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Add new authors (#795). Closes #561.
* Order new authors

* Merge author metadata

* Add new authors to contribution statement

* Add new authors to funding statement

* Use middle initial

* Add city and state to affiliation
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agitter committed Jan 16, 2018
1 parent fef6e3a commit 88d4a7f
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24 changes: 19 additions & 5 deletions authors/author-order.ipynb
Expand Up @@ -54,10 +54,12 @@
"After initial ordering\n",
"@traversc, @dhimmel, @brettbj, @alxndrkalinin, @bdo311, @gwaygenomics, @enricoferrero, @agapow, @XieConnect, @gailrosen, @blengerich, @jisraeli, @jacklanchantin, @sw1, @AnneCarpenter, @AvantiShri, @j3xugit, @evancofer, @davharris, @DaveDeCaprio, @qiyanjun, @akundaje, @yfpeng, @laurakwiley, @mrwns, @agitter, @cgreene\n",
"\n",
"After adding authors (not yet applicable)\n",
"@traversc, @dhimmel, @brettbj, @alxndrkalinin, @bdo311, @gwaygenomics, @enricoferrero, @agapow, @XieConnect, @gailrosen, @blengerich, @jisraeli, @jacklanchantin, @sw1, @AnneCarpenter, @AvantiShri, @j3xugit, @evancofer, @davharris, @DaveDeCaprio, @qiyanjun, @akundaje, @yfpeng, @laurakwiley, @mrwns, @agitter, @cgreene\n",
"After adding authors\n",
"@traversc, @dhimmel, @brettbj, @alxndrkalinin, @bdo311, @gwaygenomics, @enricoferrero, @agapow, @zietzm, @michaelmhoffman, @XieConnect, @gailrosen, @blengerich, @jisraeli, @jacklanchantin, @sw1, @AnneCarpenter, @AvantiShri, @j3xugit, @evancofer, @lavenderca, @SriniTuraga, @alexandari, @luzh2, @davharris, @DaveDeCaprio, @qiyanjun, @akundaje, @yfpeng, @laurakwiley, @mrwns, @SiminaB, @swamidass, @austinvhuang, @agitter, @cgreene\n",
"\n",
"27 total authors\n"
"27 original authors\n",
"9 new authors\n",
"36 total authors\n"
]
}
],
Expand All @@ -83,6 +85,8 @@
"# corresponding authors\n",
"contrib_map['04_corresponding'] = ['@agitter', '@cgreene']\n",
"\n",
"original_count = reduce((lambda x,y: x+y), map(len, contrib_map.values()))\n",
"\n",
"print('Before ordering')\n",
"print_authors(contrib_map)\n",
"\n",
Expand All @@ -97,17 +101,27 @@
"\n",
"# new authors after revisions\n",
"new_contrib_map = defaultdict(list)\n",
"# lead contribution\n",
"new_contrib_map['01_lead'] = ['@michaelmhoffman', '@zietzm']\n",
"# default contribution\n",
"new_contrib_map['02_default'] = ['@alexandari', '@lavenderca', '@luzh2', '@SriniTuraga']\n",
"# other contribution\n",
"new_contrib_map['03_other'] = ['@austinvhuang', '@SiminaB', '@swamidass']\n",
"\n",
"new_count = reduce((lambda x,y: x+y), map(len, new_contrib_map.values()))\n",
"\n",
"# add new authors to the end of the existing category in a random order\n",
"for contrib_type in contrib_types:\n",
" random.shuffle(new_contrib_map[contrib_type])\n",
" contrib_map[contrib_type].extend(new_contrib_map[contrib_type])\n",
"\n",
"print('After adding authors (not yet applicable)')\n",
"print('After adding authors')\n",
"print_authors(contrib_map)\n",
"\n",
"# total number of authors\n",
"print('{} total authors'.format(reduce((lambda x,y: x+y), map(len, contrib_map.values()))))"
"print('{} original authors'.format(original_count))\n",
"print('{} new authors'.format(new_count))\n",
"print('{} total authors'.format(original_count + new_count))"
]
}
],
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2 changes: 1 addition & 1 deletion content/00.front-matter.md
Expand Up @@ -26,7 +26,7 @@ on {{date}}.
{% endfor %}

