path: root/2024/info/project-after.md

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<div class="transcript transcript-mainVideo"><a name="project-mainVideo-transcript"></a><h1>Transcript</h1>


<div class="transcript-heading">[[!template new="1" text="""Introduction""" start="00:00:00.000" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""Good morning. I'm Blaine Mooers. I'm an associate""" start="00:00:00.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""professor of biochemistry and physiology at the""" start="00:00:10.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""University of Oklahoma Health Sciences in Oklahoma City.""" start="00:00:12.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""I'm going to be talking about the utilization of Org mode to""" start="00:00:15.080" video="mainVideo-project" id="subtitle"]]
[[!template text="""write a specific kind of log file for thinking about writing""" start="00:00:21.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""projects, in particular research articles. I have stored a""" start="00:00:26.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""template for this file on GitHub. You can find it at Mooers""" start="00:00:31.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""Lab. If you go to the landing page and scroll down to""" start="00:00:35.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""Emacs-related, you'll find a link to it.""" start="00:00:40.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""I am a structural biologist. I utilize X-ray""" start="00:00:47.280" video="mainVideo-project" id="subtitle"]]
[[!template text="""crystallography to determine the structures of proteins""" start="00:00:50.680" video="mainVideo-project" id="subtitle"]]
[[!template text="""and nucleic acids that are important in human health. Our""" start="00:00:53.360" video="mainVideo-project" id="subtitle"]]
[[!template text="""workflow is shown across the top. We start out with a""" start="00:00:58.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""purified material that we crystallize as shown by that""" start="00:01:01.880" video="mainVideo-project" id="subtitle"]]
[[!template text="""elongated rod-shaped crystal on the left. We will mount""" start="00:01:04.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""that in a cold stream and collect diffraction data with""" start="00:01:09.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""X-rays in the instrument to the right. That instrument will""" start="00:01:14.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""generate an image like the one to the right where you see a""" start="00:01:20.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""bunch of spots. That's a diffraction pattern from the""" start="00:01:23.560" video="mainVideo-project" id="subtitle"]]
[[!template text="""crystal. After rotating the crystal for one degree, we'll""" start="00:01:26.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""rotate the crystal 180 degrees to get a full data set that""" start="00:01:29.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""we'll process with a computer. This will lead to the""" start="00:01:33.080" video="mainVideo-project" id="subtitle"]]
[[!template text="""chicken-wire map of electron density shown further to the""" start="00:01:37.360" video="mainVideo-project" id="subtitle"]]
[[!template text="""right. Then on the far right, we have compared""" start="00:01:43.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""electrostructures of two drug molecules from two""" start="00:01:50.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""different structures, overlapped after superimposing""" start="00:01:54.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""a wild type protein and a mutant protein. We're trying to""" start="00:01:59.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""analyze how the mutant was preventing one of the drugs from""" start="00:02:02.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""binding. These kind of analyses we can develop that are""" start="00:02:05.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""drugs. In this case, the drugs are being used to treat lung""" start="00:02:12.200" video="mainVideo-project" id="subtitle"]]
[[!template text="""cancer.""" start="00:02:16.520" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Starting a new writing project""" start="00:02:20.080" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""When I start a new writing project, I will assign it a number.""" start="00:02:20.080" video="mainVideo-project" id="subtitle"]]
[[!template text="""In this case, I'm developing a review article about the""" start="00:02:24.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""detection of crystals in images collected with""" start="00:02:29.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""microscopes like the image in the upper left.""" start="00:02:32.480" video="mainVideo-project" id="subtitle"]]
