path: root/2022/info/science-after.md

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<a name="science-mainVideo-transcript"></a>
# Transcript

[[!template new="1" text="""Hello everyone, I'm Vidianos.""" start="00:00:00.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""Today I'm going to show you""" start="00:00:02.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""how I write and organize""" start="00:00:03.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""my literature notes using Emacs.""" start="00:00:04.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""I take my notes using Zettelkasten,""" start="00:00:06.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""which you may or may not have heard.""" start="00:00:08.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""It is about taking small atomic notes""" start="00:00:11.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""and linking them one another""" start="00:00:13.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""to create your so-called second brain.""" start="00:00:15.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""Here is mine.""" start="00:00:17.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""This is a graph of all the notes""" start="00:00:19.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""I have accumulated the last few years.""" start="00:00:20.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""It has various types of notes,""" start="00:00:22.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""but we're mainly going to focus on""" start="00:00:25.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""literature notes today.""" start="00:00:25.960" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""Here are the contents of my talk.""" start="00:00:28.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""We're going to start""" start="00:00:29.640" video="mainVideo-science" id="subtitle"]]
[[!template text="""with bibliography management,""" start="00:00:30.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""which is how I take bibliography""" start="00:00:31.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""from the web and import it to Emacs.""" start="00:00:33.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""Then we're going to talk about""" start="00:00:35.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""how I create literature notes""" start="00:00:37.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""using a custom org-roam-bibtex template I have.""" start="00:00:38.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""And after talking about that,""" start="00:00:42.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""we can talk about how I write literature notes,""" start="00:00:43.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""which is through annotating an article""" start="00:00:46.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""using org-noter. Org-noter is a package""" start="00:00:48.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""that allows you to annotate PDFs""" start="00:00:51.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""using the Org format""" start="00:00:53.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""and creates a supplementary Org file to your PDF.""" start="00:00:55.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""Then we're going to talk about""" start="00:00:59.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""adding the literature to your Zettelkasten,""" start="00:01:00.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""which is a simple but important topic,""" start="00:01:03.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""and how you can write permanent notes""" start="00:01:06.280" video="mainVideo-science" id="subtitle"]]
[[!template text="""based on the info you obtain from this literature.""" start="00:01:08.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""Lastly, we're going to focus on""" start="00:01:11.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""the organization problem""" start="00:01:13.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""one might find when having a lot of literature""" start="00:01:15.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""for an assignment or an article or something,""" start="00:01:17.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""and how I have tried to solve this""" start="00:01:21.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""with my package Zetteldesk.""" start="00:01:22.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""This isn't the perfect solution,""" start="00:01:24.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""but it is what I have, and I really like it.""" start="00:01:26.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""Finally, we're going to talk about""" start="00:01:29.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""how to compose the final article""" start="00:01:30.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""that you want to produce""" start="00:01:33.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""using this literature""" start="00:01:35.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""with the technique described""" start="00:01:36.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""in the rest of this talk.""" start="00:01:38.640" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""So let's begin the talk""" start="00:01:40.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""with bibliography management.""" start="00:01:42.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""Zotero is the bibliography manager I use.""" start="00:01:44.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""It is very simple to store articles with it,""" start="00:01:47.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""and it exports to .bib,""" start="00:01:49.400" video="mainVideo-science" id="subtitle"]]
[[!template text="""integrating with packages""" start="00:01:50.680" video="mainVideo-science" id="subtitle"]]
[[!template text="""such as org-roam-bibtex and ivy-bibtex.""" start="00:01:52.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""When researching, I typically find""" start="00:01:54.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""a long list of articles from a search engine.""" start="00:01:56.680" video="mainVideo-science" id="subtitle"]]
[[!template text="""I open the titles which have interesting titles""" start="00:02:00.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""through their abstracts""" start="00:02:03.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""and save to Zotero those whose abstracts""" start="00:02:05.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""are the most relevant to what I want.""" start="00:02:07.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""From these articles,""" start="00:02:10.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""I typically won't read all of them""" start="00:02:11.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""because they're a lot,""" start="00:02:13.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""but I will select a few,""" start="00:02:14.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""once I have collected as many as I want.""" start="00:02:17.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""Zotero acts as a way to store everything""" start="00:02:21.640" video="mainVideo-science" id="subtitle"]]
