Preparing Manuscripts

author — Tue, 06 Dec 2016 00:04:10 GMT

Getting Started

Any writing or presentation should reflect our own thought process on why we initiate the project, how we design the research plan, how we interpret the results, and how we troubleshoot where needed. So they should probably start by describing what problems we are trying to understand; What people already knew / what the state of the art is; What calculations we did and how you did them; What you found; What the findings tell you.
Learn from others: writing and presentations.
See Fundamentals of Data Visualization for a nice introduction to data visualization and techniques for visualizing different types of information.

Checklist

Correct use of hyphens, em dashes, and en dashes
When formatting equations and symbols, only italicize variables (but not parentheses/square brackets, operators, or labels) italic; e.g., "E / k_B [K]" should have "E" and "k" italic, but not the division sign, label "B", or the square brackets.
For journals with a double-column layout, display items such as figures and tables should target either full width (~6.5 -- 7 in) or column width (~3.25 -- 3.5 in). This will signal to copy editors that we prefer them to occupy a single column or across two columns.
To manage the placement of display items, place them and their captions into a text box with Shape Format -> Shape Outline and Wrap Text set to "None" and "Square", respectively. Preferably, the text box is then positioned to the top or the bottom of a page by using the Shape Format -> Align option. Sometimes, Word will not break a continuous paragraph to use up the whitespace in the previous page. To fix this, move the text box below the paragraph, which will allow the paragraph to flow to the previous page, and then re-align the text box to the top of the page.
Journal names are properly abbreviated. Authoritative sources for journal name abbreviations include ISSN List of Title Word Abbreviations, Web of Science Journal Title Abbreviations, and Abbreviations for Elsevier journals.
Double check the references. References imported to Zotero by DOIs often have extra whitespace in front of subscripts (e.g., "CO ₂").
Follow journal guidelines and if available, use journal-specific Word/Zotero/LaTeX/BibTeX templates. For initial submission, when citing an article with 10 or more authors, list the first 10 authors' names and then use "et al." to represent additional authors (ACS Style Guide).
When you address a comment in Word, Overleaf, etc., please take care not to remove it. If you delete and rewrite the block of text on which a comment is made, then the comment itself will also be deleted, making it very hard to follow up on them. One way we can avoid this is by first writing new text inside the commented block and then delete the old text. Another way for Word documents is to use strike-through text for the word or sentence the comment is associated with and write/edit around the strike-through text.

MS Word

Do NOT make stylistic text changes on individual blobs of text, including title and headings. For example, do not use these ribbon options to make heading text bold and centered. This is a bad practice because you have to 1) make the same style changes for all headings; 2) remember to do the same for any new sections that are added later; and 3) edit every heading all over again if you ever need to submit to another journal with different requirements on formatting.
USE appropriate Styles to mark semantics of the text (e.g., title, Heading 2, Heading 3). If say, Heading 3 does not have the desired format, click Modify to edit in the dialog that pops up. You can make more changes by clicking the Format button. A nice side effect of this is that you can turn on Navigation pane and see a clear outline of the document.
NEVER hard code Figure X / Table Y in text. Use Cross-reference. To customize cross-reference labels (e.g., "Fig." or "FIGURE" instead of "Figure"), create a new label. Do NOT make changes to the labels manually, which will not work with Cross-reference properly.
See here for how to combine multiple references. That is, do not write "Figure 1, Figure 2, Figure 3"; instead write "Figures 1 -- 3" or "Figures 1, 2, and 4" (if not continuous).
To add automatic equation numbering, use either #() syntax (available since Word 2016) or 3-column no-border tables with captions. To cross reference equations, first select the equation number and insert a bookmark. You can then use Cross-reference.
To cross reference section numbers (e.g., Section 2), in the Cross-reference dialog, select Heading as Reference type and Heading number as Insert reference to. For this to work though, the numbers in section heading (e.g., "2. Methods") must be added using the numbered list functionality, rather than by hand.
The above points are very useful when adding new figures as the document will auto-update the figure/table numbering. To update cross-reference labels (in the text itself, not the captions), right-click the label and select "update field" for manual updating. See here for updating all fields at once.
NEVER use text boxes for figure labels. Text boxes often move out of alignment with the figures they are supposed to annotate. Instead, annotate the figure in PowerPoint. When you are done, select everything for the figure, right click, and either 1) Save as Picture or 2) Copy, right click in Word, and Paste as Picture.