[[!template text="""The article is about the utilization of AI to help with that""" start="00:02:33.862" video="mainVideo-project" id="subtitle"]]
[[!template text="""detection of crystals. I start the name of the folder with""" start="00:02:42.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""this index number, and I store the manuscript folders in the""" start="00:02:49.040" video="mainVideo-project" id="subtitle"]]
[[!template text="""top level of my home directory to ease navigation.""" start="00:02:55.080" video="mainVideo-project" id="subtitle"]]
[[!template text="""Whenever I pop open a terminal window, I just enter 0573, hit""" start="00:02:59.160" video="mainVideo-project" id="subtitle"]]
[[!template text="""TAB to autocomplete the name of the folder, and I'll be right""" start="00:03:03.840" video="mainVideo-project" id="subtitle"]]
[[!template text="""in the appropriate folder. I also use that index number to""" start="00:03:07.280" video="mainVideo-project" id="subtitle"]]
[[!template text="""label the names of the files. I start every project with""" start="00:03:11.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""three files: a manuscript, the log file that I'll be talking""" start="00:03:14.880" video="mainVideo-project" id="subtitle"]]
[[!template text="""about today, and an annotated bibliography, which is kind""" start="00:03:19.520" video="mainVideo-project" id="subtitle"]]
[[!template text="""of like one on steroids. Annotated bibliography for the""" start="00:03:22.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""21st century, not the 20th century annotated bibliography""" start="00:03:26.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""you worked on as an undergraduate.""" start="00:03:30.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""I have developed templates not only for Org Mode, but also""" start="00:03:37.240" video="mainVideo-project" id="subtitle"]]
[[!template text="""for other markup languages, like R Markdown and LaTeX. I""" start="00:03:40.280" video="mainVideo-project" id="subtitle"]]
[[!template text="""actually developed this""" start="00:03:45.360" video="mainVideo-project" id="subtitle"]]
[[!template text="""log file template over a dozen years ago in LaTeX. I also""" start="00:03:49.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""have developed it for Typst. Typst is independent of LaTeX.""" start="00:03:54.840" video="mainVideo-project" id="subtitle"]]
[[!template text="""It's inspired by LaTeX, but it's written in Rust, and""" start="00:03:58.160" video="mainVideo-project" id="subtitle"]]
[[!template text="""it's extremely fast.""" start="00:04:04.080" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""The writing log""" start="00:04:05.480" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""My writing process involves having the writing log at the""" start="00:04:05.480" video="mainVideo-project" id="subtitle"]]
[[!template text="""center of the process. That's where I began the writing""" start="00:04:11.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""project. On the right, I have the manuscript and all its""" start="00:04:14.480" video="mainVideo-project" id="subtitle"]]
[[!template text="""components highlighted in yellow. On the right,""" start="00:04:19.680" video="mainVideo-project" id="subtitle"]]
[[!template text="""hopefully I said on the right, I have the manuscript with all""" start="00:04:25.840" video="mainVideo-project" id="subtitle"]]
[[!template text="""its components highlighted in yellow. On the left, I have""" start="00:04:29.840" video="mainVideo-project" id="subtitle"]]
[[!template text="""the annotated bibliography.""" start="00:04:33.200" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Starting the research paper""" start="00:04:36.960" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""When I start a research paper, I will do this after I have""" start="00:04:36.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""built up a strong idea from various sources, and then I'll""" start="00:04:42.200" video="mainVideo-project" id="subtitle"]]
[[!template text="""sit down and go through a series of steps outlined in the""" start="00:04:49.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""writing log to develop that central hypothesis into""" start="00:04:54.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""several paragraphs that are used in the introduction of the""" start="00:04:59.840" video="mainVideo-project" id="subtitle"]]
[[!template text="""manuscript. The rest of the manuscript is built around that""" start="00:05:03.840" video="mainVideo-project" id="subtitle"]]
[[!template text="""central hypothesis, so the results section will include""" start="00:05:08.160" video="mainVideo-project" id="subtitle"]]
[[!template text="""experiments that address the central hypothesis, and it""" start="00:05:11.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""will exclude experiments that have nothing to do with it.""" start="00:05:15.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""Likewise, the discussion points address the central""" start="00:05:19.480" video="mainVideo-project" id="subtitle"]]
