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Hardcode v1 authors and remove them from metadata #998

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b7221d1
make v1.0 content fixed; randomize v2.0
cgreene Mar 10, 2020
6181775
remove v1 authors
cgreene Mar 10, 2020
77a8da6
merge w/ v2 authors
cgreene Mar 10, 2020
8cd7707
Merge branch 'master' into use-random-order
cgreene Mar 10, 2020
38c2e9d
add two lines for breaks
cgreene Mar 10, 2020
031daee
fix subtle spacing issue
cgreene Mar 10, 2020
ca18e93
Update content/00.front-matter.md
cgreene Mar 10, 2020
cb20daa
Remove spaces following affiliations
dhimmel Mar 10, 2020
6cb5767
Try alternative solution
dhimmel Mar 10, 2020
c4daec3
Update content/00.front-matter.md
dhimmel Mar 10, 2020
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135 changes: 119 additions & 16 deletions content/00.front-matter.md
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Expand Up @@ -37,33 +37,136 @@ on {{manubot.date}}.
{% if author.orcid is defined -%}
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/{{author.orcid}})
{%- endif %}
{{author.name}}<sup>{{author.affiliation_numbers | join(',')}}♠{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}</sup>
{{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 %}
{% endfor %},
[The Version 1.0 Deep Review Authors](#version-1.0-authors)

<sup>♠</sup> --- Author order for version 2.0 is currently arbitrary.<br>
<sup>♠</sup> --- Author order for version 2.0 is currently randomized [with each new build](https://github.com/greenelab/deep-review/pull/997).<br>
<sup>†</sup> --- To whom correspondence should be addressed: greenescientist@gmail.com (C.S.G.)

<small>

{% for affiliation in manubot.affiliations %}
2.{{affiliation.affiliation_number}}. {{affiliation.affiliation}}<br>
{%- endfor %}
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</small>

### Version 1.0 Authors

{% for author in manubot.authors %}
{% if author.v1 -%}
{% if author.orcid is defined -%}
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/{{author.orcid}})
{%- endif %}
{{author.name}}<sup>{{author.affiliation_numbers | join(',')}}{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}</sup>
{%- if not loop.last -%}, {%- endif -%}
{%- endif -%}
{% endfor %}
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-5577-3516)
Travers Ching<sup>1.1,☯</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-3012-7446)
Daniel S. Himmelstein<sup>1.2</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-6700-1468)
Brett K. Beaulieu-Jones<sup>1.3</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-4563-3226)
Alexandr A. Kalinin<sup>1.4</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-4992-2623)
Brian T. Do<sup>1.5</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-0503-9348)
Gregory P. Way<sup>1.2</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-8362-100X)
Enrico Ferrero<sup>1.8</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-1126-1479)
Paul-Michael Agapow<sup>1.9</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-0539-630X)
Michael Zietz<sup>1.2</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-4517-1562)
Michael M. Hoffman<sup>1.10,1.11,1.12</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-1871-6846)
Wei Xie<sup>1.13</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-1763-5750)
Gail L. Rosen<sup>1.14</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0001-8690-9554)
Benjamin J. Lengerich<sup>1.15</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-1633-5780)
Johnny Israeli<sup>1.16</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-0811-0944)
Jack Lanchantin<sup>1.17</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-0568-298X)
Stephen Woloszynek<sup>1.14</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-1555-8261)
Anne E. Carpenter<sup>1.18</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-6443-4671)
Avanti Shrikumar<sup>1.19</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0001-7111-4839)
Jinbo Xu<sup>1.20</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-3877-0433)
Evan M. Cofer<sup>1.21,1.22</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-7762-1089)
Christopher A. Lavender<sup>1.23</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-3247-6487)
Srinivas C. Turaga<sup>1.24</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0001-8655-8109)
Amr M. Alexandari<sup>1.19</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0001-9998-916X)
Zhiyong Lu<sup>1.25</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-3332-9307)
David J. Harris<sup>1.26</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0001-8931-9461)
Dave DeCaprio<sup>1.27</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-5796-7453)
Yanjun Qi<sup>1.17</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-3084-2287)
Anshul Kundaje<sup>1.19,1.28</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0001-9309-8331)
Yifan Peng<sup>1.25</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0001-6681-9754)
Laura K. Wiley<sup>1.29</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0001-8008-0546)
Marwin H.S. Segler<sup>1.30</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-1400-3398)
Simina M. Boca<sup>1.31</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-2191-0778)
S. Joshua Swamidass<sup>1.32</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0003-1349-4030)
Austin Huang<sup>1.33</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0002-5324-9833)
Anthony Gitter<sup>1.34,1.35,†</sup>,
[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/0000-0001-8713-9213)
Casey S. Greene<sup>1.2,†</sup>

<sup>☯</sup> --- Author order was determined with a randomized algorithm<br>
<sup>†</sup> --- To whom correspondence should be addressed: gitter@biostat.wisc.edu (A.G.) and greenescientist@gmail.com (C.S.G.)

