Tips on writing biology in LaTeX on Overleaf

1. Compress figure PDFs (in Preview on Mac) to speed up compilation. However, this method severely reduces the image quality and should never be used in the final edition.

2. Create a supplementary information section where the numbering of all tables and figures has an "S" prefix:

   \setcounter{table}{0}
   \renewcommand{\thetable}{S\arabic{table}}
   \setcounter{figure}{0}
   \renewcommand{\thefigure}{S\arabic{figure}}

3. Use the textgreek package for upright greek letters in text.

4. Follow specific font setting rules in chemistry (for more chemistry-related subjects, see The IUPAC Compendium of Chemical Terminology):

   \textsc{l}-glutamine
   % use small capital L and D as chirality prefixes
   
   puromycin \textit{N}-acetyltransferase
   % use italic chemical element symbols in names

5. BibLaTeX option setting: \usepackage[backend=biber,sortcites,sorting=none,uniquename=false]{biblatex}. The sortcites option enables sorting of numbers associated with multiple citations within a single citing bracket. The sorting=none option assigns number to citations based on the order in which they appear in the text. The uniquename=false option guarantees that authors are referred to their last names only (when a citation is referred not by a number but rather a name-year pair in the text), even if multiple authors in the list of all citations share the same last name.

6. Utilize the siunit package for all quantities. Set up digit grouping by including the line \sisetup{group-digits=integer,group-separator={,}} in the preamble. Use absolute units instead of relative units when possible (this applies to experiment notes in general). For example, use 18,200 g instead of 15,000 rpm, and use 40 nM instead of 40 pmole/well.

7. By default, LaTeX enables ligature. I have tested that without specification of encoding, copying from an Overleaf output PDF opened by Acrobat Reader on Windows leads to misinterpretation of "filter" (with the "fi" ligature), resulting in "__lter" after pasting. The solution is adding the following lines to the preamble as suggested:

   \input{glyphtounicode}
   \pdfgentounicode=1

8. Use \frenchspacing, which has been commonly accepted as of now (see the Wikipedia entry on sentence spacing).

9. To export in PDF/A-1b (see section 2.1.1 of the manual of the pdfx package), include the following in the preamble. Note that doing this does NOT guarantee that the generated PDF file conforms to the standard. Use the Prefight tool in Adobe Acrobat Pro DC for a compliance check.

   \begin{filecontents*}{\jobname.xmpdata} % do not change the ``\jobname'' here
      ... % add metadata
   \end{filecontents*}
   \RequirePackage[a-1b]{pdfx}

Tips on making figures in Adobe Illustrator

1. Use a colorblind-friendly palette. For example, instead of green/red to represent down/up regulated genes, use blue/red. In Illustrator, check how an colored image looks like from a colorblind perspective by clicking View->Proof Setup->Color blindness.

2. When importing PDFs generated by Prism/Keynote to an Illustrator file, click View->Outline (or press Ctrl/Command + Y) to show all clipping masks and then clean them up accordingly. Click View->Preview (or press Ctrl/Command + Y again) to revert back to the normal mode.

3. For figure portability: convert texts of an uncommon font or texts with a known portability issue to outlines (or use the "Expand..." command) and embed all images (especially when sharing with other people) in an Illustrator file.

4. Select->Same is a convenient tool when modifying dot plots.

5. The functionality to center texts vertically in a text box has been added since version 24.3.

Miscellaneous

1. A UMich thesis LaTeX template (1988-current) hosted on Overleaf. Contact its.software@umich.edu to acquire an Overleaf Professional License for convenient backup and version control by synchronizing to GitHub. Note that as the author of an Elsevier article, you retain the right to include it in a thesis or dissertation, provided it is not published commercially. Permission is not required, but please ensure that you reference the journal as the original source.

2. Zotero with Better BibTeX.

3. Title case standard.

4. List of LaTeX templates for peer-reviewed journals on Overleaf: Annual Reviews

5. The default color for all axes/ticks/axis labels/tick labels in MATLAB is gray ([0.15, 0.15, 0.15]). To change it to pure black, check this.

6. Taxonomy nomenclature and others.

7. Avoid writing: $x$-fold higher/increase.

8. Free softwares for drawing chemical structures: Marvin JS (wherein structures can be saved and later reloaded into the web application again) and ChemSketch (Windows and academic/personal use only).

9. On the use of italic and roman fonts for symbols in scientific text (IUPAC).

10. Conventions for naming zebrafish genes, alleles, and proteins.