WEBVTT captioned by sachac
NOTE Introduction
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Good morning. I'm Blaine Mooers. I'm an associate
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professor of biochemistry and physiology at the
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University of Oklahoma Health Sciences in Oklahoma City.
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I'm going to be talking about the utilization of Org mode to
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write a specific kind of log file for thinking about writing
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projects, in particular research articles. I have stored a
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template for this file on GitHub. You can find it at Mooers
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Lab. If you go to the landing page and scroll down to
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Emacs-related, you'll find a link to it.
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I am a structural biologist. I utilize X-ray
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crystallography to determine the structures of proteins
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and nucleic acids that are important in human health. Our
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workflow is shown across the top. We start out with a
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purified material that we crystallize as shown by that
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elongated rod-shaped crystal on the left. We will mount
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that in a cold stream and collect diffraction data with
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X-rays in the instrument to the right. That instrument will
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generate an image like the one to the right where you see a
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bunch of spots. That's a diffraction pattern from the
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crystal. After rotating the crystal for one degree, we'll
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rotate the crystal 180 degrees to get a full data set that
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we'll process with a computer. This will lead to the
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chicken-wire map of electron density shown further to the
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right. Then on the far right, we have compared
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electrostructures of two drug molecules from two
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different structures, overlapped after superimposing
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a wild type protein and a mutant protein. We're trying to
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analyze how the mutant was preventing one of the drugs from
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binding. These kind of analyses we can develop that are
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drugs. In this case, the drugs are being used to treat lung
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cancer.
NOTE Starting a new writing project
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When I start a new writing project, I will assign it a number.
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In this case, I'm developing a review article about the
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detection of crystals in images collected with
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microscopes like the image in the upper left.
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The article is about the utilization of AI to help with that
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detection of crystals. I start the name of the folder with
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this index number, and I store the manuscript folders in the
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top level of my home directory to ease navigation.
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Whenever I pop open a terminal window, I just enter 0573, hit
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TAB to autocomplete the name of the folder, and I'll be right
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in the appropriate folder. I also use that index number to
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label the names of the files. I start every project with
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three files: a manuscript, the log file that I'll be talking
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about today, and an annotated bibliography, which is kind
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of like one on steroids. Annotated bibliography for the
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21st century, not the 20th century annotated bibliography
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you worked on as an undergraduate.
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I have developed templates not only for Org Mode, but also
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for other markup languages, like R Markdown and LaTeX. I
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actually developed this
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log file template over a dozen years ago in LaTeX. I also
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have developed it for Typst. Typst is independent of LaTeX.
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It's inspired by LaTeX, but it's written in Rust, and
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it's extremely fast.
NOTE The writing log
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My writing process involves having the writing log at the
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center of the process. That's where I began the writing
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project. On the right, I have the manuscript and all its
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components highlighted in yellow. On the right,
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hopefully I said on the right, I have the manuscript with all
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its components highlighted in yellow. On the left, I have
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the annotated bibliography.
NOTE Starting the research paper
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When I start a research paper, I will do this after I have
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built up a strong idea from various sources, and then I'll
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sit down and go through a series of steps outlined in the
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writing log to develop that central hypothesis into
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several paragraphs that are used in the introduction of the
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manuscript. The rest of the manuscript is built around that
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central hypothesis, so the results section will include
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experiments that address the central hypothesis, and it
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will exclude experiments that have nothing to do with it.
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Likewise, the discussion points address the central
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hypothesis.
NOTE Outline
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When I'm done developing that introduction
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in, say, three or four hours, I'll have an outline in hand. At
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least for the results and discussion section, the outline
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will be detailed down to at least a sub-heading level.
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I'll move those components over to the manuscript on the
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right. As work is done to address that central
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hypothesis, the manuscript will be updated. Also as
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exploration of the literature continues, new ideas will
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flow in to the manuscript through the log file.
NOTE Another kind of writing log - accountability
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You've probably heard of another kind of writing log, which
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is more of an accountability tool, a tool you use to hold
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yourself accountable in terms of your commitment to work on
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your writing projects.
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So, this idea of carrying out this
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documentation is supported by research done by
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Robert Boice. He found that those academics
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who record their writing
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are four times more productive than those that do not.
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Those that actually share their writing with
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colleagues are nine times more productive. This is sort of a
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case in point. This is a snapshot of a Google sheet of such a
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writing log that I was sharing as part of a Google workbook.
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I was sharing it with three other colleagues. I had the
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possibility of them taking a peek at my Google sheet, and that
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possibility I found to be highly motivating.
