gypsum

2 files changed, 285 insertions, 0 deletions

diff --git a/2024/talks/gypsum.md b/2024/talks/gypsum.md
index f1d6aecd..a76afb02 100644
--- a/2024/talks/gypsum.md
+++ b/2024/talks/gypsum.md
@@ -362,6 +362,68 @@ professionally.
 You may also like another talk by this speaker:
 [EmacsConf - 2022 - talks - Build a Zettelkasten with the Hyperbole Rolodex](https://emacsconf.org/2022/talks/rolodex/)
 
+# Discussion
+
+## Questions and answers
+
+-   Q: Would it be possible to support a GUI toolkit other than GTK? Like how GNU Emacs still supports Lucid
+    -   A: Yes this planed by having proper backend: emacs-lisp running
+        into a module and the GUI being another module. So normalized
+        communication. Currently GTK being standard implementation, also
+        done here.
+-   Q: Do you plan to provide improvements to Elisp as a language, or is the focus on a compatibility layer to facilitate doing all new extensions, etc. in Scheme?
+    -   A: Plan is to keep up-to-date with new releases. So new GNU
+        feature should be included with each release. But also intend to
+        have support for pure Scheme features.
+-   Q: \<janneke\> If Emacs Lisp support for Guile was documented
+    better, could you be nudged/convinced to (re)start using, and
+    contributing to that?
+    -   A: Compatibility is the most important things. Documentation not
+        sufficient to convince users to switch.
+-   Q: Why is being able to interpret all of \`init.el\` an useful goal?
+    Sure, there is a lot of code written in elisp - can we consider a
+    translator like utility to convert elisp to scheme, once guile-emacs
+    becomes a reality? 
+    -   A: Probably, but first step is getting the interpretter working.
+        Emacs-lisp basically compiled down to intermediate
+        representation of the guile compiler \[this was one of the hard
+        things to get to work\]. But unclear how this works for other
+        schemes. Best solution probably translation elisp -\> scheme,
+        but this is not the approach that was done. Would be very cool
+        to have. Feel free to give a PR.
+-   Q: What is the plan to handle elisp packages that depend on 3rd party/external libraries? (libgit/magit or rg/ripgrep)? 
+    -   A: Will be tricky. If loading directly into the elisp process,
+        very hard. Cairo could help, but you need emacs lisp binding on
+        top of that. For magit, you can call regular process
+        communication via stdin/stdout; so you can reuse existing scheme
+        libraries. Dynamic libraries not a goal. Rg/ripgrep probably the
+        same with process communication.
+-   Q: \<xlarsx\`\> Why is it not feasible for the Emacs layer that interprets Emacs Lisp (the core in C) ot have a Scheme interpreter, instead of using Guile?
+    -   A: \<gringo\> Guile is a scheme. Not sure what you mean.
+    -   A: Check presentation later of Robin Templeton (\"Beguiling
+        Emacs: Guile-Emacs relaunched!\"): the attempt exists by
+        translating elisp to guile. 
+        -   thank you
+
+- Q: Not really a question, but how about Schemacs as a name?
+
+-   -   A: Cool name, but did not check if it is already used. Feel free
+        to discuss by email.
+-   Q: \<gringo\> I'm curious to know how the hell guile-emacs deals with all of the dynamically scoped modules out there. Is there any effort to automatically modularize and namespace stuff?
+
+## Notes
+
+-   \<robin\> oo neat, i didn\'t know about that first bit of history
+-   \<janneke\> i\'ve heard rms say that scheme (guile) is just a nicer
+    lisp; but didn\'t know there were concrete talks/attempts to use
+    guile for emacs that early
+-   \<tusharhero\> Q: Not really a question, but how about Schemacs as a
+    name?
+-   \<janneke\> robin: yes, guile-elisp not being portable might be a
+    showstopper
+-                       for ramin
+
+
 [[!inline pages="internal(2024/info/gypsum-after)" raw="yes"]]
 
 [[!inline pages="internal(2024/info/gypsum-nav)" raw="yes"]]
diff --git a/2024/talks/project.md b/2024/talks/project.md
index 65c33ac1..84f2959a 100644
--- a/2024/talks/project.md
+++ b/2024/talks/project.md
@@ -56,6 +56,229 @@ He switched from using LaTeX to Org-mode recently.
 He will discuss the features of the writing log and the joys of editing it in Org-mode.
 
 
+# Discussion
+
+## Questions and answers
+
+-   Q: what does 0573 means in your init. file name?
