Manuscript Title

This manuscript (permalink) was automatically generated from manubot/rootstock@957ff8e on July 31, 2024.

Authors

✉ — Correspondence possible via GitHub Issues or email to Jane Roe <jane.roe@whatever.edu>.

Abstract

This manuscript is a template (aka “rootstock”) for Manubot, a tool for writing scholarly manuscripts. Use this template as a starting point for your manuscript.

The rest of this document is a full list of formatting elements/features supported by Manubot. Compare the input (.md files in the /content directory) to the output you see below.

Basic formatting

Bold text

Semi-bold text

Centered text

Right-aligned text

Italic text

Combined italics and bold

Strikethrough

  1. Ordered list item
  2. Ordered list item
    1. Sub-item
    2. Sub-item
      1. Sub-sub-item
  3. Ordered list item
    1. Sub-item

subscript: H2O is a liquid

superscript: 210 is 1024.

unicode superscripts⁰¹²³⁴⁵⁶⁷⁸⁹

unicode subscripts₀₁₂₃₄₅₆₇₈₉

A long paragraph of text. Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Putting each sentence on its own line has numerous benefits with regard to editing and version control.

Line break without starting a new paragraph by putting
two spaces at end of line.

Document organization

Document section headings:

Heading 1

Heading 2

Heading 3

Heading 4

Heading 5
Heading 6

A heading centered on its own printed page

Horizontal rule:

Heading 1’s are recommended to be reserved for the title of the manuscript.

Heading 2’s are recommended for broad sections such as Abstract, Methods, Conclusion, etc.

Heading 3’s and Heading 4’s are recommended for sub-sections.

Bare URL link: https://manubot.org

Long link with lots of words and stuff and junk and bleep and blah and stuff and other stuff and more stuff yeah

Link with text

Link with hover text

Link by reference

Citations

Citation by DOI [1].

Citation by PubMed Central ID [2].

Citation by PubMed ID [3].

Citation by Wikidata ID [4].

Citation by ISBN [5].

Citation by URL [6].

Citation by alias [7].

Multiple citations can be put inside the same set of brackets [1,5,7]. Manubot plugins provide easier, more convenient visualization of and navigation between citations [2,3,7,8].

Citation tags (i.e. aliases) can be defined in their own paragraphs using Markdown’s reference link syntax:

Referencing figures, tables, equations

Figure 1

Figure 2

Figure 3

Figure 4

Table 1

Equation 1

Equation 2

Quotes and code

Quoted text

Quoted block of text

Two roads diverged in a wood, and I—
I took the one less traveled by,
And that has made all the difference.

Code in the middle of normal text, aka inline code.

Code block with Python syntax highlighting:

from manubot.cite.doi import expand_short_doi

def test_expand_short_doi():
    doi = expand_short_doi("10/c3bp")
    # a string too long to fit within page:
    assert doi == "10.25313/2524-2695-2018-3-vliyanie-enhansera-copia-i-insulyatora-gypsy-na-sintez-ernk-modifikatsii-hromatina-i-svyazyvanie-insulyatornyh-belkov-vtransfetsirovannyh-geneticheskih-konstruktsiyah"

Code block with no syntax highlighting:

Exporting HTML manuscript
Exporting DOCX manuscript
Exporting PDF manuscript

Figures

Figure 1: A square image at actual size and with a bottom caption. Loaded from the latest version of image on GitHub.
Figure 2: An image too wide to fit within page at full size. Loaded from a specific (hashed) version of the image on GitHub.
Figure 3: A tall image with a specified height. Loaded from a specific (hashed) version of the image on GitHub.
Figure 4: A vector .svg image loaded from GitHub. The parameter sanitize=true is necessary to properly load SVGs hosted via GitHub URLs. White background specified to serve as a backdrop for transparent sections of the image. Note that if you want to export to Word (.docx), you need to download the image and reference it locally (e.g. content/images/vector.svg) instead of using a URL.

