Manuscript Writing Guidelines#

This guide outlines key steps for preparing a manuscript in the BHK Lab to streamline review and feedback from Benjamin and co-authors.

1. Initial Setup#

Step	Action
1	Create a shared Google Drive folder for all manuscript materials
2	Share it with `bhaibeka@gmail.com`, co-authors, and add `bhklab.research@gmail.com` as Editor
3	Transfer ownership to `bhklab.research@gmail.com`
4	Organize into subfolders: Figures, Tables, Supplementary, Code, etc.

2. Add Legend & Highlighting Guide at the Top of Manuscript#

Add the following legend at the top of your manuscript:

Purpose	Style
Shared Directory	"[Google Drive URL]"
Editable Figures	"[Miro URL]"
Figures Tables_Supplementary_Info	"[Overleaf URL]"
Computer Code	"[GitHub URL]"
Executable Container	"[Code Ocean URL] (optional, if applicable)"
References	"[Paperpile link]"

Then, use these highlighting rules consistently throughout the manuscript draft:

Text highlighting colour code for mansucript writing. Blue text references figures, tables, or supplementary information; Yellow text is to be updated/modified; Red text is to be deleted; and Green text needs a reference.

3. Manuscript Format Checklist#

Element	Requirement
Font	Arial 11
Section Titles	Use `HEADING 1` (uppercase)
Subtitles	Use `HEADING 2`
Figures	Created in Miro
Tables	Use Google Docs for small; Sheets or CSV for large
Figure, Table, Supplementary References	Placed in (parentheses) e.g. (Figure x), not "Figure x shows..."
Captions	Start with one bolded sentence summarizing its content. A figure/table caption must be sufficiently detailed to be understood on its own (i.e., without reading the rest of the manuscript).
Supplementary Info	Store in Overleaf (optional, if applicable)
Code & Scripts	Upload to BHK GitHub
Data	Store and run in Code Ocean capsule (optional, if applicable)
References	Use Paperpile

4. Author & Institution Formatting#

List authors under the title with superscript numbers.

Example

Authors:
Sarah Lee², Benjamin Haibe-Kains¹ ³

Affiliations:
¹ Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
² Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
³ Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada

List of common collaborators

  Here is a list of departments and institutions that the BHK lab often collaborates with or works for:

  1. Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.  
  2. Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.  
  3. Joint Department of Medical Imaging, University of Toronto, Toronto, Canada  
  4. Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.  
  5. Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada.

📝 Note

Before making any changes to formatting, structure, or manuscript components, please consult with the project lead and the corresponding author(s). All updates should align with the target journal’s submission guidelines and policies.

📌 Follow these guidelines to ensure fast, focused feedback from Benjamin. Consistency helps everyone involved.