+    -   A: Index number used to \"name\"/ describe a project.  My
+        project folders in my home directory are of the format
+        ####stubOfTheProjectsFullName. Maybe i will describe my project
+        numbering system in a future talk. It helps enormously in
+        navigating between projects and stayting organized. I store the
+        project ID number and the folder name in a sqlite database that
+        I pop open with a bash alias to the DB Browser for SQlite. I
+        also use the Project ID to track time spent on each project to
+        the nearest 15 minues increment. I do this time tracking once
+        every several hours 2-4 times a day. If I cannot remember what I
+        was doing, nothing is recorded. This is important for keeping
+        the data accurate. This practive is a pain but the data are
+        valuable for self-assessments and annual reports.
+-   Q: \<gringo\> What does Zettelkasten mean?
+    -   A: \<vidianos\> It\'s a notetaking method \<Neil\>Useful
+        overview at
+        [https://zettelkasten.de/introduction/](https://zettelkasten.de/introduction/){rel="noreferrer noopener"}
+    -   A: Pls cf.
+        [https://en.wikipedia.org/wiki/Zettelkasten](https://en.wikipedia.org/wiki/Zettelkasten){rel="noreferrer noopener"}
+        An augmented org-roam is found in the zetteldesk.el project by
+        Vidianos
+        [https://github.com/Vidianos-Giannitsis/zetteldesk.el](https://github.com/Vidianos-Giannitsis/zetteldesk.el){rel="noreferrer noopener"}.
+        See  his talk from EmacsConf 2022: 
+        [https://www.youtube.com/watch?v=dJ859kiFRLg&t=0s](https://www.youtube.com/watch?v=dJ859kiFRLg&t=0s){rel="noreferrer noopener"}
+    -   A: A great resource is Sönke Ahrens\'s \"How to Take Smart
+        Notes\" (to get you thinking about the progressive evolution of
+        your note taking; and a solid walk through of Zettlekasten in
+        practice/implementation) . There also is a German edition of the
+        book, it\'s called: \"Das Zettelkasten-Prinzip\". The book
+        \"Antinet Zettelkasten\" by Scott Scheper clarifies several
+        misconceptions about the Zettelkasten Method (see chapter 3). He
+        spent months replicating the analog version that Luhman used and
+        gained a number of important insights. I have seen the method
+        applied in ways that were never intended. I think that these
+        vairant approaches are innovative and can enhance productivity,
+        but they can cause some confusion. The ultimate source is the
+        [https://niklas-luhmann-archiv.de/](https://niklas-luhmann-archiv.de/){rel="noreferrer noopener"}.
+    -   Smart notes are linked to one another. They make up a kind of
+        hypertext, similar to a wiki, as a whole.
+    -   Org-Roam and Denote are two implementations that can support the
+        slipcase; backlinks are important (and also/perhaps a
+        consideration of the hierarchy)
+-   Q: How many papers are you writing at the same time?
+    -   A: Working on 10--15/y, publishing 1--8/y
+    -   On a given day, 2 papers/day usually, sometimes up to 5
+        papers/day
+-   Q: How you capture those ideas when when you are away from Emacs?+3
+    -   A: Digital recorder for recording thoughts, especially during
+        daily commute. I also mentioned caputing thoughts in
+        750words.com. I was an early user (May 2012) and was
+        grandfathered in with a free subscription for life. This is why
+        I am reluctant to give it up. I started learning to use Emacs
+        in 2000. I have not yet moved all of my workflow to Emacs, but I
+        am getting there. The other site that I use when I exceed the
+        5000 word limit at 750words.com is WriteHoney
+        [https://app.writehoney.com/write](https://app.writehoney.com/write){rel="noreferrer noopener"}.
+    -   Whisper AI to transcribe the recordings. See this site for the
+        post transcription scripts that I apply to clean up the text
+        before I see the trasncript:
+        [https://github.com/MooersLab/bash-whisper-transcription](https://github.com/MooersLab/bash-whisper-transcription){rel="noreferrer noopener"}.
+        I also jot down notes but not so much after I started using the
+        digitial voice recorder (DVR). Dragging the audo file to the
+        folder where I do the transcriptions does take a wee bit of time
+        so I try to be judicious about selecting when I turn on the DVR.
+        I should probably write a Elisp function to transcribe the audio
+        recording from the DVR, save the transcript, and delete the
+        audio recording so that I can streamline this process. There is
+        alawys a way to do things more efficiently with Emacs!
+		- sachac: oooh, I can recommend getting an inexpensive lapel mic if you don't already have one. I'm also experimenting with using keywords to organize my audio braindumps.	
+-   Q: What if an ideas does not belong to any current working manuscript?
+    -   A: Sandbox area in a log file. The Sandbox area is called
+        \"Future additions and tangents\" in the template log file and
+        is also used to draft sections of the paper that I am uncertain
+        that I will retain.
