Use this template to store in one document outside of your writing project's main document (e.g., journal article, grant application, book chapter, book, lecture notes, seminar notes, talk notes, poster notes) the data and the thinking behind your writing project. This document is meant to be specific to one project; create a separate document for additional projects. This template addresses the problem of cluttering the writing project document with notes about decisions made and plans for the work. This template provides a safe place for notes that tend to get deleted and lost upon manuscript submission.
Use this writing log in parallel to the main writing project document to support these workflows:
- project ideation and initiation (usually a 3-4 hour work session on day one)
- Data inventory (update as needed)
- Daily log to record decisions made, actions completed or attempted, and correspondence.
- Periodic project assessment against timeline with milestones (once a week, month, or quarter -- whatever is appropriate)
- Project completion and archiving (one to several days at manuscript submission or acceptance or a bit of both)
- Eases restarting a project that has been interrupted.
- Supports working on several projects concurrently.
- Updates the fear of losing momentum.
- Abates the fear of forgetting where you left off.
- Supports the planning of related projects as you make progress on the current project. You will have a running start on the next writing project.
- This is not an extended annotated bibliography to store your thoughts about the literature you read. You can find elsewhere on the site repositories that support the assembly of classical annotated bibliographies. You will also find repositories for templates for modern bibliographies that support multi-paragraph entries illustrated with figures, tables, code listings, equations, and URLs to relevant websites, including videos.
- This is not an accountability tool where you record your minutes spent on words written per day across one or more writing projects. You can find several different approaches to writing accountability on this website and the corresponding tools to support those approaches. You can choose one approach that you think you can use daily. Do not try to use more than one approach at a time. You will exhaust yourself and give up. If you schedule your writing activities and show up at the appointed time, the need for tracking your progress will be diminished when following the writing schedule becomes a deeply ingrained habit.
Org-mode is a rich variant of markdown (see cheatsheet) that can read some LaTeX code directly. The remaining LaTeX code can be used in a code block for LaTeX.
- 20 considerations for planning a manuscript.
- A table of contents that is automatically generated and hyperlinked.
- An automatically generated index that is hyperlinked.
- Support for generating a references cited section from a BibTeX library.
- A writing log section for recording notes about each day's accomplishments.
- Plot of the word count by writing session to track your progress.
- Use org-clock and clock tables to track and summarize your effort.
- A GUIDANCE drawer that stores advice on how to use a section. The drawer is opened by placing the cursor on it and entering the tab.
The writing log is a document that is external to the manuscript. It stores the plans and progress made on one manuscript. It is a tool for enhancing your focus and sustaining forward momentum on the writing project. It is also a tool that eases re-engagement in an interrupted writing project. It is like a master thinking document or a second brain for a writing project.
Instructions for using the writing log are found in the annotations in the template. You can delete these after they are no longer needed.
Version 0.8 of the writing log is divided into these sections:
- project initiation
- project data
- plans to support the project
- timely completion
- daily entries
- future additions and tangents
- Guidelines, checklists, protocols, and helpful tips
The subsections of these sections are shown below.
- Rationale
- Audience
- Target journals
- Related projects
- Potential Introduction
- Potential Results
- Potential Discussion points
- Prior discussion points
- Potential titles
- Potential keywords
- Potential abstract
- Abbreviations
- Potential collaborators
- Potential competitors
- Potential reviewers
- Draft cover letter
- Inventory of data on hand
- Inventory of project's required external software
- Inventory of the project's software repositories
- Relevant videos
- Relevant blogs
- Relevant literature sources
- Relevant collections of PDFs
- Project's progress summary for the annual grant report
- Project's progress summary for the annual report to college
- Budget
- Relation to specific aims of funded grants.
- Secure funding for the research and manuscript.
- Timeline to do the required experiments to test the hypothesis.
- Secure access to required national laboratory resources at experimental stations (i.e., general user proposal and beamtime requests).
- Secure access to computing resources.
- Gather the appropriate information from the literature.
- Recruit collaborators
- Recruit lab members to do the work.
- Individual career development for lab members, including yourself.
- Biosafety.
- Authentication of key biological and chemical resources.
- Rigorous statistical sampling and data analysis
- Data management, including backups and archives.
- Data sharing.
- The NIH PEDP.
- Advertising plan: posters, talks, seminars, YouTube videos, social media posts.
- Checklist for manuscript completion.
- Timeline and Milestones.