Tables

Table 1: A table with a top caption and specified relative column widths.
Bowling Scores Jane John Alice Bob
Game 1 150 187 210 105
Game 2 98 202 197 102
Game 3 123 180 238 134
Table 2: A table too wide to fit within page.
Digits 1-33 Digits 34-66 Digits 67-99 Ref.
pi 3.14159265358979323846264338327950 288419716939937510582097494459230 781640628620899862803482534211706 piday.org
e 2.71828182845904523536028747135266 249775724709369995957496696762772 407663035354759457138217852516642 nasa.gov
Table 3: A table with merged cells using the attributes plugin.
Colors
Size Text Color Background Color
big blue orange
small black white

Equations

A LaTeX equation:

\[\int_0^\infty e^{-x^2} dx=\frac{\sqrt{\pi}}{2}\](1)

An equation too long to fit within page:

\[x = a + b + c + d + e + f + g + h + i + j + k + l + m + n + o + p + q + r + s + t + u + v + w + x + y + z + 1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9\](2)

Special

WARNING The following features are only supported and intended for .html and .pdf exports. Journals are not likely to support them, and they may not display correctly when converted to other formats such as .docx.

Link styled as a button

Adding arbitrary HTML attributes to an element using Pandoc’s attribute syntax:

Manubot Manubot Manubot Manubot Manubot. Manubot Manubot Manubot Manubot. Manubot Manubot Manubot. Manubot Manubot. Manubot.

Adding arbitrary HTML attributes to an element with the Manubot attributes plugin (more flexible than Pandoc’s method in terms of which elements you can add attributes to):

Manubot Manubot Manubot Manubot Manubot. Manubot Manubot Manubot Manubot. Manubot Manubot Manubot. Manubot Manubot. Manubot.

Available background colors for text, images, code, banners, etc:

white lightgrey grey darkgrey black lightred lightyellow lightgreen lightblue lightpurple red orange yellow green blue purple

Using the Font Awesome icon set:

References

1.
Sci-Hub provides access to nearly all scholarly literature
Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
eLife (2018-03-01) https://doi.org/ckcj
DOI: 10.7554/elife.32822 · PMID: 29424689 · PMCID: PMC5832410
2.
Reproducibility of computational workflows is automated using continuous analysis
Brett K Beaulieu-Jones, Casey S Greene
Nature biotechnology (2017-04) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103790/
DOI: 10.1038/nbt.3780 · PMID: 28288103 · PMCID: PMC6103790
3.
Bitcoin for the biological literature.
Douglas Heaven
Nature (2019-02) https://www.ncbi.nlm.nih.gov/pubmed/30718888
DOI: 10.1038/d41586-019-00447-9 · PMID: 30718888
4.
Plan S: Accelerating the transition to full and immediate Open Access to scientific publications
cOAlition S
(2018-09-04) https://www.wikidata.org/wiki/Q56458321
5.
Open access
Peter Suber
MIT Press (2012)
ISBN: 9780262517638
6.
Open collaborative writing with Manubot
Daniel S Himmelstein, Vincent Rubinetti, David R Slochower, Dongbo Hu, Venkat S Malladi, Casey S Greene, Anthony Gitter
Manubot (2020-05-25) https://greenelab.github.io/meta-review/
7.
Opportunities and obstacles for deep learning in biology and medicine
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, … Casey S Greene
Journal of The Royal Society Interface (2018-04) https://doi.org/gddkhn
DOI: 10.1098/rsif.2017.0387 · PMID: 29618526 · PMCID: PMC5938574
8.
Open collaborative writing with Manubot
Daniel S Himmelstein, Vincent Rubinetti, David R Slochower, Dongbo Hu, Venkat S Malladi, Casey S Greene, Anthony Gitter
PLOS Computational Biology (2019-06-24) https://doi.org/c7np
DOI: 10.1371/journal.pcbi.1007128 · PMID: 31233491 · PMCID: PMC6611653