+    -   If not related, kept in an external diary
+-   Q: It looks like you have daily log per project, what do you think
+    about just using single daily notes and cross referencing different
+    projects?
+    -   A: I have \> 800 projects per year in 10 categories. Several
+        years ago, I made org files for each category with 1000
+        headlines, but this proved to be too unwieldy for me at the time
+        as a noivice org-mode user. The log files for the manuscript
+        projects wind up with 50-100 pages of content each so the
+        single-threaded nature of Emacs hampers scrolling through such
+        huge org files. In addition, I want to keep all other projects
+        out of sight and mind while focused on the project at hand.
+-   Q: \<gringo\> If there were one habit from your process (referencing your extensive flow chart) that you want active learners/professional researchers to adopt, which would it be and why?
+    -   Keeping a daily diary is essential for overcoming the fears of
+        forgetting and losing momentum. These fears are the maiin
+        barriers to switching between projects on a given day. The
+        in-grained preference is to do binge writing, which I still
+        succumb to doing sometimes, but I am trying to avoid binge
+        writing with this system.
+-   Q: \<gs-101\> I see that you use checkboxes for tasks. Did you know
+    you can format headings to support tracking them? Like this: TODO
+    Heading \[0/4\]
+    -   A: Yes, I convert some of my most important todo items into
+        \*\*\* TODO headline to be picked up by arg agenda. I add the
+        writing-project log file to the list of org files that org
+        agenda searches. I use a Elisp function to add new \*\*\*TODO
+        items to the list when they come to mind. I will post this
+        function shortly on the AAAreadme of
+        [https://github.com/MooersLab/writingLogTemplateInOrg](https://github.com/MooersLab/writingLogTemplateInOrg){rel="noreferrer noopener"}.
+        This eliminates the need to refile the idea, which I am too
+        undisciplined to do.
+-   Q: I actually love this one! But it creates as much separated log as
+    there is project. You limit yourself to work only on how many
+    project per day? How do you explore them back (if you ever)?  I
+    assume your org files is growing exponantially over time. You said
+    about \"valuable when receiving critiques?\" (Donovan)  
+-   A: Thank you for the opportunity to make clarifications. I try to
+    work on two writing projects a day on average terms of doing
+    generative writing tasks. Yes, there is one writing-project log file
+    per project. They tend to grow to a length of 50-100 pages by the
+    time the paper is published. Because of the ability to fold
+    sections, I have not run into trouble with the longer lengths.  I
+    use the template on GitHub to start the log file for a new writing
+    probject. I could consider retaining a log file for a sequel paper
+    to retain the history of decisions made in the first paper but I
+    would duplicate it and rename the copy with the new project number.
+    I will go through an old log file for a published paper from years
+    ago to recover details on how I carried out certain procedures. The
+    history of decisions in the daily log is invaluable for responding
+    to probing questions by reviewers about why we decided to do certain
+    procedures.
+-   \<\_viz\> Q: Sorry, not really related to the talk\'s topic but can
+    you share the pymol project that shown in the writing log slide
+    earlier in the talk? I am interested in the paper/project.
+    -   A: Thank you for your interest on the PyMOL project. I have not
+        published that particular project yet, but a number of related
+        PyMOL projects are on my GitHub site. The most popular is
+        MooersLab/PyMOLshortcuts
+        [https://github.com/MooersLab/pymolshortcuts](https://github.com/MooersLab/pymolshortcuts){rel="noreferrer noopener"}.
+        The associated paper is here
+        [https://onlinelibrary.wiley.com/doi/10.1002/pro.3781](https://onlinelibrary.wiley.com/doi/10.1002/pro.3781){rel="noreferrer noopener"}.
+        I have run PyMOL in Jupyter
+        [https://github.com/MooersLab/jupyterlabpymolpysnips](https://github.com/MooersLab/jupyterlabpymolpysnips){rel="noreferrer noopener"} 
+        [https://pubmed.ncbi.nlm.nih.gov/33967632/](https://pubmed.ncbi.nlm.nih.gov/33967632/){rel="noreferrer noopener"}
+        ,  Colab  
+        [https://github.com/MooersLab/colabOpenSourcePyMOLpySnips](https://github.com/MooersLab/colabOpenSourcePyMOLpySnips){rel="noreferrer noopener"} 
+        [https://proceedings.scipy.org/articles/majora-1b6fd038-002](https://proceedings.scipy.org/articles/majora-1b6fd038-002){rel="noreferrer noopener"},
+        RStudio 
+        [https://github.com/MooersLab/rstudiopymolpysnips](https://github.com/MooersLab/rstudiopymolpysnips){rel="noreferrer noopener"},
+        and Org-mode
+        [https://github.com/MooersLab/orgpymolpysnips](https://github.com/MooersLab/orgpymolpysnips){rel="noreferrer noopener"}.