TeX/LaTeX

Special symbols

Text mode Angstrom: \AA Math mode: Angstrom: \mathring{A}, \r{A}, \r{\rm A} degree symbol: ^{\circ}

For quick referencing, Kire Labs made a tool called Dexterify which uses symbol recognition to identify which LaTeX commands will give the user-drawn character. For example, you can draw a tilde symbol in the drawing box, and Dexterify will output various options for tildes.

Figures

When embedding figures in latex, the float default is usually h for "here." For publications this should be t for "top." For figures that are too large, the default behavior is to put the figure at the end. Putting an exclamation point will gurantee this:

\begin{figure}[t!]

Controlling figure and table placement in LaTeX explains how to place float objects to places they belong.

For the Xmgrace files, use figures in .eps format. Make sure that the figure has the correct size in Xmgrace by providing the correct number of pixels. Font size in labels and legends should be commensurate with text size in the journal.
ACS journal column widths are 3.25 in. So make sure to never go below that in width. It is not necessary to make the figures 3.25" in size unless otherwise requested by the journal.

Software

When preparing manuscripts, keep all LaTeX as simple as possible. Do NOT use any packages and only use the documentclass provided by the journal. Always follow the author guidelines from the journal as closely as possible.
Neither ACS, AIP, Elsevier, nor Nature use "pdflatex". Thus, we must use regular "latex".
Data management plans now require extensive Supporting Information. Essentially all simulation data that appears somewhere in a figure, also need to be as numerical data in a table in the supporting info. This is quite labor intensive.
Relative paths should be used
Some publisher programs will have difficulty with lines of longer than 255 characters.
Make sure to name the PDF something appropriate. For example, the ACS supporting info file name is named based on the main paper. So, for example, don't submit full_article.pdf
ACS journals have a mistake with mathematical symbols. The statement

The result is about 5.2

would be translated to

The result is ~5.2

This is the wrong symbol for about; you should use the approximate equals yourself; the program will think it's a mathematical equation instead and it will correctly translate.

Latex differentiates between opening and closing quotes.

BibTeX

Correct format

An example BibTeX entry that has multiple issues:

@article{X22,
author = {Gupta, Prashant Kumar and Meuwly, Markus},
journal = {The journal of physical chemistry. B},
number = {35},
pages = {10951--9},
volume = {116},
year = {2012}
}

Title: This is sometimes missing from the output of reference manager software, but is needed for all proposals and for some journals (e.g., ACS journals now want the titles for citations). Also be careful that the Web of Science may use the wrong capitalization: only the first word and names should be capitalized (sentence case). The BibTeX style file should change titles to the journal format automatically (e.g., title case for ACS journals). However, there is a problem with names. For example, the name of our method has to be typed as "{M}onte {C}arlo" otherwise the first letter of these names will be lowercase.
Author: Edit so that only the initials are included. No journal wants the full middle name of the authors. Also NEVER use "et al." in your .bib file. For the few journals that want fewer names, we will modify the BibTeX style file or directly edit the .bbl file.
Journal: Edit to use the correct abbreviation. LaTex does not automatically find the correct abbreviations for the journal title. When using Zotero, double check "Journal Abbr" is set correctly.
Number: Remove or make sure the BibTeX template removes them. There is no single journal that requires the issue number in the list of references.
Pages: Page numbers need to be given in full. That is, "10951-9" should read "10951-10959".
Some journals do not allow a separate .bib file, in which case the references need to be embedded in the main .tex file.
When a problem is found for a reference, make sure to fix the citation source in Zotero or BibTeX. Develop the habit of checking the title and journal abbr fields whenever you import a new reference, either by DOI lookups or by extracting PDF metadata.

Writing

Skillful writing of an awful research paper (Royce Murray, 2011)

Paper writing gone Hollywood (2017)

Siepmann's comments on clarity and precision of language

Scrapbook (Posts about writing)