diff --git a/README.md b/README.md index 91cf3d9f..e9ae1444 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # Output directory containing the formatted manuscript The [`gh-pages`](https://github.com/manubot/rootstock/tree/gh-pages) branch hosts the contents of this directory at . -The permalink for this webpage version is . +The permalink for this webpage version is . To redirect to the permalink for the latest manuscript version at anytime, use the link . ## Files @@ -35,4 +35,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc ## Source The manuscripts in this directory were built from -[`e5b62395d10a2b475c914726aafb510e41ce9015`](https://github.com/manubot/rootstock/commit/e5b62395d10a2b475c914726aafb510e41ce9015). +[`ca748bf4e80a830d7bee69a20b1fae18e028d9e6`](https://github.com/manubot/rootstock/commit/ca748bf4e80a830d7bee69a20b1fae18e028d9e6). diff --git a/index.html b/index.html index c626cda5..6fe09335 100644 --- a/index.html +++ b/index.html @@ -6,7 +6,7 @@ - + Manuscript Title + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+

Manuscript Title

+
+

+This manuscript +(permalink) +was automatically generated +from manubot/rootstock@ca748bf +on December 20, 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. +
  2. Ordered list item +
      +
    1. Sub-item
      2. +
    2. Sub-item +
        +
      1. Sub-sub-item
        2. +
      3. +
    3. +
  3. Ordered list item +
      +
    1. Sub-item
      2. +
    4. +
+
    +
  • List item
    • +
  • List item
    • +
  • List 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 ScoresJaneJohnAliceBob
Game 1150187210105
Game 298202197102
Game 3123180238134
+
+
+ + +++++++ + + + + + + + + + + + + + + + + + + + + + + + + + +
Table 2: A table too wide to fit within page. +
Digits 1-33Digits 34-66Digits 67-99Ref.
pi3.14159265358979323846264338327950288419716939937510582097494459230781640628620899862803482534211706piday.org
e2.71828182845904523536028747135266249775724709369995957496696762772407663035354759457138217852516642nasa.gov
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
Table 3: A table with merged cells using the attributes plugin. +
Colors
SizeText ColorBackground Color
bigblueorange
smallblackwhite
+
+

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
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/v/ca748bf4e80a830d7bee69a20b1fae18e028d9e6/index.html.ots b/v/ca748bf4e80a830d7bee69a20b1fae18e028d9e6/index.html.ots new file mode 100644 index 00000000..9d1a2fc9 Binary files /dev/null and b/v/ca748bf4e80a830d7bee69a20b1fae18e028d9e6/index.html.ots differ diff --git a/v/ca748bf4e80a830d7bee69a20b1fae18e028d9e6/manuscript.pdf b/v/ca748bf4e80a830d7bee69a20b1fae18e028d9e6/manuscript.pdf new file mode 100644 index 00000000..51e079fd Binary files /dev/null and b/v/ca748bf4e80a830d7bee69a20b1fae18e028d9e6/manuscript.pdf differ diff --git a/v/ca748bf4e80a830d7bee69a20b1fae18e028d9e6/manuscript.pdf.ots b/v/ca748bf4e80a830d7bee69a20b1fae18e028d9e6/manuscript.pdf.ots new file mode 100644 index 00000000..05426bcc Binary files /dev/null and b/v/ca748bf4e80a830d7bee69a20b1fae18e028d9e6/manuscript.pdf.ots differ diff --git a/v/e5b62395d10a2b475c914726aafb510e41ce9015/index.html.ots b/v/e5b62395d10a2b475c914726aafb510e41ce9015/index.html.ots index c9c10d81..99f5cd8e 100644 Binary files a/v/e5b62395d10a2b475c914726aafb510e41ce9015/index.html.ots and b/v/e5b62395d10a2b475c914726aafb510e41ce9015/index.html.ots differ diff --git a/v/e5b62395d10a2b475c914726aafb510e41ce9015/manuscript.pdf.ots b/v/e5b62395d10a2b475c914726aafb510e41ce9015/manuscript.pdf.ots index 0389c4c3..9afa0d44 100644 Binary files a/v/e5b62395d10a2b475c914726aafb510e41ce9015/manuscript.pdf.ots and b/v/e5b62395d10a2b475c914726aafb510e41ce9015/manuscript.pdf.ots differ diff --git a/v/freeze/index.html b/v/freeze/index.html index f65472e7..d0b96d28 100644 --- a/v/freeze/index.html +++ b/v/freeze/index.html @@ -7,13 +7,13 @@ - + Page Redirection - If you are not redirected automatically, follow this link. + If you are not redirected automatically, follow this link. diff --git a/v/latest/index.html b/v/latest/index.html index c626cda5..6fe09335 100644 --- a/v/latest/index.html +++ b/v/latest/index.html @@ -6,7 +6,7 @@ - + Manuscript Title