<small>

{% for affiliation in manubot.affiliations %}
{{affiliation.affiliation_number}}. {{affiliation.affiliation}}
{%- endfor %}

</small>
1.1. Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI
1.2. Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
1.3. Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
1.4. Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI
1.5. Harvard Medical School, Boston, MA
1.6. Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH
1.7. Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH
1.8. Computational Biology and Stats, Target Sciences, GlaxoSmithKline, Stevenage, United Kingdom
1.9. Data Science Institute, Imperial College London, London, United Kingdom
1.10. Princess Margaret Cancer Centre, Toronto, ON, Canada
1.11. Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
1.12. Department of Computer Science, University of Toronto, Toronto, ON, Canada
1.13. Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN
1.14. Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA
1.15. Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
1.16. Biophysics Program, Stanford University, Stanford, CA
1.17. Department of Computer Science, University of Virginia, Charlottesville, VA
1.18. Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA
1.19. Department of Computer Science, Stanford University, Stanford, CA
1.20. Toyota Technological Institute at Chicago, Chicago, IL
1.21. Department of Computer Science, Trinity University, San Antonio, TX
1.22. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
1.23. Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
1.24. Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA
1.25. National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD
1.26. Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
1.27. ClosedLoop.ai, Austin, TX
1.28. Department of Genetics, Stanford University, Stanford, CA
1.29. Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO
1.30. Institute of Organic Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
1.31. Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
1.32. Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO
1.33. Department of Medicine, Brown University, Providence, RI
1.34. Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
1.35. Morgridge Institute for Research, Madison, WI
91 changes: 67 additions & 24 deletions content/08.methods.md
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Expand Up @@ -31,12 +31,20 @@ The ability to irrefutably prove manuscript existence at a past time could be im

#### Version 2.0

We continued using the open repository on the GitHub version control platform ([`greenelab/deep-review`](https://github.com/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 %}
We continued using the open repository on the GitHub version control platform ([`greenelab/deep-review`](https://github.com/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 %}

##### Version 2.0 Competing Interests

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

##### Version 2.0 Funding Statement

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.).

#### Version 1.0

Expand All @@ -48,27 +56,54 @@ 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.
{% for v1, authors in manubot.authors|groupby('v1') %}
{% if v1|length %}
{{ v1 }}:{% for author in authors %} {{author.name }}{%- if not loop.last -%}, {%- endif -%}{% endfor %}.
{% endif %}
{% endfor %}
Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion: Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M. Hoffman.
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.

### Competing interests
##### Version 1.0 Competing interests

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

### Acknowledgements

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.

### Funding statement
|Author|Competing Interests|Last Reviewed|
|---|---|---|
|Travers Ching|None|2017-05-26|
|Daniel S. Himmelstein|None|2017-05-26|
|Brett K. Beaulieu-Jones|None|2017-05-26|
|Alexandr A. Kalinin|None|2017-05-26|
|Brian T. Do|None|2017-05-26|
|Gregory P. Way|None|2017-05-26|
|Enrico Ferrero|Full-time employee of GlaxoSmithKline.|2017-05-26|
|Paul-Michael Agapow|None|2017-05-26|
|Michael Zietz|None|2017-05-26|
|Michael M. Hoffman|None|2017-05-26|
|Wei Xie|None|2017-05-26|
|Gail L. Rosen|None|2017-05-26|
|Benjamin J. Lengerich|None|2017-05-26|
|Johnny Israeli|None|2017-05-26|
|Jack Lanchantin|None|2017-05-26|
|Stephen Woloszynek|None|2017-05-26|
|Anne E. Carpenter|None|2017-05-26|
|Avanti Shrikumar|None|2017-05-26|
|Jinbo Xu|None|2017-05-26|
|Evan M. Cofer|None|2017-05-26|
|Christopher A. Lavender|None|2017-05-26|
|Srinivas C. Turaga|None|2017-05-26|
|Amr M. Alexandari|None|2017-05-26|
|Zhiyong Lu|None|2017-05-26|
|David J. Harris|None|2017-05-26|
|Dave DeCaprio|None|2017-05-26|
|Yanjun Qi|None|2017-05-26|
|Anshul Kundaje|Advisory Board of Deep Genomics Inc.|2017-05-26|
|Yifan Peng|None|2017-05-26|
|Laura K. Wiley|None|2017-05-26|
|Marwin H.S. Segler|None|2017-05-26|
|Simina M. Boca|None|2017-05-26|
|S. Joshua Swamidass|None|2017-05-26|
|Austin Huang|None|2017-05-26|
|Anthony Gitter|None|2017-05-26|
|Casey S. Greene|None|2017-05-26|

##### Version 1.0 Funding Statement

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.);
Expand All @@ -77,3 +112,11 @@ the National Institutes of Health Intramural Research Program and National Libra
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.).

### Acknowledgements

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.
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