finish intro edits

content/60.methods.md

@@ -35,24 +35,28 @@ While not all of the manuscripts are specifically about SARS-CoV-2 or COVID-19,
 Additionally, with information being produced rapidly both in traditional publishing venues and as preprints, some papers that are published face scrutiny after their initial release.
 Concerns have been raised that the number of COVID-19 papers being retracted may be higher, or potentially much higher, than is typical, although a thorough investigation of this question will not be possible until more time has elapsed [@doi:10.1080/08989621.2020.1782203; @doi:10.1080/08989621.2020.1793675].
 Other papers are updated with corrections or expressions of concern [@doi:10.1080/08989621.2020.1793675; @url:https://retractionwatch.com/retracted-coronavirus-covid-19-papers].
-These include both preprints and papers that are published in more traditional venues [@url:https://retractionwatch.com/retracted-coronavirus-covid-19-papers].
+These include both preprints and papers that are published in more traditional venues [@url:https://retractionwatch.com/retracted-coronavirus-covid-19-papers; @url:https://asapbio.org/preprints-and-covid-19].
 Preprints provide a venue for scientists to release findings rapidly, but have both the advantage and disadvantage of making research available before it has undergone the peer review process.
 However, some traditional publishing venues have also fast-tracked COVID-19 through peer review, leading to questions about whether this research is being held to the usual standards for publication [@doi:10.1111/bioe.12772].
 Therefore, monitoring the COVID-19 literature requires not only digesting the high volume of information being released, but also critically evaluating it and/or monitoring for subsequent adjustments.
 
 Because of the fast-moving nature of the topic, many efforts to summarize and synthesize COVID-19 literature have been undertaken. 
-A number of groups have sought to track and review COVID-19 preprints<!--To Do: add refrences-->.
-However, any static review is likely to quickly become dated as new research is released or existing research is retracted or superseded, and the explosive rate of publication made localized efforts to curate new publications increasingly difficult.
-Additionally, the complex nature of COVID-19 means that significant advantages can be gained from examining the virus and disease in a multidisciplinary context.
+These efforts include newsletters [@url:https://depts.washington.edu/pandemicalliance/covid-19-literature-report/latest-reports/; @doi:10.1080/10872981.2020.1770562], web portals (such as [@url:https://outbreaksci.prereview.org/] or the now-defunct http://covidpreprints.com/, which was described in [@url:https://asapbio.org/preprints-and-covid-19]), comments on preprint servers [@doi:10.1038/s41577-020-0319-0; @url:https://disqus.com/by/sinaiimmunologyreviewproject/], and even a journal [@url:https://rapidreviewscovid19.mitpress.mit.edu/].
+However, the explosive rate of publication presents challenges for such efforts, many of which are no longer publishing summaries.
+Similarly, many literature reviews have been written on the available COVID-19 literature [@doi:10.1016/j.molmed.2020.02.008; @doi:10.1016/j.immuni.2020.05.002; @doi:10.1126/scitranslmed.abc1931; @doi:10.1016/j.immuni.2020.05.002; @doi:10.1001/jama.2020.6019; @doi:10.1038/d41591-020-00026-w; @doi:10.1001/jama.2020.12839].
+However, static reviews quickly become outdated as new research is released or existing research is retracted or superseded
 Therefore, the COVID-19 publishing climate presented a challenge where curation of the literature by a diverse group of experts in a format that could respond quickly to high-volume, high-velocity information was desirable.
 