NOTE Reducing switching costs
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As you can see, on July 24th, 2023, I worked on five different writing
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projects. This would not have been possible if it had not
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been for having five separate writing logs where I could
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figure out where I had started and where I would report the
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day's progress before maybe taking a break and then
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switching to another writing project. The writing log
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helps reduce switching costs between projects.
NOTE Motivation
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My motivation for developing this project-specific log
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that I'm presenting here is to support clearer thinking
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about the science that I'm trying to do, hopefully leading
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to better science, as well as accelerating the completion
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of the writing project. The secondary purpose is to enable
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working on multiple writing projects in parallel. This is
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important to be able to harness your subconscious. If you
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work on project A for a few hours in the morning, say early
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morning, then late morning you work on project B.
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While you're working on project B,
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your subconscious is busy working away on project A.
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As a result, perhaps the following morning,
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when you wake up or while you're taking a shower or
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commuting, new ideas will emerge for projects A and B as a
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result of these background jobs that you have launched. If
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you don't work on project A, then you're not going to get the
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benefit the following morning. The side effects of using
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this writing log are that it reduces the fear of forgetting
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and also reduces the fear of losing momentum. These are two
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barriers to attempting to carry out work on multiple
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writing projects in a given day. This problem of dealing
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with multiple writing projects is one that is not discussed
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in books about writing. It's apparently a very difficult
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problem. I think my writing log is a successful solution to
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that problem.
NOTE Overview of the writing log
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This is an overview of the writing log in Org mode. It has
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various components. I don't have time to go through all of
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them in detail, but you can see its structure. We get this
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summary view when you open up the file. You have this in the
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header for a startup command overview. Then I just click
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on the heading and hit TAB to see the contents below. So
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normally, I'm just going to go straight to the daily log.
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In this case, it starts on line 944.
NOTE LaTeX preamble in opened drawer
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I don't have to scroll all the way down to it,
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because thanks to the support
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for folding of these sections in Org mode, if I open up the
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drawer labeled :PREAMBLE:, you can see that I have imported a
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number of LaTeX packages to enhance the format of the PDF
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file that is upon export.
NOTE Informative header
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I have commands that are listed
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below at the bottom for providing a fancy header. This
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header has the current date as well as a running title and the
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current page number and total number of pages. You can see
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in the center the header at the start of page 2. You can see the
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bottom of page 1 where the page number is at the bottom of the
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page. These headers are very useful if you happen to print
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out several log files and their corresponding manuscripts
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and take them with you to work on them while traveling.
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Invariably, the pages will get intermingled, and you'll have
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to sort them out when you return home. These headers ease
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that problem. You can see that the table of contents that begin
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the writing log is hyperlinked to various sections. In
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addition to the table of contents, the log file, of course,
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will support various graphical objects like images,
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tables, equations, code listings. I also have added
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LaTeX support for an index, a list of acronyms, glossary,
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mathematical notation, and literature cited. It takes no
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effort to add these in, so why not have them available? These
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features are also available in the annotated bibliography
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template, which helps support making that annotated
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bibliography far more relevant and interesting.
NOTE Four workflows
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This shows a list of four workflows that I'm going to
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discuss, since I don't have time to go through each
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of the items. Obviously, project initiation
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occurs on day one. If I have a three- or four-hour block of time,
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that's sufficient to finish project initiation. Then
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the daily workflow is obviously what occurs every day to
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move the project forward. The periodic assessments are
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done on a monthly or weekly basis, generally on the weekly
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basis as the submission deadline approaches. Then
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after you have received the galley proofs and sent them
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back, there are a few chores that need to be done in terms of
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project closeout. This is an example of a protocol
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that could be followed to do that, and an example of the kinds
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of more or less appendix material that could be included in
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the writing log to help get these things done.
NOTE Project initiation workflow
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This shows a project initiation section of the workflow.
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I go through a series of sections that include advice
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about what I need to do to complete each section. The
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rationale section asks me like, why are you doing this? Why
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should you do this? Why not somebody else? Those sort of
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fundamental questions. Then I have
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a drawer labeled guidance that I have,
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and that headline immediately above,
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I have this :noexport: keyword so that guidance is not
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written out upon export to the PDF unless you want it. If you
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want it, you have to remove the :noexport: tag. Then I have the
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response to these questions--in this case, a list of
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journals that I'm targeting for submission of this review
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article. I have a plan B journal picked out in case the
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editors decide to reject it. Having a plan B journal
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picked out is a decision you can make at the time of
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submission, so that you're prepared to move quickly if the
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article is rejected.
