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+WEBVTT
+
+
+00:00:00.000 --> 00:02:20.079
+Introduction
+
+00:02:20.080 --> 00:04:05.479
+Starting a new writing project
+
+00:04:05.480 --> 00:04:36.959
+The writing log
+
+00:04:36.960 --> 00:05:25.309
+Starting the research paper
+
+00:05:25.310 --> 00:06:11.439
+Outline
+
+00:06:11.440 --> 00:07:17.457
+Another kind of writing log - accountability
+
+00:07:17.458 --> 00:07:46.479
+Reducing switching costs
+
+00:07:46.480 --> 00:09:31.519
+Motivation
+
+00:09:31.520 --> 00:10:17.294
+Overview of the writing log
+
+00:10:17.295 --> 00:10:42.667
+LaTeX preamble in opened drawer
+
+00:10:42.668 --> 00:12:21.399
+Informative header
+
+00:12:21.400 --> 00:13:28.079
+Four workflows
+
+00:13:28.080 --> 00:14:56.959
+Project initiation workflow
+
+00:14:56.960 --> 00:17:05.750
+Daily workflow
+
+00:17:05.751 --> 00:17:48.884
+Metadata and metacognition
+
+00:17:48.885 --> 00:18:56.959
+Periodic assessment workflow
+
+00:18:56.960 --> 00:19:49.639
+Project closeout workflow
+
+00:19:49.640 --> 00:20:34.519
+Conclusions
+
+00:20:34.520 --> 00:21:37.720
+Acknowledgements
diff --git a/2024/captions/emacsconf-2024-project--managing-writing-project-metadata-with-orgmode--blaine-mooers--main.vtt b/2024/captions/emacsconf-2024-project--managing-writing-project-metadata-with-orgmode--blaine-mooers--main.vtt
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+WEBVTT captioned by sachac
+
+NOTE Introduction
+
+00:00:00.000 --> 00:00:09.999
+Good morning. I'm Blaine Mooers. I'm an associate
+
+00:00:10.000 --> 00:00:12.399
+professor of biochemistry and physiology at the
+
+00:00:12.400 --> 00:00:15.079
+University of Oklahoma Health Sciences in Oklahoma City.
+
+00:00:15.080 --> 00:00:21.639
+I'm going to be talking about the utilization of Org mode to
+
+00:00:21.640 --> 00:00:26.799
+write a specific kind of log file for thinking about writing
+
+00:00:26.800 --> 00:00:31.599
+projects, in particular research articles. I have stored a
+
+00:00:31.600 --> 00:00:35.919
+template for this file on GitHub. You can find it at Mooers
+
+00:00:35.920 --> 00:00:40.759
+Lab. If you go to the landing page and scroll down to
+
+00:00:40.760 --> 00:00:47.279
+Emacs-related, you'll find a link to it.
+
+00:00:47.280 --> 00:00:50.679
+I am a structural biologist. I utilize X-ray
+
+00:00:50.680 --> 00:00:53.359
+crystallography to determine the structures of proteins
+
+00:00:53.360 --> 00:00:58.919
+and nucleic acids that are important in human health. Our
+
+00:00:58.920 --> 00:01:01.879
+workflow is shown across the top. We start out with a
+
+00:01:01.880 --> 00:01:04.959
+purified material that we crystallize as shown by that
+
+00:01:04.960 --> 00:01:09.599
+elongated rod-shaped crystal on the left. We will mount
+
+00:01:09.600 --> 00:01:14.959
+that in a cold stream and collect diffraction data with
+
+00:01:14.960 --> 00:01:20.399
+X-rays in the instrument to the right. That instrument will
+
+00:01:20.400 --> 00:01:23.559
+generate an image like the one to the right where you see a
+
+00:01:23.560 --> 00:01:26.319
+bunch of spots. That's a diffraction pattern from the
+
+00:01:26.320 --> 00:01:29.799
+crystal. After rotating the crystal for one degree, we'll
+
+00:01:29.800 --> 00:01:33.079
+rotate the crystal 180 degrees to get a full data set that
+
+00:01:33.080 --> 00:01:37.359
+we'll process with a computer. This will lead to the
+
+00:01:37.360 --> 00:01:43.719
+chicken-wire map of electron density shown further to the
+
+00:01:43.720 --> 00:01:49.999
+right. Then on the far right, we have compared
+
+00:01:50.000 --> 00:01:54.799
+electrostructures of two drug molecules from two
+
+00:01:54.800 --> 00:01:59.399
+different structures, overlapped after superimposing
+
+00:01:59.400 --> 00:02:02.919
+a wild type protein and a mutant protein. We're trying to
+
+00:02:02.920 --> 00:02:05.959
+analyze how the mutant was preventing one of the drugs from
+
+00:02:05.960 --> 00:02:12.199
+binding. These kind of analyses we can develop that are
+
+00:02:12.200 --> 00:02:16.519
+drugs. In this case, the drugs are being used to treat lung
+
+00:02:16.520 --> 00:02:20.079
+cancer.
