>1.17</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-0568-298X)Inline HTML Stephen Woloszynek<sup>1.14</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-1555-8261)Inline HTML Anne E. Carpenter<sup>1.18</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-6443-4671)Inline HTML Avanti Shrikumar<sup>1.19</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0001-7111-4839)Inline HTML Jinbo Xu<sup>1.20</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-3877-0433)Inline HTML Evan M. Cofer<sup>1.21,1.22</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-7762-1089)Inline HTML Christopher A. Lavender<sup>1.23</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-3247-6487)Inline HTML Srinivas C. Turaga<sup>1.24</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0001-8655-8109)Inline HTML Amr M. Alexandari<sup>1.19</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0001-9998-916X)Inline HTML Zhiyong Lu<sup>1.25</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-3332-9307)Inline HTML David J. Harris<sup>1.26</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0001-8931-9461)Inline HTML Dave DeCaprio<sup>1.27</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-5796-7453)Inline HTML Yanjun Qi<sup>1.17</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-3084-2287)Inline HTML Anshul Kundaje<sup>1.19,1.28</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0001-9309-8331)Inline HTML Yifan Peng<sup>1.25</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0001-6681-9754)Inline HTML Laura K. Wiley<sup>1.29</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0001-8008-0546)Inline HTML Marwin H.S. Segler<sup>1.30</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-1400-3398)Inline HTML Simina M. Boca<sup>1.31</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-2191-0778)Inline HTML S. Joshua Swamidass<sup>1.32</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0003-1349-4030)Inline HTML Austin Huang<sup>1.33</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0002-5324-9833)Inline HTML Anthony Gitter<sup>1.34,1.35,†</sup>, [{height="11px" width="11px"}](https://orcid.org/0000-0001-8713-9213)Inline HTML Casey S. Greene<sup>1.2,†</sup> Inline HTML<sup>☯</sup> --- Author order was determined with a randomized algorithm<br>Inline HTML<sup>†</sup> --- To whom correspondence should be addressed: gitter@biostat.wisc.edu (A.G.) and greenescientist@gmail.com (C.S.G.) Inline HTML<small> Trailing spaces1.1. Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI Trailing spaces1.2. Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA Trailing spaces1.3. Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA Trailing spaces1.4. Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI Trailing spaces1.5. Harvard Medical School, Boston, MA Trailing spaces1.6. Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH Trailing spaces1.7. Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH Trailing spaces1.8. Computational Biology and Stats, Target Sciences, GlaxoSmithKline, Stevenage, United Kingdom Trailing spaces1.9. Data Science Institute, Imperial College London, London, United Kingdom Trailing spaces1.10. Princess Margaret Cancer Centre, Toronto, ON, Canada Trailing spaces1.11. Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada Trailing spaces1.12. Department of Computer Science, University of Toronto, Toronto, ON, Canada Trailing spaces1.13. Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN Trailing spaces1.14. Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA Trailing spaces1.15. Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA Trailing spaces1.16. Biophysics Program, Stanford University, Stanford, CA Trailing spaces1.17. Department of Computer Science, University of Virginia, Charlottesville, VA Trailing spaces1.18. Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA Trailing spaces1.19. Department of Computer Science, Stanford University, Stanford, CA Trailing spaces1.20. Toyota Technological Institute at Chicago, Chicago, IL Trailing spaces1.21. Department of Computer Science, Trinity University, San Antonio, TX Trailing spaces1.22. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ Trailing spaces1.23. Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC Trailing spaces1.24. Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA Trailing spaces1.25. National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD Trailing spaces1.26. Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL Trailing spaces1.27. ClosedLoop.ai, Austin, TX Trailing spaces1.28. Department of Genetics, Stanford University, Stanford, CA Trailing spaces1.29. Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO Trailing spaces1.30. Institute of Organic Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany Trailing spaces1.31. Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC Trailing spaces1.32. Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO Trailing spaces1.33. Department of Medicine, Brown University, Providence, RI Trailing spaces1.34. Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI Trailing spaces1.35. Morgridge Institute for Research, Madison, WI </small>