NOTE Daily workflow
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This shows the daily workflow section. Each entry has a
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date. I sometimes annotate the dated entries with a small
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phrase to highlight certain events. Within a given entry,
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I'll have a list of accomplishments. That's sort of the bare
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minimum of what I include. This just demonstrates how
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relatively brief these entries are. Just whatever
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distinct accomplishments were made are listed.
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Sometimes I'll include the goals for that day.
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I'll always include the correspondence related to the
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project. I'll copy and paste an email into a quote
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environment from LaTeX.
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I have a snippet template for auto-generating these
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entries. It will insert the date, for example, in the
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subheading. Then below that, I'll have the next action,
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following David Allen's Getting Things Done approach
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where you identify the next thing that needs to be done.
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That may have come from a to-do list that's indicated below that.
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Beyond that, there's sections for some writing
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accountability, and then a reminder to go about updating
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your Zettelkasten and Org-roam if you have come across any
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nuggets of knowledge you want to add to your Org-roam. Then
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below that, there's another section for the storage of
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additions to be made to the manuscript. Maybe they're not
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ready to go yet, so this provides a spot for them to be
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incubated, a sandbox, if you will, where you have room to
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develop them further before they're ready to be
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transferred over to the main manuscript. I also have a
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section there too for the incubation of new ideas for new
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projects.
NOTE Metadata and metacognition
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So this kind of metadata and metacognition about
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the project are often stored in commented out regions or in
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comments, like MS Word documents. These are often stripped
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out in the rush to submit the manuscript, and they're quite
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often lost. Yet they can be invaluable, not only for the
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preparation of future manuscripts, but they can be very
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invaluable for responding to critiques by reviewers. This
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writing log provides ample room for the safe storage of such
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information, such knowledge.
NOTE Periodic assessment workflow
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Then periodically, every several months or weeks,
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we'll carry out an assessment of
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the project. We go through a checklist for the completion of
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the manuscript. We also have a timeline with milestones
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identified.
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Of course, Org has these wonderful tables that are very
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dynamic. If you need a wider column to accommodate a new
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entry, it self-adjusts. These self-adjusting tables
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are one reason why I was attracted to Org mode, because coming
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from LaTex, where trying to make changes to
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tables is quite difficult. Below that, there's a
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section to make assessments. There are four questions that
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I address about the status of the project. One really good
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question is, why can't you submit this project today?
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What's holding it back?
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Other such existential questions
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are important to ask from time to time.
NOTE Project closeout workflow
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Then finally, the project closeout workflow.
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So this is in the form of a checklist.
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This checklist in the main template
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is already included, but you could include it from an
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external file. Of course, that checklist will be only in
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the PDF when it's included in this fashion. It won't be in the
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Org file, but you can view that checklist by clicking on its
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file path. It serves as a link that will open up in an Org
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buffer. The advantage of taking a modular approach to this
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sort of appendix material is that you can update your
00:19:43.000 --> 00:19:46.399
protocols and the updated protocols will be available to
00:19:46.400 --> 00:19:49.639
all log files across all projects.
NOTE Conclusions
00:19:49.640 --> 00:19:56.319
In conclusion, this project-specific log file helps
00:19:56.320 --> 00:20:02.759
narrow the focus on one project. It provides space to harbor
00:20:02.760 --> 00:20:08.679
the thinking about that project, and it helps support the
00:20:08.680 --> 00:20:13.999
project initiation and sustain its momentum and
00:20:14.000 --> 00:20:21.799
facilitate its completion. The side effects of using this
00:20:21.800 --> 00:20:27.399
log file for one project is that it dampens the fear of
00:20:27.400 --> 00:20:31.439
forgetting, the fear of losing momentum, which inhibits us
00:20:31.440 --> 00:20:34.519
working on more than one project in a given day.
NOTE Acknowledgements
00:20:34.520 --> 00:20:42.559
I would like to thank my friends at the Oklahoma Data Science
00:20:42.560 --> 00:20:47.799
Workshop. We hold this workshop every third Friday at noon
00:20:47.800 --> 00:20:53.759
central time by Zoom. It's open to participation by people
00:20:53.760 --> 00:20:56.879
from all around the world. Send me an email if you are
00:20:56.880 --> 00:21:01.519
interested in the applications of computing to scientific
00:21:01.520 --> 00:21:06.799
research. I participate occasionally in these Emacs
00:21:06.800 --> 00:21:11.359
meetups, and I have shared this writing blog with members of
00:21:11.360 --> 00:21:18.719
the UK Research Software Engineer group through the Emacs
00:21:18.720 --> 00:21:24.279
Research Slack channel. My efforts are supported by
00:21:24.280 --> 00:21:28.799
funding from these grants. I'll be happy to take any
00:21:28.800 --> 00:21:37.720
questions.