[[!template text="""that might be interesting,""" start="00:02:24.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""while Emacs and my Zettelkasten""" start="00:02:25.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""stores everything that is definitely interesting,""" start="00:02:28.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""and I have read it already.""" start="00:02:30.960" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""And then we can move to""" start="00:02:35.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""how I create literature notes.""" start="00:02:36.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""I set the default action of ivy-bibtex""" start="00:02:38.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""to ivy-bibtex-edit-notes,""" start="00:02:41.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""which will prompt-- which""" start="00:02:43.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""with org-roam-bibtex-mode active,""" start="00:02:44.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""prompts you for an org-capture template""" start="00:02:46.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""when selecting something""" start="00:02:48.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""if the node doesn't exist,""" start="00:02:50.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""or takes you to the existing node.""" start="00:02:52.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""And obviously you need to have this here,""" start="00:02:54.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""to set the default action""" start="00:02:58.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""that was already there""" start="00:03:00.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""to a letter.""" start="00:03:02.600" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""Then we can move to my org-roam reference template,""" start="00:03:04.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""using org-roam-bibtex.""" start="00:03:08.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""This isn't so complicated,""" start="00:03:11.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""but it has some important stuff""" start="00:03:12.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""I want to highlight.""" start="00:03:14.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""Save it to the ref directory,""" start="00:03:14.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""so I can remember where it is,""" start="00:03:17.400" video="mainVideo-science" id="subtitle"]]
[[!template text="""and it's classified as a literature note.""" start="00:03:19.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""The file name is the cite key,""" start="00:03:23.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""which is easy and small,""" start="00:03:25.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""but the title is the actual article's title.""" start="00:03:27.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""Give it a tag of the entry-type;""" start="00:03:30.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""this is typically &quot;article,&quot;""" start="00:03:32.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""but it's easy to sort things this way""" start="00:03:35.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""because not all literature notes are articles.""" start="00:03:37.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""And then give the keywords""" start="00:03:41.400" video="mainVideo-science" id="subtitle"]]
[[!template text="""that are given by Zotero, because why not?""" start="00:03:43.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""Tags here are tags from Zettelkasten.""" start="00:03:47.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""These are the links to""" start="00:03:51.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""other files which are relevant,""" start="00:03:53.640" video="mainVideo-science" id="subtitle"]]
[[!template text="""but its initialization is empty, obviously.""" start="00:03:55.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""And then this heading is where""" start="00:03:58.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""all the magic happens.""" start="00:03:59.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""The name is just not really so relevant;""" start="00:04:00.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""I just needed something that made sense.""" start="00:04:04.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""The properties are what matters,""" start="00:04:07.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""and mainly this one here.""" start="00:04:10.400" video="mainVideo-science" id="subtitle"]]
[[!template text="""The ${file} attribute finds""" start="00:04:12.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""the file of this specific literature""" start="00:04:18.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""and makes sure that org-noter works""" start="00:04:24.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""by default here.""" start="00:04:27.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""As I'm going to show you in a moment,""" start="00:04:29.640" video="mainVideo-science" id="subtitle"]]
[[!template text="""this way [of] initializing the literature note,""" start="00:04:32.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""org-noter works by default.""" start="00:04:34.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""That's all, basically, for the template.""" start="00:04:37.000" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""This is the point of the talk""" start="00:04:40.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""where we reach the first demo.""" start="00:04:42.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""This is about opening ivy-bibtex,""" start="00:04:44.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""selecting an article I want to annotate,""" start="00:04:47.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""initializing the literature note.""" start="00:04:50.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""We can see that everything""" start="00:04:53.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""is inserted in for me,""" start="00:04:55.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""and if I open org-noter on this heading,""" start="00:04:56.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""it opens the article, as expected.""" start="00:05:01.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""I can read the article,""" start="00:05:03.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""I can say I want to""" start="00:05:06.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""annotate something here.""" start="00:05:08.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""Obviously, annotation is not that simple as here,""" start="00:05:20.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""but I don't really have the time""" start="00:05:24.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""to actually annotate an article live.""" start="00:05:26.