+
+NOTE Starting a new writing project
+
+00:02:20.080 --> 00:02:24.919
+When I start a new writing project, I will assign it a number.
+
+00:02:24.920 --> 00:02:29.639
+In this case, I'm developing a review article about the
+
+00:02:29.640 --> 00:02:32.479
+detection of crystals in images collected with
+
+00:02:32.480 --> 00:02:33.861
+microscopes like the image in the upper left.
+
+00:02:33.862 --> 00:02:42.639
+The article is about the utilization of AI to help with that
+
+00:02:42.640 --> 00:02:49.039
+detection of crystals. I start the name of the folder with
+
+00:02:49.040 --> 00:02:55.079
+this index number, and I store the manuscript folders in the
+
+00:02:55.080 --> 00:02:59.159
+top level of my home directory to ease navigation.
+
+00:02:59.160 --> 00:03:03.839
+Whenever I pop open a terminal window, I just enter 0573, hit
+
+00:03:03.840 --> 00:03:07.279
+TAB to autocomplete the name of the folder, and I'll be right
+
+00:03:07.280 --> 00:03:11.599
+in the appropriate folder. I also use that index number to
+
+00:03:11.600 --> 00:03:14.879
+label the names of the files. I start every project with
+
+00:03:14.880 --> 00:03:19.519
+three files: a manuscript, the log file that I'll be talking
+
+00:03:19.520 --> 00:03:22.759
+about today, and an annotated bibliography, which is kind
+
+00:03:22.760 --> 00:03:25.999
+of like one on steroids. Annotated bibliography for the
+
+00:03:26.000 --> 00:03:30.759
+21st century, not the 20th century annotated bibliography
+
+00:03:30.760 --> 00:03:37.239
+you worked on as an undergraduate.
+
+00:03:37.240 --> 00:03:40.279
+I have developed templates not only for Org Mode, but also
+
+00:03:40.280 --> 00:03:45.359
+for other markup languages, like R Markdown and LaTeX. I
+
+00:03:45.360 --> 00:03:49.399
+actually developed this
+
+00:03:49.400 --> 00:03:54.839
+log file template over a dozen years ago in LaTeX. I also
+
+00:03:54.840 --> 00:03:58.159
+have developed it for Typst. Typst is independent of LaTeX.
+
+00:03:58.160 --> 00:04:04.079
+It's inspired by LaTeX, but it's written in Rust, and
+
+00:04:04.080 --> 00:04:05.479
+it's extremely fast.
+
+NOTE The writing log
+
+00:04:05.480 --> 00:04:11.799
+My writing process involves having the writing log at the
+
+00:04:11.800 --> 00:04:14.479
+center of the process. That's where I began the writing
+
+00:04:14.480 --> 00:04:19.679
+project. On the right, I have the manuscript and all its
+
+00:04:19.680 --> 00:04:25.839
+components highlighted in yellow. On the right,
+
+00:04:25.840 --> 00:04:29.839
+hopefully I said on the right, I have the manuscript with all
+
+00:04:29.840 --> 00:04:33.199
+its components highlighted in yellow. On the left, I have
+
+00:04:33.200 --> 00:04:36.959
+the annotated bibliography.
