Managing writing project metadata with org-mode

Blaine Mooers (he/him) - Pronunciation: Blane Moors, blaine-mooers@ouhsc.edu

The following image shows where the talk is in the schedule for Sat 2024-12-07. Solid lines show talks with Q&A via BigBlueButton. Dashed lines show talks with Q&A via IRC or Etherpad.

Format: 22-min talk; Q&A: BigBlueButton conference room https://media.emacsconf.org/2024/current/bbb-project.html
Discuss on IRC: #emacsconf
Status: Quality check

Description

The planning and writing of a scientific manuscript is an intricate process that requires focused effort. Scientists must make many decisions about what to include and exclude from the paper, often capturing these decisions in notes in the margins, appended notes, or external files. This ad hoc approach becomes unmanageable when the notes exceed the length of the manuscript, which is often the case. Nonetheless, these notes can be vital when responding to reviewers' critiques.

Great scientists like Linus Pauling effectively utilized laboratory notebooks to store metadata on his manuscripts. His cross-referencing system resembled that of Niklas Luhmann in his physical zettelkasten. These paper-based approaches have pros and cons, but they are no longer popular because of the hard work required to make them work well. In comparison, the org-roam-ui view of my zettelkasten provides a garden of endlessly forking paths I can wander in all day.

I sought a more focused approach to managing my attention and the metadata for one writing project. I developed a project-specific writing log for this purpose about a decade ago. The writing log helps me manage anxieties about forgetting where I left off on an interrupted project (Fear of Forgetting, FoF). In this talk, I will highlight the features of my writing log template in org-mode.

The first section supports gathering the initial thoughts about the project needed to assemble a central hypothesis around which to build the paper. Subsections support listing the experiments required to address the central hypothesis and the key discussion points. These subsections include plans for graphical items like images, data plots, tables, equations, and code blocks. Of course, this section will evolve as the results accumulate. When largely completed, this section supports drafting a quarter to a third of a manuscript on day one of the project.

The following two sections support project administration and assessment. The administration section includes plans to apply for funding and approvals for the work. The assessment section supports periodic checks of the project's current state, what holds the manuscript from submission today, and what is missing that makes a larger impact. This section includes a timeline and milestones to finish the project promptly. These can be displayed in tables that org-mode so strongly supports.

The central section of the template contains daily accounts of accomplishments, decisions, and correspondence about the project. I read this section after a hiatus to resume work on the project quickly. An open-ended to-do list and a section for collecting ideas for future projects follow the daily log. The last section contains protocols and guidelines for the various tasks involved in completing the project.

Here, context switching between the writing log and the manuscript is fine because it usually happens only at the beginning and the end of the writing session. My project-specific approach keeps my mind focused on the project at hand and my FoF under control. I share my writing log template in org-mode on GitHub.

About the speaker:

Blaine Mooers is an associate professor of Biochemistry and Physiology at the University of Oklahoma. He uses X-ray diffraction to study the molecular structure of proteins and RNAs important in disease. He writes grant applications, progress reports, manuscripts, lectures, seminars, and talks each year in Emacs. To control his fear of forgetting (FoF), he uses an external document, the writing log, to store metadata about each writing project. He switched from using LaTeX to Org-mode recently. He will discuss the features of the writing log and the joys of editing it in Org-mode.

Questions or comments? Please e-mail blaine-mooers@ouhsc.edu