[[!template text="""hypothesis.""" start="00:05:22.720" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Outline""" start="00:05:25.310" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""When I'm done developing that introduction""" start="00:05:25.310" video="mainVideo-project" id="subtitle"]]
[[!template text="""in, say, three or four hours, I'll have an outline in hand. At""" start="00:05:27.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""least for the results and discussion section, the outline""" start="00:05:33.440" video="mainVideo-project" id="subtitle"]]
[[!template text="""will be detailed down to at least a sub-heading level.""" start="00:05:38.200" video="mainVideo-project" id="subtitle"]]
[[!template text="""I'll move those components over to the manuscript on the""" start="00:05:44.200" video="mainVideo-project" id="subtitle"]]
[[!template text="""right. As work is done to address that central""" start="00:05:47.240" video="mainVideo-project" id="subtitle"]]
[[!template text="""hypothesis, the manuscript will be updated. Also as""" start="00:05:53.080" video="mainVideo-project" id="subtitle"]]
[[!template text="""exploration of the literature continues, new ideas will""" start="00:05:58.120" video="mainVideo-project" id="subtitle"]]
[[!template text="""flow in to the manuscript through the log file.""" start="00:06:01.360" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Another kind of writing log - accountability""" start="00:06:11.440" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""You've probably heard of another kind of writing log, which""" start="00:06:11.440" video="mainVideo-project" id="subtitle"]]
[[!template text="""is more of an accountability tool, a tool you use to hold""" start="00:06:13.520" video="mainVideo-project" id="subtitle"]]
[[!template text="""yourself accountable in terms of your commitment to work on""" start="00:06:16.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""your writing projects.""" start="00:06:20.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""So, this idea of carrying out this""" start="00:06:24.717" video="mainVideo-project" id="subtitle"]]
[[!template text="""documentation is supported by research done by""" start="00:06:29.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""Robert Boice. He found that those academics""" start="00:06:32.717" video="mainVideo-project" id="subtitle"]]
[[!template text="""who record their writing""" start="00:06:35.839" video="mainVideo-project" id="subtitle"]]
[[!template text="""are four times more productive than those that do not.""" start="00:06:39.101" video="mainVideo-project" id="subtitle"]]
[[!template text="""Those that actually share their writing with""" start="00:06:42.003" video="mainVideo-project" id="subtitle"]]
[[!template text="""colleagues are nine times more productive. This is sort of a""" start="00:06:44.120" video="mainVideo-project" id="subtitle"]]
[[!template text="""case in point. This is a snapshot of a Google sheet of such a""" start="00:06:47.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""writing log that I was sharing as part of a Google workbook.""" start="00:06:55.480" video="mainVideo-project" id="subtitle"]]
[[!template text="""I was sharing it with three other colleagues. I had the""" start="00:07:03.280" video="mainVideo-project" id="subtitle"]]
[[!template text="""possibility of them taking a peek at my Google sheet, and that""" start="00:07:06.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""possibility I found to be highly motivating.""" start="00:07:14.320" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Reducing switching costs""" start="00:07:17.458" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""As you can see, on July 24th, 2023, I worked on five different writing""" start="00:07:17.458" video="mainVideo-project" id="subtitle"]]
[[!template text="""projects. This would not have been possible if it had not""" start="00:07:22.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""been for having five separate writing logs where I could""" start="00:07:25.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""figure out where I had started and where I would report the""" start="00:07:29.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""day's progress before maybe taking a break and then""" start="00:07:32.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""switching to another writing project. The writing log""" start="00:07:36.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""helps reduce switching costs between projects.""" start="00:07:41.200" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Motivation""" start="00:07:46.480" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""My motivation for developing this project-specific log""" start="00:07:46.480" video="mainVideo-project" id="subtitle"]]