+        I gave a talk about the later at emacsconf 2021
+        [https://emacsconf.org/2021/talks/molecular/](https://emacsconf.org/2021/talks/molecular/){rel="noreferrer noopener"}. 
+-   \<jsiegel62\> Q: Have you tweaked your Emacs configuration at all
+    \-- with cus keybindings, etc \-- to support the process you
+    demonstrated? Thank for the good question because my talk was
+    focused on a template org document. I use org-ref heavily. I use it
+    to add Bibtex entries, download PDFs of research articles by their
+    DOIs, and rename them with the citekey. I made several Elisp
+    functions that do minor tasks to support my worflow. I will post
+    them github. 
+-   \<PlasmaStrike\> I like to Seperate my ZettelKasten and GTD  with
+    Daily and global, Zettelkasten daily would be a journal, The reason
+    to keep them seperated is daily is to start with a black sheet and
+    can be thrown ignored if not done well, If good enough goes into
+    zettel etc. That is a good suggestion. Thank you for sharing it.
+
+## Notes
+
+-   Hi, This is Blaine. I am checkin in!
+    -   Hey :)
+-   Hello from Madagascar :) Hello from Brazil (there\'s an old song
+    about madagascar:
+    [https://www.youtube.com/watch?v=k206JIkXJbk](https://www.youtube.com/watch?v=k206JIkXJbk){rel="noreferrer noopener"})
+    :) Hello from Uganda Hello from ISS\^\^ The International Space
+    Station? 0_0 Hello from US Hello world and outer space!!!!
+-   It\'s so awesome seeing these talks that are not strictly software
+    development relatedThank you!
+-   It\'s amazing to see how much people do with emacs Thank you!
+-   \<Neil\> \[MooersLab/writingLogTemplateInOrg: Template for
+    writing.log in
+    org-mode\]([https://github.com/MooersLab/writingLogTemplateInOrg](https://github.com/MooersLab/writingLogTemplateInOrg){rel="noreferrer noopener"})
+-   \<mickeynp\> it\'s really impressive. it also makes me realise that
+    people are a lot more organised than could ever be. I have been
+    studying time management for decades; it is still a stuggle for me.
+-   \<gg\> That chart looks complicated. It can get pretty complicated
+    as its deeply personal and has seen several revisions.  (Sounds like
+    the chart is descriptive and not prescriptive) Right, is just
+    descriptive. Yes, that concept map it a bit overwhelming. I plann to
+    make a slimed down version. Thank you for the feedback.
+-   \<jsiegel62\> I love the fact. that \"shower\" is called out as an
+    Ideation \"feed\" in the writing process chart :-) Takes shower
+    thoughts to a whole new level\...It is a feature of our insane 24-7
+    culture. 
+-   \<gringo\> The man is trying to treat cancer, I expected nothing
+    less complicated than this gg Thank you! Yes, our work has added
+    years of additional life to many cancer patients. 
+-   \<jsiegel62\> There is a package \-- I think it is \'org-tracktable
+    \-- that records word counts by session in an inline block within
+    org files 
+    [https://github.com/tty-tourist/org-tracktable](https://github.com/tty-tourist/org-tracktable){rel="noreferrer noopener"}
+    i will check it out. Thank you for the link! My time tracking
+    databse has 10,848 rows after 2.5 years. It may be over 100,000 rows
+    long by the time that I expire. I decided that a org-mode table
+    would be not appropriate. I adandoned the Google Sheet Workbook over
+    a year ago because it is reduant with entries in my timespent.db. I
+    did not like the duplicated effort.  I am now testing the use of a
+    heat map for a similar writing accountability purpose. It tallies my
+    writing effort per day from my timespent.db file. I enter \`hmj\`
+    for Heat Map of Journal article writing to effort.  This is a long
+    bash alias to to script and commands that generate the heatmap and
+    post it on Github. The GitHub repo for the script is here
+    [https://github.com/MooersLab/writing-time-spent-heatmap](https://github.com/MooersLab/writing-time-spent-heatmap){rel="noreferrer noopener"}.
+    I have similar aliases for makng heatmps for grant writing,
+    teaching, and service, but my daily focus is on article writing.
+-   \<\_viz\> oohhh using a drawer for stashing these details away is a
+    nice idea! Thank you! Org-mode has so many niffty feature like
+    drawers.
+-   \<gg\> I\'m impressed by how systematic he is about everything.Thank
+    you!
+-   \<gringo\> I\'m thankful for people like the presenter that dedicate
+    so much of their time to researching treatments for the horrible
+    diseases that people suffer. \[10:09\] Thank you!
+
 
 [[!inline pages="internal(2024/info/project-after)" raw="yes"]]