+
+NOTE Starting the research paper
+
+00:04:36.960 --> 00:04:42.199
+When I start a research paper, I will do this after I have
+
+00:04:42.200 --> 00:04:49.639
+built up a strong idea from various sources, and then I'll
+
+00:04:49.640 --> 00:04:54.919
+sit down and go through a series of steps outlined in the
+
+00:04:54.920 --> 00:04:59.839
+writing log to develop that central hypothesis into
+
+00:04:59.840 --> 00:05:03.839
+several paragraphs that are used in the introduction of the
+
+00:05:03.840 --> 00:05:08.159
+manuscript. The rest of the manuscript is built around that
+
+00:05:08.160 --> 00:05:11.599
+central hypothesis, so the results section will include
+
+00:05:11.600 --> 00:05:15.799
+experiments that address the central hypothesis, and it
+
+00:05:15.800 --> 00:05:19.479
+will exclude experiments that have nothing to do with it.
+
+00:05:19.480 --> 00:05:22.719
+Likewise, the discussion points address the central
+
+00:05:22.720 --> 00:05:25.309
+hypothesis.
+
+NOTE Outline
+
+00:05:25.310 --> 00:05:27.919
+When I'm done developing that introduction
+
+00:05:27.920 --> 00:05:33.439
+in, say, three or four hours, I'll have an outline in hand. At
+
+00:05:33.440 --> 00:05:38.199
+least for the results and discussion section, the outline
+
+00:05:38.200 --> 00:05:44.199
+will be detailed down to at least a sub-heading level.
+
+00:05:44.200 --> 00:05:47.239
+I'll move those components over to the manuscript on the
+
+00:05:47.240 --> 00:05:53.079
+right. As work is done to address that central
+
+00:05:53.080 --> 00:05:58.119
+hypothesis, the manuscript will be updated. Also as
+
+00:05:58.120 --> 00:06:01.359
+exploration of the literature continues, new ideas will
+
+00:06:01.360 --> 00:06:11.439
+flow in to the manuscript through the log file.
+
+NOTE Another kind of writing log - accountability
+
+00:06:11.440 --> 00:06:13.519
+You've probably heard of another kind of writing log, which
+
+00:06:13.520 --> 00:06:16.719
+is more of an accountability tool, a tool you use to hold
+
+00:06:16.720 --> 00:06:20.599
+yourself accountable in terms of your commitment to work on
+
+00:06:20.600 --> 00:06:24.716
+your writing projects.
+
+00:06:24.717 --> 00:06:28.999
+So, this idea of carrying out this
+
+00:06:29.000 --> 00:06:32.716
+documentation is supported by research done by
+
+00:06:32.717 --> 00:06:35.838
+Robert Boice. He found that those academics
+
+00:06:35.839 --> 00:06:39.100
+who record their writing
+
+00:06:39.101 --> 00:06:42.002
+are four times more productive than those that do not.
+
+00:06:42.003 --> 00:06:44.119
+Those that actually share their writing with
+
+00:06:44.120 --> 00:06:47.719
+colleagues are nine times more productive. This is sort of a
+
+00:06:47.720 --> 00:06:55.479
+case in point. This is a snapshot of a Google sheet of such a
+
+00:06:55.480 --> 00:07:03.279
+writing log that I was sharing as part of a Google workbook.
+
+00:07:03.280 --> 00:07:06.959
+I was sharing it with three other colleagues. I had the
+
+00:07:06.960 --> 00:07:14.319
+possibility of them taking a peek at my Google sheet, and that
+
+00:07:14.320 --> 00:07:17.457
+possibility I found to be highly motivating.
+
+NOTE Reducing switching costs
+
+00:07:17.458 --> 00:07:22.599
+As you can see, on July 24th, 2023, I worked on five different writing
+
+00:07:22.600 --> 00:07:25.959
+projects. This would not have been possible if it had not
+
+00:07:25.960 --> 00:07:29.399
+been for having five separate writing logs where I could
+
+00:07:29.400 --> 00:07:32.759
+figure out where I had started and where I would report the
+
+00:07:32.760 --> 00:07:36.959
+day's progress before maybe taking a break and then
+
+00:07:36.960 --> 00:07:41.199
+switching to another writing project. The writing log
+
+00:07:41.200 --> 00:07:46.479
+helps reduce switching costs between projects.