[[!template text="""that I'm presenting here is to support clearer thinking""" start="00:07:57.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""about the science that I'm trying to do, hopefully leading""" start="00:08:02.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""to better science, as well as accelerating the completion""" start="00:08:06.880" video="mainVideo-project" id="subtitle"]]
[[!template text="""of the writing project. The secondary purpose is to enable""" start="00:08:10.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""working on multiple writing projects in parallel. This is""" start="00:08:13.440" video="mainVideo-project" id="subtitle"]]
[[!template text="""important to be able to harness your subconscious. If you""" start="00:08:17.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""work on project A for a few hours in the morning, say early""" start="00:08:21.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""morning, then late morning you work on project B.""" start="00:08:25.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""While you're working on project B,""" start="00:08:28.211" video="mainVideo-project" id="subtitle"]]
[[!template text="""your subconscious is busy working away on project A.""" start="00:08:33.861" video="mainVideo-project" id="subtitle"]]
[[!template text="""As a result, perhaps the following morning,""" start="00:08:39.142" video="mainVideo-project" id="subtitle"]]
[[!template text="""when you wake up or while you're taking a shower or""" start="00:08:43.480" video="mainVideo-project" id="subtitle"]]
[[!template text="""commuting, new ideas will emerge for projects A and B as a""" start="00:08:46.280" video="mainVideo-project" id="subtitle"]]
[[!template text="""result of these background jobs that you have launched. If""" start="00:08:52.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""you don't work on project A, then you're not going to get the""" start="00:08:55.240" video="mainVideo-project" id="subtitle"]]
[[!template text="""benefit the following morning. The side effects of using""" start="00:08:58.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""this writing log are that it reduces the fear of forgetting""" start="00:09:04.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""and also reduces the fear of losing momentum. These are two""" start="00:09:07.440" video="mainVideo-project" id="subtitle"]]
[[!template text="""barriers to attempting to carry out work on multiple""" start="00:09:10.200" video="mainVideo-project" id="subtitle"]]
[[!template text="""writing projects in a given day. This problem of dealing""" start="00:09:15.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""with multiple writing projects is one that is not discussed""" start="00:09:19.240" video="mainVideo-project" id="subtitle"]]
[[!template text="""in books about writing. It's apparently a very difficult""" start="00:09:22.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""problem. I think my writing log is a successful solution to""" start="00:09:26.040" video="mainVideo-project" id="subtitle"]]
[[!template text="""that problem.""" start="00:09:29.760" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Overview of the writing log""" start="00:09:31.520" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""This is an overview of the writing log in Org mode. It has""" start="00:09:31.520" video="mainVideo-project" id="subtitle"]]
[[!template text="""various components. I don't have time to go through all of""" start="00:09:39.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""them in detail, but you can see its structure. We get this""" start="00:09:42.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""summary view when you open up the file. You have this in the""" start="00:09:48.680" video="mainVideo-project" id="subtitle"]]
[[!template text="""header for a startup command overview. Then I just click""" start="00:09:54.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""on the heading and hit TAB to see the contents below. So""" start="00:10:04.120" video="mainVideo-project" id="subtitle"]]
[[!template text="""normally, I'm just going to go straight to the daily log.""" start="00:10:08.080" video="mainVideo-project" id="subtitle"]]
[[!template text="""In this case, it starts on line 944.""" start="00:10:11.440" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""LaTeX preamble in opened drawer""" start="00:10:17.295" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""I don't have to scroll all the way down to it,""" start="00:10:17.295" video="mainVideo-project" id="subtitle"]]
[[!template text="""because thanks to the support""" start="00:10:19.256" video="mainVideo-project" id="subtitle"]]
[[!template text="""for folding of these sections in Org mode, if I open up the""" start="00:10:21.240" video="mainVideo-project" id="subtitle"]]