<sup>☯</sup> --- Author order was determined with a randomized algorithm<br>
<sup>†</sup> --- To whom correspondence should be addressed: gitter@biostat.wisc.edu (AG) and greenescientist@gmail.com (CSG)
<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 affiliations %}
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13 changes: 8 additions & 5 deletions content/08.methods.md
Expand Up @@ -37,9 +37,9 @@ 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: A.A.K., B.K.B., B.T.D., D.S.H., E.F., G.P.W., P.A., T.C.
Drafted one or more sub-sections: A.E.C., A.S., B.J.L., E.M.C., G.L.R., J.I., J.L., J.X., S.W., W.X.
Revised specific sub-sections or supervised drafting one or more sub-sections: A.K., D.D., D.J.H., L.K.W., M.H.S.S., Y.P., Y.Q.
Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion: A.A.K., B.K.B., B.T.D., D.S.H., E.F., G.P.W., M.M.H., M.Z., P.A., T.C.
Drafted one or more sub-sections: A.E.C., A.M.A., A.S., B.J.L., C.A.L., E.M.C., G.L.R., J.I., J.L., J.X., S.C.T., S.W., W.X., Z.L.
Revised specific sub-sections or supervised drafting one or more sub-sections: A.H., A.K., D.D., D.J.H., L.K.W., M.H.S.S., S.J.S., S.M.B., Y.P., Y.Q.
Drafted sub-sections, edited the manuscript, reviewed pull requests, and coordinated co-authors: A.G., C.S.G.

### Competing interests
Expand All @@ -55,6 +55,9 @@ We would like to thank Aaron Sheldon, who contributed text but did not formally
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 Robert Gieseke, Ruibang Luo, and Sourav Singh for correcting typos, formatting, and references.
Finally, 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 National Institutes of Health awards DP2GM123485 (A.K.), R01AI116794 (B.K.B.), R01GM089652 (A.E.C.), R01GM089753 (J.X.), T32GM007753 (B.T.D.), and U54AI117924 (A.G.);
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.), 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.);
and the National Institutes of Health Intramural Research Program and National Library of Medicine (Y.P.).
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.).
73 changes: 72 additions & 1 deletion content/metadata.yaml
Expand Up @@ -63,6 +63,24 @@ author_info:
email: p.agapow@imperial.ac.uk
affiliations:
- Data Science Institute, Imperial College London, London, United Kingdom
- github: zietzm
name: Michael Zietz
initials: MZ
orcid: 0000-0003-0539-630X
email: zietz@sas.upenn.edu
affiliations:
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
funders: Roy and Diana Vagelos Scholars Program in the Molecular Life Sciences
- github: michaelmhoffman
name: Michael M. Hoffman
initials: MMH
orcid: 0000-0002-4517-1562
email: michael.hoffman@utoronto.ca
affiliations:
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, Toronto, ON, Canada
- Department of Computer Science, Toronto, ON, Canada
funders: NSERC RGPIN-2015-3948
- github: xieconnect
name: Wei Xie
orcid: 0000-0002-1871-6846
Expand Down Expand Up @@ -127,6 +145,36 @@ author_info:
affiliations:
- Department of Computer Science, Trinity University, San Antonio, TX
funders: NSF 1531594
- github: lavenderca
name: Christopher A. Lavender
initials: CAL
orcid: 0000-0002-7762-1089
email: christopher.lavender@nih.gov
affiliations:
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
- github: SriniTuraga
name: Srinivas C. Turaga
initials: SCT
orcid: 0000-0003-3247-6487
email: turagas@janelia.hhmi.org
affiliations:
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA
funders: Howard Hughes Medical Institute
- github: alexandari
name: Amr M. Alexandari
initials: AMA
orcid: 0000-0001-8655-8109
email: amr.alexandari@gmail.com
affiliations:
- Department of Computer Science, Stanford University, Stanford, CA
- github: luzh2
name: Zhiyong Lu
initials: ZL
orcid: 0000-0001-9998-916X
email: zhiyong.lu@nih.gov
affiliations:
- National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD
funders: National Institutes of Health Intramural Research Program and National Library of Medicine
- github: davharris
name: David J. Harris
orcid: 0000-0003-3332-9307
Expand Down Expand Up @@ -173,12 +221,35 @@ author_info:
email: marwin.segler@uni-muenster.de
affiliations:
- Institute of Organic Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
- github: SiminaB
name: Simina M. Boca
initials: SMB
orcid: 0000-0002-1400-3398
email: smb310@georgetown.edu
affiliations:
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
funders: NIH R21CA220398, NIH P30CA051008
- github: swamidass
name: S. Joshua Swamidass
initials: SJS
orcid: 0000-0003-2191-0778
email: swamidass@wustl.edu
affiliations:
- Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO
funders: NIH R01LM012222, NIH R01LM012482
- github: austinvhuang
name: Austin Huang
initials: AH
orcid: 0000-0003-1349-4030
email: austinh@alum.mit.edu
affiliations:
- Department of Medicine, Brown University, Providence, RI
- github: agitter
name: Anthony Gitter
orcid: 0000-0002-5324-9833
email: gitter@biostat.wisc.edu
affiliations:
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
- Morgridge Institute for Research, Madison, WI
funders: NIH U54AI117924
symbol_str: ""
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73 changes: 0 additions & 73 deletions content/new-author-metadata.yaml

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