+We therefore sought to develop a platform for scientific discussion and collaboration around COVID-19 by adapting open publishing infrastructure to accommodate the scale of the COVID-19 publishing boom.
 Recent advances in open publishing have created an infrastructure that facilitates distributed, version-controlled collaboration on manuscripts [@doi:10.1371/journal.pcbi.1007128].<!--To Do: possibly cite some other efforts here-->
 Manubot [@doi:10.1371/journal.pcbi.1007128] is a collaborative framework developed to adapt open-source software development techniques and version control for manuscript writing.
 With Manubot, manuscripts are managed and maintained using GitHub, a popular, online version control interface that also provides the infrastructure via continuous integration (CI) to incorporate code into the manuscript building process to allow, for example, figures to be continuously updated based on an external data set.
-This open-publishing platform has been used to develop large-scale collaborative efforts such as <!--To Do: brief summary of deep review and one other use case-->.
-However, although synthesis and discussion of the emerging literature by biomedical scientists and clinicians would be expected to provide novel insights into how various areas of COVID-19 research intersect, such tools are not typically associated with biomedical research and the reliance on git can present a significant technical barrier to entry for biomedical scientists.
-The problem of synthesizing the COVID-19 literature lends itself well to a crowd-sourced approach to writing through open collaboration, but in biology, such efforts often rely on WYSIWYG tools such as Google Docs despite the significant limitations of such approaches.<!--To Do: recheck what the Manubot paper says about this and possibly pull some other refs-->
-Therefore, in addition to the unprecedented release of information, COVID-19 presents a unique challenge because most subject matter experts have limited technical training.
+This open-publishing platform has been used to develop large-scale collaborative efforts such as a review of developments in deep learning [@doi:10.1098/rsif.2017.0387].
+Collaboration via massively open online papers (MOOPs) has been identified as a strategy for promoting inclusion and interdisciplinary thought [@doi:10.5334/kula.63].
+Manubot is an ideal platform for the analysis of COVID-19 literature because it facilitates the automatic integration of new data through CI.
+However, the Manubot workflow can appear intimidating to contributors who are not well-versed in git [@doi:10.5334/kula.63].
+The synthesis and discussion of the emerging literature by biomedical scientists and clinicians is imperative to a robust interpretation of COVID-19 research, but in biology, such efforts often rely on WYSIWYG tools such as Google Docs despite the significant limitations of these platforms in the face of excessive publication.
+Therefore, we recognized that the problem of synthesizing the COVID-19 literature lent itself well to the Manubot platform, but that the potential technical expertise required to work with Manubot present a significant technical barrier to domain experts.
 
 Here, we describe efforts to adapt Manubot to handle the extreme case of the COVID-19 infodemic, with the objective of extending simply reviewing preprints to develop a centralized platform for summarizing and synthesizing a massive amount of preprints, news stories, journal publications, and data.
 Unlike prior collaborations built on Manubot, here most contributors came from a traditional biological or medical background.
@@ -160,7 +164,6 @@ The manuscripts pull data from XX data sources, allowing for information and vis
 This computational approach allows for the information in the manuscripts to be kept up to date automatically.
 
 Beyond the immediate goal of applying Manubot to the challenges of COVID-19, we have also expanded Manubot to allow for broader participation in open publishing from fields where computational training in tools like version control is uncommon. 
-Several review articles on aspects of COVID-19 have already been published, including reviews on the disease epidemiology [@doi:10.1016/j.molmed.2020.02.008], immunological response [@doi:10.1016/j.immuni.2020.05.002], diagnostics [@doi:10.1126/scitranslmed.abc1931], and pharmacological treatments [@doi:10.1016/j.immuni.2020.05.002; @doi:10.1001/jama.2020.6019] and others that provide narrative reviews of progress on some important ongoing COVID-19 research questions [@doi:10.1038/d41591-020-00026-w; @doi:10.1001/jama.2020.12839].
 However, the broader topic of COVID-19 intersects with a wide range of fields, including virology, immunology, medicine, pharmacology, evolutionary biology, public health, and more, and any effort to comprehensively document and evaluate this body of literature would require insight from scientists across a number of fields.
 Furthermore, during the initial phase of the COVID-19 pandemic during spring and summer 2020, and much longer in some part of the world, many biological scientists were unable to access their research spaces.
 As a result, early career researchers (ECR) and students were likely to lose out on valuable time for conducting experiments. <!--To Do: look at equity analyses of the effects on the pandemic to see if there is any data on this yet?-->