+
+NOTE Motivation
+
+00:07:46.480 --> 00:07:57.959
+My motivation for developing this project-specific log
+
+00:07:57.960 --> 00:08:02.959
+that I'm presenting here is to support clearer thinking
+
+00:08:02.960 --> 00:08:06.879
+about the science that I'm trying to do, hopefully leading
+
+00:08:06.880 --> 00:08:10.399
+to better science, as well as accelerating the completion
+
+00:08:10.400 --> 00:08:13.439
+of the writing project. The secondary purpose is to enable
+
+00:08:13.440 --> 00:08:17.719
+working on multiple writing projects in parallel. This is
+
+00:08:17.720 --> 00:08:21.799
+important to be able to harness your subconscious. If you
+
+00:08:21.800 --> 00:08:25.919
+work on project A for a few hours in the morning, say early
+
+00:08:25.920 --> 00:08:28.210
+morning, then late morning you work on project B.
+
+00:08:28.211 --> 00:08:33.860
+While you're working on project B,
+
+00:08:33.861 --> 00:08:39.141
+your subconscious is busy working away on project A.
+
+00:08:39.142 --> 00:08:43.479
+As a result, perhaps the following morning,
+
+00:08:43.480 --> 00:08:46.279
+when you wake up or while you're taking a shower or
+
+00:08:46.280 --> 00:08:51.999
+commuting, new ideas will emerge for projects A and B as a
+
+00:08:52.000 --> 00:08:55.239
+result of these background jobs that you have launched. If
+
+00:08:55.240 --> 00:08:58.799
+you don't work on project A, then you're not going to get the
+
+00:08:58.800 --> 00:09:04.319
+benefit the following morning. The side effects of using
+
+00:09:04.320 --> 00:09:07.439
+this writing log are that it reduces the fear of forgetting
+
+00:09:07.440 --> 00:09:10.199
+and also reduces the fear of losing momentum. These are two
+
+00:09:10.200 --> 00:09:14.999
+barriers to attempting to carry out work on multiple
+
+00:09:15.000 --> 00:09:19.239
+writing projects in a given day. This problem of dealing
+
+00:09:19.240 --> 00:09:22.719
+with multiple writing projects is one that is not discussed
+
+00:09:22.720 --> 00:09:26.039
+in books about writing. It's apparently a very difficult
+
+00:09:26.040 --> 00:09:29.759
+problem. I think my writing log is a successful solution to
+
+00:09:29.760 --> 00:09:31.519
+that problem.
+
+NOTE Overview of the writing log
+
+00:09:31.520 --> 00:09:39.919
+This is an overview of the writing log in Org mode. It has
+
+00:09:39.920 --> 00:09:42.959
+various components. I don't have time to go through all of
+
+00:09:42.960 --> 00:09:48.679
+them in detail, but you can see its structure. We get this
+
+00:09:48.680 --> 00:09:54.319
+summary view when you open up the file. You have this in the
+
+00:09:54.320 --> 00:10:04.119
+header for a startup command overview. Then I just click
+
+00:10:04.120 --> 00:10:08.079
+on the heading and hit TAB to see the contents below. So
+
+00:10:08.080 --> 00:10:11.439
+normally, I'm just going to go straight to the daily log.
+
+00:10:11.440 --> 00:10:17.294
+In this case, it starts on line 944.
+
+NOTE LaTeX preamble in opened drawer
+
+00:10:17.295 --> 00:10:19.255
+I don't have to scroll all the way down to it,
+
+00:10:19.256 --> 00:10:21.239
+because thanks to the support
+
+00:10:21.240 --> 00:10:27.319
+for folding of these sections in Org mode, if I open up the
+
+00:10:27.320 --> 00:10:31.319
+drawer labeled :PREAMBLE:, you can see that I have imported a
+
+00:10:31.320 --> 00:10:38.879
+number of LaTeX packages to enhance the format of the PDF
+
+00:10:38.880 --> 00:10:42.667
+file that is upon export.
