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diff --git a/2024/info/project-after.md b/2024/info/project-after.md index eca2de19..c85fa07b 100644 --- a/2024/info/project-after.md +++ b/2024/info/project-after.md @@ -1,13 +1,10 @@ <!-- Automatically generated by emacsconf-publish-after-page --> -<div class="transcript transcript-mainVideo"><a name="project-mainVideo-transcript"></a> -# Transcript +<div class="transcript transcript-mainVideo"><a name="project-mainVideo-transcript"></a><h1>Transcript</h1> -[[!template new="1" text="""Introduction""" start="00:00:00.000" video="mainVideo-project" id="subtitle"]] - -[[!template text="""Good morning. I'm Blaine Mooers. I'm an associate""" start="00:00:00.000" video="mainVideo-project" id="subtitle"]] +<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"]] @@ -39,9 +36,7 @@ [[!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"]] -[[!template new="1" text="""Starting a new writing project""" start="00:02:20.080" video="mainVideo-project" id="subtitle"]] - -[[!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"]] +<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"]] @@ -66,9 +61,7 @@ [[!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"]] -[[!template new="1" text="""The writing log""" start="00:04:05.480" video="mainVideo-project" id="subtitle"]] - -[[!template text="""My writing process involves having the writing log at the""" start="00:04:05.480" 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"]] @@ -76,9 +69,7 @@ [[!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"]] -[[!template new="1" text="""Starting the research paper""" start="00:04:36.960" video="mainVideo-project" id="subtitle"]] - -[[!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"]] +<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"]] @@ -90,9 +81,7 @@ [[!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"]] -[[!template new="1" text="""Outline""" start="00:05:25.310" video="mainVideo-project" id="subtitle"]] - -[[!template text="""When I'm done developing that introduction""" start="00:05:25.310" 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"]] @@ -102,9 +91,7 @@ [[!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"]] -[[!template new="1" text="""Another kind of writing log - accountability""" start="00:06:11.440" video="mainVideo-project" id="subtitle"]] - -[[!template text="""You've probably heard of another kind of writing log, which""" start="00:06:11.440" 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"]] @@ -121,9 +108,7 @@ [[!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"]] -[[!template new="1" text="""Reducing switching costs""" start="00:07:17.458" video="mainVideo-project" id="subtitle"]] - -[[!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"]] +<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"]] @@ -131,9 +116,7 @@ [[!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"]] -[[!template new="1" text="""Motivation""" start="00:07:46.480" video="mainVideo-project" id="subtitle"]] - -[[!template text="""My motivation for developing this project-specific log""" start="00:07:46.480" 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"]] @@ -159,9 +142,7 @@ [[!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"]] -[[!template new="1" text="""Overview of the writing log""" start="00:09:31.520" video="mainVideo-project" id="subtitle"]] - -[[!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"]] +<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"]] @@ -170,18 +151,14 @@ [[!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"]] -[[!template new="1" text="""LaTeX preamble in opened drawer""" start="00:10:17.295" video="mainVideo-project" id="subtitle"]] - -[[!template text="""I don't have to scroll all the way down to it,""" start="00:10:17.295" 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"]] -[[!template new="1" text="""Informative header""" start="00:10:42.668" video="mainVideo-project" id="subtitle"]] - -[[!template text="""I have commands that are listed""" start="00:10:42.668" 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"]] @@ -204,9 +181,7 @@ [[!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"]] -[[!template new="1" text="""Four workflows""" start="00:12:21.400" video="mainVideo-project" id="subtitle"]] - -[[!template text="""This shows a list of four workflows that I'm going to""" start="00:12:21.400" 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"]] @@ -222,9 +197,7 @@ [[!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"]] -[[!template new="1" text="""Project initiation workflow""" start="00:13:28.080" video="mainVideo-project" id="subtitle"]] - -[[!template text="""This shows a project initiation section of the workflow.""" start="00:13:28.080" 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"]] @@ -243,9 +216,7 @@ [[!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"]] -[[!template new="1" text="""Daily workflow""" start="00:14:56.960" video="mainVideo-project" id="subtitle"]] - -[[!template text="""This shows the daily workflow section. Each entry has a""" start="00:14:56.960" 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"]] @@ -275,9 +246,7 @@ [[!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"]] -[[!template new="1" text="""Metadata and metacognition""" start="00:17:05.751" video="mainVideo-project" id="subtitle"]] - -[[!template text="""So this kind of metadata and metacognition about""" start="00:17:05.751" 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"]] @@ -287,9 +256,7 @@ [[!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"]] -[[!template new="1" text="""Periodic assessment workflow""" start="00:17:48.885" video="mainVideo-project" id="subtitle"]] - -[[!template text="""Then periodically, every several months or weeks,""" start="00:17:48.885" 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"]] @@ -307,9 +274,7 @@ [[!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"]] -[[!template new="1" text="""Project closeout workflow""" start="00:18:56.960" video="mainVideo-project" id="subtitle"]] - -[[!template text="""Then finally, the project closeout workflow.""" start="00:18:56.960" 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"]] @@ -322,9 +287,7 @@ [[!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"]] -[[!template new="1" text="""Conclusions""" start="00:19:49.640" video="mainVideo-project" id="subtitle"]] - -[[!template text="""In conclusion, this project-specific log file helps""" start="00:19:49.640" 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"]] @@ -333,9 +296,7 @@ [[!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"]] -[[!template new="1" text="""Acknowledgements""" start="00:20:34.520" video="mainVideo-project" id="subtitle"]] - -[[!template text="""I would like to thank my friends at the Oklahoma Data Science""" start="00:20:34.520" 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"]] |