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""But you can keep going, and it's a good setup.""" start="00:05:28.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""Then close org-noter,""" start="00:05:34.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""and let's go presentation again.""" start="00:05:39.880" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""Moving on, this section is some stuff""" start="00:05:40.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""about my annotation process.""" start="00:05:44.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""As I said, there is not enough time for me""" start="00:05:45.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""to actually annotate an article live,""" start="00:05:49.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""but here are some things about it.""" start="00:05:51.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""First, is that I annotate with org-noter,""" start="00:05:53.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""which I absolutely love.""" start="00:05:55.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""It is great for annotations""" start="00:05:56.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""because you do them in org,""" start="00:05:59.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""which is an amazing format""" start="00:06:02.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""and gives you a lot of flexibility,""" start="00:06:03.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""such as adding to the Zettelkasten,""" start="00:06:05.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""being initialized by a capture template,""" start="00:06:07.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""and other things.""" start="00:06:11.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""But also, you don't need to look for""" start="00:06:13.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""the notes inside the PDF,""" start="00:06:15.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""which is a problem you can have""" start="00:06:17.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""if you annotate on the PDF,""" start="00:06:19.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""and it is very annoying in my opinion.""" start="00:06:20.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""So I prefer having these notes,""" start="00:06:23.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""and I can only focus on them,""" start="00:06:26.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""but I can also see where they refer.""" start="00:06:27.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""The other scenarios are not so good.""" start="00:06:29.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""Annotating on the PDF,""" start="00:06:33.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""you search for it,""" start="00:06:35.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""and if you don't know which section it refers to,""" start="00:06:36.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""then you need to look about it,""" start="00:06:41.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""and that is very tiring.""" start="00:06:42.760" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""Also, I am always annotating in English.""" start="00:06:44.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""This is not my mother tongue,""" start="00:06:48.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""but it helps me avoid""" start="00:06:50.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""the necessary mental overhead""" start="00:06:52.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""of translating while reading.""" start="00:06:53.680" video="mainVideo-science" id="subtitle"]]
[[!template text="""I want to pay attention to what I read""" start="00:06:55.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""and not to translate stuff.""" start="00:06:57.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""I will translate later.""" start="00:06:59.680" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""And when finishing an article,""" start="00:07:02.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""I write a mini-abstract myself,""" start="00:07:05.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""which contains what I think about the article.""" start="00:07:07.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""It doesn't need to be much,""" start="00:07:10.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""it's usually like 3 or 4 paragraphs,""" start="00:07:11.640" video="mainVideo-science" id="subtitle"]]
[[!template text="""and it shows things that are useful in the article,""" start="00:07:14.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""and what is mentioned that matters to me.""" start="00:07:18.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""So I can look back at it,""" start="00:07:21.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""and it is very easy for me to find""" start="00:07:22.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""what I got from this article,""" start="00:07:24.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""so where I will cite it on my actual project.""" start="00:07:26.600" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""Then last thing you need to do""" start="00:07:30.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""is add a note to your Zettelkasten.""" start="00:07:33.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""This is very easy due to it being in an org format.""" start="00:07:35.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""You can just have it in the org-roam directory,""" start="00:07:38.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""which it automatically goes to,""" start="00:07:41.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""and link it to other relevant notes,""" start="00:07:43.640" video="mainVideo-science" id="subtitle"]]
[[!template text="""which is its index""" start="00:07:46.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""because everything in my Zettelkasten""" start="00:07:48.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""(at least) has an index,""" start="00:07:50.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""but also every other permanent note""" start="00:07:51.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""whose contents are in one way or another""" start="00:07:54.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""mentioned inside the article.""" start="00:07:56.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""This way the article is in a network with notes""" start="00:07:58.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""that are similar to it.""" start="00:08:00.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""Then we move on to the second demo,""" start="00:08:02.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""which is about a full-fledged literature note.""" start="00:08:05.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""We can go on org-roam-node-find,""" start="00:08:08.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""search for references,""" start="00:08:11.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""go to this, and you can see""" start="00:08:13.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""it is linked to other notes.""" start="00:08:15.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""And here is the mini-abstract,""" start="00:08:17.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""and here are my notes on it.""" start="00:08:20.040" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""The last thing you need to do""" start="00:08:21.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""when creating a literature note,""" start="00:08:27.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""is obviously create permanent notes""" start="00:08:29.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""based on what you read.""" start="00:08:31.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""If you never create these literature notes,""" start="00:08:32.280" video="mainVideo-science" id="subtitle"]]