- Periodic assessments of the current state of the manuscript.
Create the following yasnippet snippet with the tab trigger of daily to auto-generate a subsection heading, property box, and index key using today's date.
Save it to a file named daily-entry-for-writing-log inside ./snippets/org-mode.
# -*- coding: utf-8 -*-
# group: writing-log
# name: daily-entry-for-writing-log
# key: daily
# --
** `(format-time-string "%Y-%m-%d")`
:PROPERTIES:
:CUSTOM_ID: `(format-time-string "%Y-%m-%d")`
:END:
#+Latex:\index{`(format-time-string "%Y-%m-%d")`}
$0Now type entry followed by tab to start a new subsection for the current day's entry.
- Daily Log
- Update writing progress notebook
- Update personal knowledge base
- Timeline or Benchmarks
- Next action
- To be done
- Word Count
- Ideas to consider adding to the manuscript
- Introduction
- Results
- Discussion
- To be done someday
- Spin-off writing projects
This part of the writing project log may require customization. You may want to include project-specific protocols. You May have already written down your own protocols that you want to include, or the space for such protocols May stimulate you to develop protocols for multi-step processes you must go through in your work. Having those multi-step processes recorded in a protocol and readily accessible in this document increases the probability that the protocol will be followed and that you will save time by avoiding mistakes.
We have made a variant of this writing log where this section is modular. The modularity eases the inclusion and exclusion of various protocols and guidelines so that you can customize this section of the writing log to be most relevant to the writing project at hand. Seek repositories on this website with the words modular and writing log.
Below is a list of protocols you can delete, supplement, or expand upon.
- Daily Protocol
- Tips for using Overleaf
- Protocol for running Grammarly in Overleaf
- Guidelines for debugging the annotated bibliography
- Graphical Abstract
- Guidelines for benchmarks
- Guidelines for using the Writing Progress Notebook
- Guidelines for using a personal knowledge base
- Protocol for wrapping up the project and archiving data.
We store files containing established protocols in the home directory.
These files can be included in all writing-project log files.
This enables updating one file and propagating these updates to all log files.
In an org file, you can use the org-mode #+INCLUDE: or the LaTeX \include{}.
These included files will only be injected into the log file upon export to PDF.
To inject the contents of the external file into an org-mode file so that you see the protocol in the org file, use the following function. It includes the file path of the injected file and a timestamp of when the external file was injected.
(defun org-insert-external-file (file-path)
"Insert the contents of an external file into the current org-mode file.
Prompts for a file path via minibuffer and includes a timestamp in a comment."
(interactive "fFile to be inserted: ")
(let ((timestamp (format-time-string "%Y-%m-%d %H:%M:%S")))
(insert (format "#+BEGIN_COMMENT\n# File %s inserted on %s\n#+END_COMMENT\n\n" file-path timestamp))
(insert-file-contents file-path)
(goto-char (point-max))))
(global-set-key (kbd "C-c S") 'org-insert-external-file)Here is an example of the output.
** Protocol to generate a bib file with only cited references
#+BEGIN_COMMENT
# File ~/protocols-org/bibfileCitedOnly-writing-checklist.org inserted on 2024-12-06 04:16:21
#+END_COMMENT
- [ ] Run the following code to generate a bib file of the papers cited in a manuscript:
- [ ] bibtool --preserve.key.case=on -x main.aux > cited.bib
- [ ] main.tex is the manuscript file.
- [ ] Note that the *main.aux* file is hidden on Overleaf under the "Logs and outputs" pulldown menu.
- [ ] The first flag in the command will preserve the letter case in the cite key.
Here is a modified form of the above function that prepends the file path to the protocols directory:
(defun org-insert-protocol-file (file-path)
"Insert the contents of a protocol file from ~/protocols-org into the current org-mode file.
Prompts for a file path via minibuffer and includes a timestamp in a comment."
(interactive (list (read-file-name "Directory `~/protocols-org/`: " "~/" "protocols-org/")))
(let ((full-path (expand-file-name file-path))
(timestamp (format-time-string "%Y-%m-%d %H:%M:%S")))
(insert (format "#+BEGIN_COMMENT\n# File %s inserted on %s\n#+END_COMMENT\n\n" full-path timestamp))
(insert-file-contents full-path)
(goto-char (point-max))))
(global-set-key (kbd "C-c P") 'org-insert-protocol-file)Disclosure: the last two functions were generated with Lama 3.1 70B via the Sider plugin for Google Chrome. The functions were tested and worked as advertised.
git clone https://github.com/MooersLab/writingLogTemplateInOrginto the folder containing your current writing project.- Start Emacs, perhaps using this Emacs configuration.