[[!template text="""drawer labeled :PREAMBLE:, you can see that I have imported a""" start="00:10:27.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""number of LaTeX packages to enhance the format of the PDF""" start="00:10:31.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""file that is upon export.""" start="00:10:38.880" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Informative header""" start="00:10:42.668" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""I have commands that are listed""" start="00:10:42.668" video="mainVideo-project" id="subtitle"]]
[[!template text="""below at the bottom for providing a fancy header. This""" start="00:10:44.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""header has the current date as well as a running title and the""" start="00:10:49.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""current page number and total number of pages. You can see""" start="00:10:54.520" video="mainVideo-project" id="subtitle"]]
[[!template text="""in the center the header at the start of page 2. You can see the""" start="00:10:58.200" video="mainVideo-project" id="subtitle"]]
[[!template text="""bottom of page 1 where the page number is at the bottom of the""" start="00:11:04.200" video="mainVideo-project" id="subtitle"]]
[[!template text="""page. These headers are very useful if you happen to print""" start="00:11:09.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""out several log files and their corresponding manuscripts""" start="00:11:17.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""and take them with you to work on them while traveling.""" start="00:11:22.880" video="mainVideo-project" id="subtitle"]]
[[!template text="""Invariably, the pages will get intermingled, and you'll have""" start="00:11:25.360" video="mainVideo-project" id="subtitle"]]
[[!template text="""to sort them out when you return home. These headers ease""" start="00:11:29.440" video="mainVideo-project" id="subtitle"]]
[[!template text="""that problem. You can see that the table of contents that begin""" start="00:11:33.680" video="mainVideo-project" id="subtitle"]]
[[!template text="""the writing log is hyperlinked to various sections. In""" start="00:11:39.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""addition to the table of contents, the log file, of course,""" start="00:11:44.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""will support various graphical objects like images,""" start="00:11:48.520" video="mainVideo-project" id="subtitle"]]
[[!template text="""tables, equations, code listings. I also have added""" start="00:11:51.560" video="mainVideo-project" id="subtitle"]]
[[!template text="""LaTeX support for an index, a list of acronyms, glossary,""" start="00:11:56.040" video="mainVideo-project" id="subtitle"]]
[[!template text="""mathematical notation, and literature cited. It takes no""" start="00:12:00.280" video="mainVideo-project" id="subtitle"]]
[[!template text="""effort to add these in, so why not have them available? These""" start="00:12:05.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""features are also available in the annotated bibliography""" start="00:12:10.040" video="mainVideo-project" id="subtitle"]]
[[!template text="""template, which helps support making that annotated""" start="00:12:12.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""bibliography far more relevant and interesting.""" start="00:12:16.360" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Four workflows""" start="00:12:21.400" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""This shows a list of four workflows that I'm going to""" start="00:12:21.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""discuss, since I don't have time to go through each""" start="00:12:28.080" video="mainVideo-project" id="subtitle"]]
[[!template text="""of the items. Obviously, project initiation""" start="00:12:32.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""occurs on day one. If I have a three- or four-hour block of time,""" start="00:12:36.280" video="mainVideo-project" id="subtitle"]]
[[!template text="""that's sufficient to finish project initiation. Then""" start="00:12:39.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""the daily workflow is obviously what occurs every day to""" start="00:12:45.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""move the project forward. The periodic assessments are""" start="00:12:49.360" video="mainVideo-project" id="subtitle"]]
[[!template text="""done on a monthly or weekly basis, generally on the weekly""" start="00:12:54.240" video="mainVideo-project" id="subtitle"]]
[[!template text="""basis as the submission deadline approaches. Then""" start="00:12:57.080" video="mainVideo-project" id="subtitle"]]
[[!template text="""after you have received the galley proofs and sent them""" start="00:13:02.560" video="mainVideo-project" id="subtitle"]]
[[!template text="""back, there are a few chores that need to be done in terms of""" start="00:13:05.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""project closeout. This is an example of a protocol""" start="00:13:09.840" video="mainVideo-project" id="subtitle"]]