+
+NOTE Informative header
+
+00:10:42.668 --> 00:10:44.319
+I have commands that are listed
+
+00:10:44.320 --> 00:10:48.999
+below at the bottom for providing a fancy header. This
+
+00:10:49.000 --> 00:10:54.519
+header has the current date as well as a running title and the
+
+00:10:54.520 --> 00:10:58.199
+current page number and total number of pages. You can see
+
+00:10:58.200 --> 00:11:04.199
+in the center the header at the start of page 2. You can see the
+
+00:11:04.200 --> 00:11:09.399
+bottom of page 1 where the page number is at the bottom of the
+
+00:11:09.400 --> 00:11:17.719
+page. These headers are very useful if you happen to print
+
+00:11:17.720 --> 00:11:22.879
+out several log files and their corresponding manuscripts
+
+00:11:22.880 --> 00:11:25.359
+and take them with you to work on them while traveling.
+
+00:11:25.360 --> 00:11:29.439
+Invariably, the pages will get intermingled, and you'll have
+
+00:11:29.440 --> 00:11:33.679
+to sort them out when you return home. These headers ease
+
+00:11:33.680 --> 00:11:39.799
+that problem. You can see that the table of contents that begin
+
+00:11:39.800 --> 00:11:44.759
+the writing log is hyperlinked to various sections. In
+
+00:11:44.760 --> 00:11:48.519
+addition to the table of contents, the log file, of course,
+
+00:11:48.520 --> 00:11:51.559
+will support various graphical objects like images,
+
+00:11:51.560 --> 00:11:56.039
+tables, equations, code listings. I also have added
+
+00:11:56.040 --> 00:12:00.279
+LaTeX support for an index, a list of acronyms, glossary,
+
+00:12:00.280 --> 00:12:04.999
+mathematical notation, and literature cited. It takes no
+
+00:12:05.000 --> 00:12:10.039
+effort to add these in, so why not have them available? These
+
+00:12:10.040 --> 00:12:12.919
+features are also available in the annotated bibliography
+
+00:12:12.920 --> 00:12:16.359
+template, which helps support making that annotated
+
+00:12:16.360 --> 00:12:21.399
+bibliography far more relevant and interesting.
+
+NOTE Four workflows
+
+00:12:21.400 --> 00:12:28.079
+This shows a list of four workflows that I'm going to
+
+00:12:28.080 --> 00:12:32.599
+discuss, since I don't have time to go through each
+
+00:12:32.600 --> 00:12:36.279
+of the items. Obviously, project initiation
+
+00:12:36.280 --> 00:12:39.719
+occurs on day one. If I have a three- or four-hour block of time,
+
+00:12:39.720 --> 00:12:45.759
+that's sufficient to finish project initiation. Then
+
+00:12:45.760 --> 00:12:49.359
+the daily workflow is obviously what occurs every day to
+
+00:12:49.360 --> 00:12:54.239
+move the project forward. The periodic assessments are
+
+00:12:54.240 --> 00:12:57.079
+done on a monthly or weekly basis, generally on the weekly
+
+00:12:57.080 --> 00:13:02.559
+basis as the submission deadline approaches. Then
+
+00:13:02.560 --> 00:13:05.639
+after you have received the galley proofs and sent them
+
+00:13:05.640 --> 00:13:09.839
+back, there are a few chores that need to be done in terms of
+
+00:13:09.840 --> 00:13:13.959
+project closeout. This is an example of a protocol
+
+00:13:13.960 --> 00:13:18.519
+that could be followed to do that, and an example of the kinds
+
+00:13:18.520 --> 00:13:21.799
+of more or less appendix material that could be included in
+
+00:13:21.800 --> 00:13:28.079
+the writing log to help get these things done.
+
+NOTE Project initiation workflow
+
+00:13:28.080 --> 00:13:31.679
+This shows a project initiation section of the workflow.