[[!template text="""you will never get new information.""" start="00:08:35.680" video="mainVideo-science" id="subtitle"]]
[[!template text="""So for your Zettelkasten to grow,""" start="00:08:37.680" video="mainVideo-science" id="subtitle"]]
[[!template text="""you need to create such notes.""" start="00:08:40.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""This means that the subject you are researching""" start="00:08:42.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""is not just literature notes""" start="00:08:45.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""but has well-structured permanent notes,""" start="00:08:47.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""which is what you will actually read.""" start="00:08:50.280" video="mainVideo-science" id="subtitle"]]
[[!template text="""You typically only read literature notes""" start="00:08:52.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""to see what gets cited where.""" start="00:08:55.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""What you will mostly read""" start="00:08:57.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""is these permanent notes""" start="00:08:58.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""that you create from this knowledge.""" start="00:08:59.840" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""So finally we are at the last part of the talk,""" start="00:09:01.680" video="mainVideo-science" id="subtitle"]]
[[!template text="""which is about organizing literature notes.""" start="00:09:05.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""And this is in my opinion""" start="00:09:07.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""the most interesting part""" start="00:09:09.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""because it is very unique.""" start="00:09:10.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""It uses a package I wrote myself,""" start="00:09:12.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""and it doesn't have as much usage""" start="00:09:14.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""as the rest of the things I described so far.""" start="00:09:18.320" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""So what is the problem you might find?""" start="00:09:21.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""Indeed, if you read a lot of things,""" start="00:09:24.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""you have a large collection of notes,""" start="00:09:27.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""and it's not the only thing you will think about.""" start="00:09:30.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""However, you do need to""" start="00:09:33.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""justify everything with citations,""" start="00:09:36.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""so you need to remember everything""" start="00:09:37.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""you read in these notes.""" start="00:09:39.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""You have done a lot of work,""" start="00:09:41.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""but there is still a lot for you""" start="00:09:43.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""to reach your final manuscript.""" start="00:09:45.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""Except if there was a handy little way""" start="00:09:47.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""to combine everything""" start="00:09:50.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""and sort it in a very easy way.""" start="00:09:52.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""Well, there is,""" start="00:09:55.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""and I think it came out pretty well.""" start="00:09:56.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""It's zetteldesk.el.""" start="00:10:00.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""It was inspired by this quote here""" start="00:10:01.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""from How to Take Smart Notes.""" start="00:10:05.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""Sönke Ahrens here talked about a desktop,""" start="00:10:06.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""which you have all the literature""" start="00:10:09.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""you want in that desktop,""" start="00:10:13.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""and you try to bring it in order.""" start="00:10:16.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""And by doing that,""" start="00:10:20.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""you can improve your ideas""" start="00:10:22.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""and have a structure""" start="00:10:24.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""so that your manuscript will then be""" start="00:10:27.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""very, very easy to write.""" start="00:10:30.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""And as I say here, in trying to do this,""" start="00:10:33.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""I made something much more general""" start="00:10:36.280" video="mainVideo-science" id="subtitle"]]
[[!template text="""than it needed to be, so yeah,""" start="00:10:38.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""you can use it for many other things.""" start="00:10:41.560" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""But before I show you some things about it,""" start="00:10:43.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""I want to introduce you to what a desktop is.""" start="00:10:46.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""It's essentially a collection of the knowledge""" start="00:10:49.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""you want to be able to see.""" start="00:10:53.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""You add things to your Zetteldesk,""" start="00:10:54.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""and using filter functions,""" start="00:10:58.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""you only see these notes and nothing else,""" start="00:11:01.680" video="mainVideo-science" id="subtitle"]]