[[!template text="""that could be followed to do that, and an example of the kinds""" start="00:13:13.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""of more or less appendix material that could be included in""" start="00:13:18.520" video="mainVideo-project" id="subtitle"]]
[[!template text="""the writing log to help get these things done.""" start="00:13:21.800" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Project initiation workflow""" start="00:13:28.080" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""This shows a project initiation section of the workflow.""" start="00:13:28.080" video="mainVideo-project" id="subtitle"]]
[[!template text="""I go through a series of sections that include advice""" start="00:13:31.680" video="mainVideo-project" id="subtitle"]]
[[!template text="""about what I need to do to complete each section. The""" start="00:13:39.120" video="mainVideo-project" id="subtitle"]]
[[!template text="""rationale section asks me like, why are you doing this? Why""" start="00:13:45.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""should you do this? Why not somebody else? Those sort of""" start="00:13:50.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""fundamental questions. Then I have""" start="00:13:54.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""a drawer labeled guidance that I have,""" start="00:14:01.288" video="mainVideo-project" id="subtitle"]]
[[!template text="""and that headline immediately above,""" start="00:14:05.330" video="mainVideo-project" id="subtitle"]]
[[!template text="""I have this :noexport: keyword so that guidance is not""" start="00:14:07.191" video="mainVideo-project" id="subtitle"]]
[[!template text="""written out upon export to the PDF unless you want it. If you""" start="00:14:11.840" video="mainVideo-project" id="subtitle"]]
[[!template text="""want it, you have to remove the :noexport: tag. Then I have the""" start="00:14:17.040" video="mainVideo-project" id="subtitle"]]
[[!template text="""response to these questions--in this case, a list of""" start="00:14:20.440" video="mainVideo-project" id="subtitle"]]
[[!template text="""journals that I'm targeting for submission of this review""" start="00:14:25.200" video="mainVideo-project" id="subtitle"]]
[[!template text="""article. I have a plan B journal picked out in case the""" start="00:14:29.200" video="mainVideo-project" id="subtitle"]]
[[!template text="""editors decide to reject it. Having a plan B journal""" start="00:14:32.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""picked out is a decision you can make at the time of""" start="00:14:43.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""submission, so that you're prepared to move quickly if the""" start="00:14:48.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""article is rejected.""" start="00:14:55.960" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Daily workflow""" start="00:14:56.960" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""This shows the daily workflow section. Each entry has a""" start="00:14:56.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""date. I sometimes annotate the dated entries with a small""" start="00:15:04.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""phrase to highlight certain events. Within a given entry,""" start="00:15:09.440" video="mainVideo-project" id="subtitle"]]
[[!template text="""I'll have a list of accomplishments. That's sort of the bare""" start="00:15:14.480" video="mainVideo-project" id="subtitle"]]
[[!template text="""minimum of what I include. This just demonstrates how""" start="00:15:17.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""relatively brief these entries are. Just whatever""" start="00:15:20.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""distinct accomplishments were made are listed.""" start="00:15:25.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""Sometimes I'll include the goals for that day.""" start="00:15:30.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""I'll always include the correspondence related to the""" start="00:15:37.240" video="mainVideo-project" id="subtitle"]]
[[!template text="""project. I'll copy and paste an email into a quote""" start="00:15:40.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""environment from LaTeX.""" start="00:15:44.440" video="mainVideo-project" id="subtitle"]]
[[!template text="""I have a snippet template for auto-generating these""" start="00:15:49.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""entries. It will insert the date, for example, in the""" start="00:15:54.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""subheading. Then below that, I'll have the next action,""" start="00:15:59.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""following David Allen's Getting Things Done approach""" start="00:16:04.240" video="mainVideo-project" id="subtitle"]]
[[!template text="""where you identify the next thing that needs to be done.""" start="00:16:06.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""That may have come from a to-do list that's indicated below that.""" start="00:16:08.551" video="mainVideo-project" id="subtitle"]]