+
+00:13:31.680 --> 00:13:39.119
+I go through a series of sections that include advice
+
+00:13:39.120 --> 00:13:45.719
+about what I need to do to complete each section. The
+
+00:13:45.720 --> 00:13:50.759
+rationale section asks me like, why are you doing this? Why
+
+00:13:50.760 --> 00:13:54.319
+should you do this? Why not somebody else? Those sort of
+
+00:13:54.320 --> 00:14:01.287
+fundamental questions. Then I have
+
+00:14:01.288 --> 00:14:05.329
+a drawer labeled guidance that I have,
+
+00:14:05.330 --> 00:14:07.190
+and that headline immediately above,
+
+00:14:07.191 --> 00:14:11.839
+I have this :noexport: keyword so that guidance is not
+
+00:14:11.840 --> 00:14:17.039
+written out upon export to the PDF unless you want it. If you
+
+00:14:17.040 --> 00:14:20.439
+want it, you have to remove the :noexport: tag. Then I have the
+
+00:14:20.440 --> 00:14:25.199
+response to these questions--in this case, a list of
+
+00:14:25.200 --> 00:14:29.199
+journals that I'm targeting for submission of this review
+
+00:14:29.200 --> 00:14:32.959
+article. I have a plan B journal picked out in case the
+
+00:14:32.960 --> 00:14:43.399
+editors decide to reject it. Having a plan B journal
+
+00:14:43.400 --> 00:14:47.999
+picked out is a decision you can make at the time of
+
+00:14:48.000 --> 00:14:55.959
+submission, so that you're prepared to move quickly if the
+
+00:14:55.960 --> 00:14:56.959
+article is rejected.
+
+NOTE Daily workflow
+
+00:14:56.960 --> 00:15:04.639
+This shows the daily workflow section. Each entry has a
+
+00:15:04.640 --> 00:15:09.439
+date. I sometimes annotate the dated entries with a small
+
+00:15:09.440 --> 00:15:14.479
+phrase to highlight certain events. Within a given entry,
+
+00:15:14.480 --> 00:15:17.319
+I'll have a list of accomplishments. That's sort of the bare
+
+00:15:17.320 --> 00:15:20.719
+minimum of what I include. This just demonstrates how
+
+00:15:20.720 --> 00:15:25.639
+relatively brief these entries are. Just whatever
+
+00:15:25.640 --> 00:15:30.599
+distinct accomplishments were made are listed.
+
+00:15:30.600 --> 00:15:37.239
+Sometimes I'll include the goals for that day.
+
+00:15:37.240 --> 00:15:40.599
+I'll always include the correspondence related to the
+
+00:15:40.600 --> 00:15:44.439
+project. I'll copy and paste an email into a quote
+
+00:15:44.440 --> 00:15:49.719
+environment from LaTeX.
+
+00:15:49.720 --> 00:15:54.319
+I have a snippet template for auto-generating these
+
+00:15:54.320 --> 00:15:59.919
+entries. It will insert the date, for example, in the
+
+00:15:59.920 --> 00:16:04.239
+subheading. Then below that, I'll have the next action,
+
+00:16:04.240 --> 00:16:06.919
+following David Allen's Getting Things Done approach
+
+00:16:06.920 --> 00:16:08.550
+where you identify the next thing that needs to be done.
+
+00:16:08.551 --> 00:16:14.759
+That may have come from a to-do list that's indicated below that.
+
+00:16:14.760 --> 00:16:19.039
+Beyond that, there's sections for some writing
+
+00:16:19.040 --> 00:16:23.919
+accountability, and then a reminder to go about updating
+
+00:16:23.920 --> 00:16:28.919
+your Zettelkasten and Org-roam if you have come across any
+
+00:16:28.920 --> 00:16:32.359
+nuggets of knowledge you want to add to your Org-roam. Then
+
+00:16:32.360 --> 00:16:38.999
+below that, there's another section for the storage of
+
+00:16:39.000 --> 00:16:42.919
+additions to be made to the manuscript. Maybe they're not
+
+00:16:42.920 --> 00:16:47.599
+ready to go yet, so this provides a spot for them to be
+
+00:16:47.600 --> 00:16:51.599
+incubated, a sandbox, if you will, where you have room to
+
+00:16:51.600 --> 00:16:53.239
+develop them further before they're ready to be
+
+00:16:53.240 --> 00:16:58.399
+transferred over to the main manuscript. I also have a
+
+00:16:58.400 --> 00:17:04.239
+section there too for the incubation of new ideas for new
+
+00:17:04.240 --> 00:17:05.750
+projects.