- Load the writingLogTemplate.org file into Emacs via
C-x C-f.
You may want to enable yasnippets to make available your latex-mode and org-mode snippets while editing the writinglog.org file in org-mode.
- In your
~/.emacs.d/snippets/latex-mode, create a file named.yas-parents. - Add the following to this file:
latex-mode
org-mode- Under the Yasnippets pulldown, select
reload everythingor in the minibuffer, enterM-x yas-reload-all.
C-gto abort current command.C-x C-cto quit EmacsC-x C-sto save the current document.C-c C-e l oto export to pdflatex and BibTeX and open the resulting PDF in the default PDF viewer.C-x uto undo the last change.M-UPorM-DOWNto shift lines up and down. UP and Down are the arrow keys.C-3 S-tabto collapse the whole document while showing headlines down to the 3rd level. Change the number to collapse to a different level.C-x C-oto show the outline view using consult. This is the same asM-x consult-outline. This consult command collapses the document into a more compact format thanC-s S-tabcommand. It is easier to navigate as a result. You have to install the consult package.
The latex-emacs profile can access org-mode because it is built into Emacs.
The daily log section is the ideal place for running a pomodoro timer.
The daily entries have a property drawer.
Place the cursor or point below the current day's heading and enter C-c o to start a pomodoro with the start and end times logged in a logbook in the property drawer.
At the start of a writing project, use this function to write a copy of the writing log template to a file with the project name in it.
Store this Dash function in the .bashrc or .zshrc file. Oh shoot too
function logorg {
echo "Copy template writing log in org with project number in title."
if [ $# -lt 1 ]; then
echo 1>&2 "$0: not enough arguments"
echo "Usage1: logorg projectID"
return 2
elif [ $# -gt 1 ]; then
echo 1>&2 "$0: too many arguments"
echo "Usage1: logorg projectID"
return 2
fi
projectID="$1"
echo "Write writing log to log$1.org file."
cp ~/6112MooersLabGitHubLabRepos/writingLogTemplateInOrg/writingLogTemplateVer5.org log$1.org
}-
Writing log template in LaTeX (compiles on Overleaf and in Emacs)
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Writing log template in reStructuredText reStructuredText is used by programmers for documentation.
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Writing log template in Markdown Markdown variant. Read and rendered to PDF by most good text editors.
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Writing log template in ODT ODT can be read by Open Office, LibreOffice and MS Word.
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Writing log template in DOCX for MS Word MS Word variant. Probably the least suitable format for this task.
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Slides from talk about GhostText, Data Science Workshop, July 2022
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Video link to talk about GhostText, Data Science Workshop, July 2022
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Slideshow about using LaTeX in Emacs, Berlin Emacs Meetup, 31 August 2022
| Version | Changes | Date |
|---|---|---|
| 0.1 | First working version. | 2022 September 10 |
| 0.5 | Added five sections to catch up with the tex version. | 2024 August 11 |
| 0.6 | Compiles now without init.el file. Moved Daily protocol to Guidelines section. Elevated Daily Log to section level. |
2024 August 18 |
| 0.7 | Moved the comments or advice prose into a GUIDANCE drawer in each section outside of the Guidelines section. | 2024 August 21 |
| 0.7.1 | Added subheading with noexport tag above each GUIDANCE drawer to prevent the export of their contents to the PDF. Added the urlx package to linewrap long URLs. | 2024 August 27 |
| 0.7.2 | Added STARTUP command to open file with the drawers closed. | 2024 September 13 |
| 0.7.3 | Explained introduction to distinguish this tool from writing accountability tools. | 2024 October 30 |
| 0.8.0 | Added :restart: tag to position the cursor at the end of the last daily entry in the Daily Log section upon opening the document in Emac. Made minor updates to the README.md file including link to talk about this document. | 2024 November 28 |
| 0.8.1 | Added function to insert contents of external files. This is very cool! | 2024 December 6 |
- NIH: R01 CA242845
- NIH: R01 AI088011
- NIH: P30 CA225520 (PI: R. Mannel)
- NIH: P20 GM103640 and P30 GM145423 (PI: A. West)