Modifications to the Manubot section

content/02.main-text.md

@@ -111,6 +111,8 @@ With Manubot, manuscripts are written as plain-text Markdown files, which is wel
 The Markdown standard itself provides limited yet crucial formatting syntax, including the ability to embed images and format text via bold, italics, hyperlinks, headers, inline code, codeblocks, blockquotes, and numbered or bulleted lists.
 In addition, Manubot relies on extensions from [Pandoc Markdown](https://pandoc.org/MANUAL.html#pandocs-markdown) to enable citations, tables, captions, and equations specified using the popular TeX math syntax.
 
+## Citation by identifier
+
 Manubot includes an additional layer of citation processing, currently unique to the system.
 All citations point to a standard identifier, for which Manubot automatically retrieves bibliographic metadata.
 Table @tbl:citations presents the supported identifiers and example citations before and after Manubot processing.
@@ -151,6 +153,8 @@ Manubot's default style emphasizes titles and electronic (rather than print) ide
 Alternatively, users can also choose from thousands of [predefined styles](http://editor.citationstyles.org/searchByName/) or build their own [@tag:techblog-csl].
 As a result, adopting the specific bibliographic format required by a journal usually just requires specifying the style's source URL in the Manubot configuration.
 
+### Format conversion
+
 Manubot uses [Pandoc](https://pandoc.org/) to convert manuscripts from Markdown to HTML, PDF, and optionally DOCX outputs.
 Pandoc supports conversion between additional formats — such as LaTeX, AsciiDoc, EPUB, and JATS — offering Manubot users broad interoperability.
 [Journal Article Tag Suite](https://jats.nlm.nih.gov/) (JATS) is a standard XML format for scholarly articles that is used by publishers, archives, and text miners [@url:http://www.niso.org/standards/z39-96-2015/; @doi:10.6087/kcse.2014.1.99; @doi:10.1080/00987913.2012.10765464].
@@ -178,6 +182,8 @@ Clarifying markups are overlaid in purple.
 The Manubot "front-end" (layout, look, controls, behavior, etc.) was developed in line with current best practices and user expectations of the modern web.
 The plugins utilize standard technology built in to most major web browsers, allowing them to be relatively lightweight, modular, and easy to configure.
 
+### Continuous publication
+
 Manubot performs continuous publication: every update to a manuscript's source is automatically reflected in the online outputs.
 The approach uses continuous integration (CI) [@doi:10.1038/550143a; @doi:10.1038/nbt.3780; @doi:10.1101/344804], specifically via [Travis CI](https://travis-ci.org/), to monitor changes.
 When changes occur, the CI service attempts to generate an updated manuscript.
@@ -191,6 +197,8 @@ If successful, the output is deployed back to GitHub (to dedicated [`output`](ht
 As a result, <https://greenelab.github.io/meta-review> stays up to date with the latest HTML manuscript.
 Furthermore, versioned URLs, such as <https://greenelab.github.io/meta-review/v/4b6396bcefd1b9c7ddf39c1d3f0b3eab2dd63f31/>, provide access to previous manuscript versions.
 
+### Timestamping
+
 The idea of the "priority of discovery" is important to science, and Vale and Hyman discuss the importance of both disclosure and validation [@doi:10.7554/eLife.16931].
 In their framework, disclosure occurs when a scientific output is released to the world.
 However, for a manuscript that is shared as it is written, being able to establish priority could be challenging.
@@ -202,6 +210,8 @@ OpenTimestamps minimizes fees by encoding many timestamps into a single Bitcoin
 Since transactions can take up to a few days to be made, Manubot initially stores incomplete timestamps and upgrades them in future continuous deployment builds.
 We find that this asynchronous design with timestamps precise to the day is suitable for the purposes of scientific writing.
 
+### TODO
+
 Manubot and its dependencies are free of charge and largely open source.
 It does rely on gratis services from two proprietary platforms: GitHub and Travis CI.
 Fortunately, lock-in to these services is minimal, and several substitutes already exist.
@@ -210,6 +220,8 @@ For example, figures can be specified using versioned URLs that refer to the cod
 In addition, manuscripts can be templated, so that numerical values or tables are inserted directly from the repository that created them.
 An [example repository](https://github.com/manubot/rootstock) demonstrates Manubot's features and serves as a template for users to write their own manuscript with Manubot.
 
+### Existing Manubot manuscripts
+
 Since its creation to facilitate the Deep Review, Manubot has been used to write a variety of scholarly documents.
 The [Sci-Hub Coverage Study](https://github.com/greenelab/scihub-manuscript) --- performed openly on GitHub from its inception --- investigated Sci-Hub's repository of pirated articles [@doi:10.7554/eLife.32822].
 Sci-Hub [reviewed](https://github.com/greenelab/scihub-manuscript/issues/17) the initial preprint from this study in a series of tweets, pointing out a major error in one of the analyses.
@@ -219,7 +231,7 @@ As such, continuous publishing via Manubot helped the authors address the error
 This Sci-Hub Coverage Study preprint was the [most viewed](http://web.archive.org/web/20171221221858/http://www.prepubmed.org/top_preprints/) 2017 _PeerJ Preprint_, while the Deep Review was the most viewed 2017 _bioRxiv_ preprint [@doi:10.1038/d41586-017-08493-x].
 Hence, in Manubot's first year, two of the most popular preprints were written using its collaborative, open, and review-driven authoring process.
 
-Additional research studies in progress are being authored using Manubot, spanning the fields of [genomics](https://vsmalladi.github.io/tfsee-manuscript/), [climate science](https://openclimatedata.github.io/global-emissions/), and [data visualization](https://yt-project.github.io/yt-3.0-paper/).
+Additional research studies in progress are being authored using Manubot, spanning the fields of [genomics](https://vsmalladi.github.io/tfsee-manuscript/), [synthetic biology](https://zach-hensel.github.io/low-noise-manuscript/) [@doi:10.1101/515940], [climate science](https://openclimatedata.github.io/global-emissions/), [machine learning](https://trang1618.github.io/tpot-ds-ms/), and [data visualization](https://yt-project.github.io/yt-3.0-paper/).
 Manubot is also being used for documents beyond traditional journal publications, such as [grant proposals](https://greenelab.github.io/manufund-2018/), [progress reports](https://greenelab.github.io/czi-hca-report/), [undergraduate research reports](https://zietzm.github.io/Vagelos2017/) [@doi:10.6084/m9.figshare.5346577], [literature reviews](https://slochower.github.io/synthetic-motor-literature/), and lab notebooks.
 Manuscripts written with other authoring systems have been successfully ported to Manubot, including the [Bitcoin Whitepaper](https://git.dhimmel.com/bitcoin-whitepaper/) [@tag:steem-post] and [Project Rephetio manuscript](https://git.dhimmel.com/rephetio-manuscript/) [@doi:10.7554/eLife.26726].
 Finally, the Kipoi model zoo for genomics [@doi:10.1101/375345] uses Manubot's citation functionality to automatically extract model authors.