+
+NOTE Metadata and metacognition
+
+00:17:05.751 --> 00:17:09.639
+So this kind of metadata and metacognition about
+
+00:17:09.640 --> 00:17:13.759
+the project are often stored in commented out regions or in
+
+00:17:13.760 --> 00:17:18.039
+comments, like MS Word documents. These are often stripped
+
+00:17:18.040 --> 00:17:21.839
+out in the rush to submit the manuscript, and they're quite
+
+00:17:21.840 --> 00:17:26.479
+often lost. Yet they can be invaluable, not only for the
+
+00:17:26.480 --> 00:17:30.239
+preparation of future manuscripts, but they can be very
+
+00:17:30.240 --> 00:17:38.279
+invaluable for responding to critiques by reviewers. This
+
+00:17:38.280 --> 00:17:42.839
+writing log provides ample room for the safe storage of such
+
+00:17:42.840 --> 00:17:48.884
+information, such knowledge.
+
+NOTE Periodic assessment workflow
+
+00:17:48.885 --> 00:17:53.666
+Then periodically, every several months or weeks,
+
+00:17:53.667 --> 00:17:55.159
+we'll carry out an assessment of
+
+00:17:55.160 --> 00:18:02.119
+the project. We go through a checklist for the completion of
+
+00:18:02.120 --> 00:18:06.319
+the manuscript. We also have a timeline with milestones
+
+00:18:06.320 --> 00:18:07.439
+identified.
+
+00:18:07.440 --> 00:18:13.759
+Of course, Org has these wonderful tables that are very
+
+00:18:13.760 --> 00:18:18.879
+dynamic. If you need a wider column to accommodate a new
+
+00:18:18.880 --> 00:18:23.359
+entry, it self-adjusts. These self-adjusting tables
+
+00:18:23.360 --> 00:18:29.639
+are one reason why I was attracted to Org mode, because coming
+
+00:18:29.640 --> 00:18:33.039
+from LaTex, where trying to make changes to
+
+00:18:33.040 --> 00:18:36.999
+tables is quite difficult. Below that, there's a
+
+00:18:37.000 --> 00:18:39.639
+section to make assessments. There are four questions that
+
+00:18:39.640 --> 00:18:43.839
+I address about the status of the project. One really good
+
+00:18:43.840 --> 00:18:46.559
+question is, why can't you submit this project today?
+
+00:18:46.560 --> 00:18:49.350
+What's holding it back?
+
+00:18:49.351 --> 00:18:55.214
+Other such existential questions
+
+00:18:55.215 --> 00:18:56.959
+are important to ask from time to time.
+
+NOTE Project closeout workflow
+
+00:18:56.960 --> 00:19:03.633
+Then finally, the project closeout workflow.
+
+00:19:03.634 --> 00:19:06.477
+So this is in the form of a checklist.
+
+00:19:06.478 --> 00:19:09.079
+This checklist in the main template
+
+00:19:09.080 --> 00:19:13.479
+is already included, but you could include it from an
+
+00:19:13.480 --> 00:19:19.959
+external file. Of course, that checklist will be only in
+
+00:19:19.960 --> 00:19:22.799
+the PDF when it's included in this fashion. It won't be in the
+
+00:19:22.800 --> 00:19:27.599
+Org file, but you can view that checklist by clicking on its
+
+00:19:27.600 --> 00:19:32.719
+file path. It serves as a link that will open up in an Org
+
+00:19:32.720 --> 00:19:40.119
+buffer. The advantage of taking a modular approach to this
+
+00:19:40.120 --> 00:19:42.999
+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.