results part 1

content/60.methods.md

@@ -133,21 +133,30 @@ Because in this implementation of Manubot, most collaborators were writing and e
 
 #### Recruitment and Manuscript Development
 
-We received a large 
+We received a large amount of interest from the broad community beginning with coverage of the project by _Nature Toolbox_ [@doi:10.1038/d41586-020-00916-6] and an associated tweet about the project on April 1, 2020 [@url:https://twitter.com/j_perkel/status/1245454628235309057].
+<!-- To Do: use comments on #17 to illustrate engagement in issue number 17 and diversity of interest (Casey independently suggested a word cloud)-->
 Because the GitHub issues and comment systems are relatively similar to other web common web activities, we found that authors were able to learn these tools fairly quickly.
 Similarly, the gitter chat also presented a low barrier to entry.
-<!--To Do: Add a graph/text describing number of unique contributors & commits over time-->
-<!-- To Do: Word Cloud of #17 to show diversity of interests?-->
-Appendix A contains summaries written by the students, post-docs, and faculty of the Immunology Institute at the Mount Sinai School of Medicine [@url:https://github.com/ismms-himc/covid-19_sinai_reviews; @doi:10.1038/s41577-020-0319-0], and two of the authors were recruited through the American Physician Scientist Association's Virtual Summer Research Program [@url:https://www.physicianscientists.org/page/summer-research-pilot-program].
-<!--To Do: Graph of contributions by individual over time and/or by career stage?-->
-<!-- To Do: unique contributors and commits over time like this: https://greenelab.github.io/meta-review/#fig:contrib-->
-<!--To Do: Other possible graphs: plot number of article issues opened over time, distribution of review contents, that is, something showing the number of comments per pull request that was merged, growth of the reference list over time and/or number of clinical trials cited (because we describe that as a necessary enhancement)-->
+While only a fraction of potential contributors ended up contributing to the development of the manuscript, many of these contributors remained engaged over the course of a full year (Figure with dots).
+
+<!--To Do: Add dot plot of unique contributors & commits over time-->
 
 In order to make the project accessible to individuals from a number of backgrounds, we developed resources explaining how to use GitHub's web interface to develop and edit text and interact with Manubot for individuals with no prior experience working with git or other version control platforms.
 We developed tutorials containing visuals to explain how to open an issue, open a pull request, and review a pull request [@url:https://github.com/greenelab/covid19-review/blob/master/CONTRIBUTING.md; @url:https://github.com/greenelab/covid19-review/blob/master/INSTRUCTIONS.md].
-
-Articles were classified as _diagnostic_, _therapeutic_, or _other_, and a template was developed to guide the review of papers and preprints in each category.
-For examples of each template, please see Appendices B-D.
+Additionally, the framework for evaluating literature was converted into issue templates to simplify review of new articles.
+Articles were classified as _diagnostic_ [@url:https://github.com/greenelab/covid19-review/blob/master/.github/ISSUE_TEMPLATE/new-diag-study-template.md], _therapeutic_ [@url:https://github.com/greenelab/covid19-review/blob/master/.github/ISSUE_TEMPLATE/new-therapy-study-template.md], or _other_ [@url:https://github.com/greenelab/covid19-review/blob/master/.github/ISSUE_TEMPLATE/new-paper-template.md], with an associated template developed to guide the review of papers and preprints in each category.
+<!-- To Do: Number of paper issue and number of unique contributors?-->
+
+Efforts to integrate with existing projects providing support for undergraduate students during COVID-19 were also successful.
+Appendix A contains summaries written by the students, post-docs, and faculty of the Immunology Institute at the Mount Sinai School of Medicine [@url:https://github.com/ismms-himc/covid-19_sinai_reviews; @doi:10.1038/s41577-020-0319-0].
+Additionally, two of the consortium authors were undergraduate students recruited through the American Physician Scientist Association's Virtual Summer Research Program [@url:https://www.physicianscientists.org/page/summer-research-pilot-program].
+<!--To Do: Other possible graphs: plot number of article issues opened over time, distribution of review contents, that is, something showing the number of comments per pull request that was merged, growth of the reference list over time and/or number of clinical trials cited (because we describe that as a necessary enhancement) -- growth of manuscript would probably be next priority for me-->
+
+Currently, three manuscripts associated with this project have been submitted to _mSystems_, with one accepted for publication [@arxiv:2102.02250] and two under revision [@arxiv:2103.02723; @arxiv:2102.01521].
+An additional four manuscripts are in preparation.
+All seven will be submitted to _mSystems_ as part of a special issue that is providing support for evolving reviews, so that they will continue to be updated as more information becomes available.
+These manuscripts cover a wide range of topics including the fundamental biology of SARS-CoV-2 (pathogenesis [@arxiv:2102.01521] and evolution [@individual-evolution]), biomedical advances in responding to the virus and COVID-19 (pharmaceutical therapeutics [@arxiv:2103.02723], nutraceutical therapeutics [@arxiv:2102.02250], vaccines [@individual-vaccines], and diagnostic technologies [@individual-diagnostics]), and biological and social factors influencing variable effects on patients [@individual-inequality].<!--To Do: add these additional individual citations-->
+To date, [number] authors are associated with the consortium.<!--To Do: break down by undergrad, grad/med student, post-doc, jr faculty?-->
 
 #### Data Analysis and Integration