[[!template text="""Beyond that, there's sections for some writing""" start="00:16:14.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""accountability, and then a reminder to go about updating""" start="00:16:19.040" video="mainVideo-project" id="subtitle"]]
[[!template text="""your Zettelkasten and Org-roam if you have come across any""" start="00:16:23.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""nuggets of knowledge you want to add to your Org-roam. Then""" start="00:16:28.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""below that, there's another section for the storage of""" start="00:16:32.360" video="mainVideo-project" id="subtitle"]]
[[!template text="""additions to be made to the manuscript. Maybe they're not""" start="00:16:39.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""ready to go yet, so this provides a spot for them to be""" start="00:16:42.920" video="mainVideo-project" id="subtitle"]]
[[!template text="""incubated, a sandbox, if you will, where you have room to""" start="00:16:47.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""develop them further before they're ready to be""" start="00:16:51.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""transferred over to the main manuscript. I also have a""" start="00:16:53.240" video="mainVideo-project" id="subtitle"]]
[[!template text="""section there too for the incubation of new ideas for new""" start="00:16:58.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""projects.""" start="00:17:04.240" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Metadata and metacognition""" start="00:17:05.751" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""So this kind of metadata and metacognition about""" start="00:17:05.751" video="mainVideo-project" id="subtitle"]]
[[!template text="""the project are often stored in commented out regions or in""" start="00:17:09.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""comments, like MS Word documents. These are often stripped""" start="00:17:13.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""out in the rush to submit the manuscript, and they're quite""" start="00:17:18.040" video="mainVideo-project" id="subtitle"]]
[[!template text="""often lost. Yet they can be invaluable, not only for the""" start="00:17:21.840" video="mainVideo-project" id="subtitle"]]
[[!template text="""preparation of future manuscripts, but they can be very""" start="00:17:26.480" video="mainVideo-project" id="subtitle"]]
[[!template text="""invaluable for responding to critiques by reviewers. This""" start="00:17:30.240" video="mainVideo-project" id="subtitle"]]
[[!template text="""writing log provides ample room for the safe storage of such""" start="00:17:38.280" video="mainVideo-project" id="subtitle"]]
[[!template text="""information, such knowledge.""" start="00:17:42.840" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Periodic assessment workflow""" start="00:17:48.885" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""Then periodically, every several months or weeks,""" start="00:17:48.885" video="mainVideo-project" id="subtitle"]]
[[!template text="""we'll carry out an assessment of""" start="00:17:53.667" video="mainVideo-project" id="subtitle"]]
[[!template text="""the project. We go through a checklist for the completion of""" start="00:17:55.160" video="mainVideo-project" id="subtitle"]]
[[!template text="""the manuscript. We also have a timeline with milestones""" start="00:18:02.120" video="mainVideo-project" id="subtitle"]]
[[!template text="""identified.""" start="00:18:06.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""Of course, Org has these wonderful tables that are very""" start="00:18:07.440" video="mainVideo-project" id="subtitle"]]
[[!template text="""dynamic. If you need a wider column to accommodate a new""" start="00:18:13.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""entry, it self-adjusts. These self-adjusting tables""" start="00:18:18.880" video="mainVideo-project" id="subtitle"]]
[[!template text="""are one reason why I was attracted to Org mode, because coming""" start="00:18:23.360" video="mainVideo-project" id="subtitle"]]
[[!template text="""from LaTex, where trying to make changes to""" start="00:18:29.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""tables is quite difficult. Below that, there's a""" start="00:18:33.040" video="mainVideo-project" id="subtitle"]]
[[!template text="""section to make assessments. There are four questions that""" start="00:18:37.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""I address about the status of the project. One really good""" start="00:18:39.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""question is, why can't you submit this project today?""" start="00:18:43.840" video="mainVideo-project" id="subtitle"]]
[[!template text="""What's holding it back?""" start="00:18:46.560" video="mainVideo-project" id="subtitle"]]
[[!template text="""Other such existential questions""" start="00:18:49.351" video="mainVideo-project" id="subtitle"]]
[[!template text="""are important to ask from time to time.""" start="00:18:55.215" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Project closeout workflow""" start="00:18:56.960" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""Then finally, the project closeout workflow.""" start="00:18:56.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""So this is in the form of a checklist.""" start="00:19:03.634" video="mainVideo-project" id="subtitle"]]
[[!template text="""This checklist in the main template""" start="00:19:06.478" video="mainVideo-project" id="subtitle"]]
[[!template text="""is already included, but you could include it from an""" start="00:19:09.080" video="mainVideo-project" id="subtitle"]]
[[!template text="""external file. Of course, that checklist will be only in""" start="00:19:13.480" video="mainVideo-project" id="subtitle"]]
[[!template text="""the PDF when it's included in this fashion. It won't be in the""" start="00:19:19.960" video="mainVideo-project" id="subtitle"]]
[[!template text="""Org file, but you can view that checklist by clicking on its""" start="00:19:22.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""file path. It serves as a link that will open up in an Org""" start="00:19:27.600" video="mainVideo-project" id="subtitle"]]
[[!template text="""buffer. The advantage of taking a modular approach to this""" start="00:19:32.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""sort of appendix material is that you can update your""" start="00:19:40.120" video="mainVideo-project" id="subtitle"]]
[[!template text="""protocols and the updated protocols will be available to""" start="00:19:43.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""all log files across all projects.""" start="00:19:46.400" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Conclusions""" start="00:19:49.640" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""In conclusion, this project-specific log file helps""" start="00:19:49.640" video="mainVideo-project" id="subtitle"]]
[[!template text="""narrow the focus on one project. It provides space to harbor""" start="00:19:56.320" video="mainVideo-project" id="subtitle"]]
[[!template text="""the thinking about that project, and it helps support the""" start="00:20:02.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""project initiation and sustain its momentum and""" start="00:20:08.680" video="mainVideo-project" id="subtitle"]]
[[!template text="""facilitate its completion. The side effects of using this""" start="00:20:14.000" video="mainVideo-project" id="subtitle"]]
[[!template text="""log file for one project is that it dampens the fear of""" start="00:20:21.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""forgetting, the fear of losing momentum, which inhibits us""" start="00:20:27.400" video="mainVideo-project" id="subtitle"]]
[[!template text="""working on more than one project in a given day.""" start="00:20:31.440" video="mainVideo-project" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Acknowledgements""" start="00:20:34.520" video="mainVideo-project" id="subtitle"]]</div>[[!template text="""I would like to thank my friends at the Oklahoma Data Science""" start="00:20:34.520" video="mainVideo-project" id="subtitle"]]
[[!template text="""Workshop. We hold this workshop every third Friday at noon""" start="00:20:42.560" video="mainVideo-project" id="subtitle"]]
[[!template text="""central time by Zoom. It's open to participation by people""" start="00:20:47.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""from all around the world. Send me an email if you are""" start="00:20:53.760" video="mainVideo-project" id="subtitle"]]
[[!template text="""interested in the applications of computing to scientific""" start="00:20:56.880" video="mainVideo-project" id="subtitle"]]
[[!template text="""research. I participate occasionally in these Emacs""" start="00:21:01.520" video="mainVideo-project" id="subtitle"]]
[[!template text="""meetups, and I have shared this writing blog with members of""" start="00:21:06.800" video="mainVideo-project" id="subtitle"]]
[[!template text="""the UK Research Software Engineer group through the Emacs""" start="00:21:11.360" video="mainVideo-project" id="subtitle"]]
[[!template text="""Research Slack channel. My efforts are supported by""" start="00:21:18.720" video="mainVideo-project" id="subtitle"]]
[[!template text="""funding from these grants. I'll be happy to take any""" start="00:21:24.280" video="mainVideo-project" id="subtitle"]]
[[!template text="""questions.""" start="00:21:28.800" video="mainVideo-project" id="subtitle"]]

</div>

Captioner: sachac

Questions or comments? Please e-mail [blaine-mooers@ouhsc.edu](mailto:blaine-mooers@ouhsc.edu?subject=Comment%20for%20EmacsConf%202023%20project%3A%20Managing%20writing%20project%20metadata%20with%20org-mode)


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