[[!template text="""which in my opinion is very handy.""" start="00:11:04.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""So having said that,""" start="00:11:07.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""we can see these things in action""" start="00:11:10.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""for the final demo of the talk.""" start="00:11:12.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""This is the third one.""" start="00:11:14.400" video="mainVideo-science" id="subtitle"]]
[[!template text="""I will go to an index file of mine.""" start="00:11:15.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""This is 3D printing,""" start="00:11:20.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""an assignment I had last semester.""" start="00:11:21.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""And this has 28 backlinks,""" start="00:11:23.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""so a lot of things that I looked at""" start="00:11:27.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""for this assignment.""" start="00:11:30.400" video="mainVideo-science" id="subtitle"]]
[[!template text="""I can say I want to add""" start="00:11:31.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""the current note's backlinks to the Zetteldesk,""" start="00:11:33.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""and now I have a filtered version""" start="00:11:35.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""of org-roam-node-find defined,""" start="00:11:38.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""which only lists these 29 notes.""" start="00:11:40.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""Very nice, right?""" start="00:11:42.000" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""I can also filter just the literature notes,""" start="00:11:45.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""which can also use other UIs beside org-roam,""" start="00:11:49.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""such as, for example,""" start="00:11:56.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""one I use a lot is the ivy-bibtex command.""" start="00:11:57.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""This takes a lot of time,""" start="00:12:00.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""much longer than the org-roam one,""" start="00:12:03.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""but has them in this UI,""" start="00:12:04.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""which in a lot of cases is more useful for me.""" start="00:12:06.480" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""The other very important thing is inserting these.""" start="00:12:09.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""For example, say I want to insert a permanent note,""" start="00:12:15.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""such as this.""" start="00:12:20.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""Its title will become a top-level heading,""" start="00:12:21.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""and everything else will be inserted as expected.""" start="00:12:25.400" video="mainVideo-science" id="subtitle"]]
[[!template text="""But the most important thing for us""" start="00:12:29.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""is inserting literature, right?""" start="00:12:35.400" video="mainVideo-science" id="subtitle"]]
[[!template text="""This is done with this command,""" start="00:12:37.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""and let's say I want to insert this.""" start="00:12:39.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""The title again becomes a heading,""" start="00:12:42.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""and this is the article title also.""" start="00:12:48.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""I store the cite key here,""" start="00:12:50.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""and everything else about it is also here.""" start="00:12:53.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""And I can add others,""" start="00:12:56.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""for example, this and this.""" start="00:12:58.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""And we have all of them here.""" start="00:13:01.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""I see it says this is the basic,""" start="00:13:09.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""so let's put it at the top.""" start="00:13:11.280" video="mainVideo-science" id="subtitle"]]
[[!template text="""And then maybe I want to put this last.""" start="00:13:12.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""And this way, you can sort things,""" start="00:13:18.840" video="mainVideo-science" id="subtitle"]]
[[!template text="""and typically, on the other side,""" start="00:13:24.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""I have a manuscript,""" start="00:13:26.320" video="mainVideo-science" id="subtitle"]]
[[!template text="""and I look at what order""" start="00:13:27.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""I want to have things in""" start="00:13:30.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""and sort the articles and the permanent notes""" start="00:13:31.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""in a way so that each section can have""" start="00:13:34.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""its own citations and its own notes,""" start="00:13:38.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""which makes writing, again, very easy, in my opinion.""" start="00:13:41.800" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""Finally, let's go to composing the final article.""" start="00:13:46.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""This is our goal: we wrote and organized""" start="00:13:53.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""all these literature notes""" start="00:13:57.280" video="mainVideo-science" id="subtitle"]]
[[!template text="""to put them in your final project.""" start="00:13:58.360" video="mainVideo-science" id="subtitle"]]
[[!template text="""This might be an assignment""" start="00:14:00.400" video="mainVideo-science" id="subtitle"]]
[[!template text="""or an actual scientific article.""" start="00:14:01.880" video="mainVideo-science" id="subtitle"]]
[[!template text="""It is apparent that you have done""" start="00:14:04.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""a lot of work for this so far,""" start="00:14:07.480" video="mainVideo-science" id="subtitle"]]
[[!template text="""but you don't need to do a lot more.""" start="00:14:09.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""In my opinion, this is the easiest part""" start="00:14:12.280" video="mainVideo-science" id="subtitle"]]
[[!template text="""of the whole workflow.""" start="00:14:14.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""People consider final article composition hard,""" start="00:14:15.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""but if you've done all these steps,""" start="00:14:19.280" video="mainVideo-science" id="subtitle"]]
[[!template text="""you already have everything you want""" start="00:14:21.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""to add in the article from your notes.""" start="00:14:23.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""It's already there,""" start="00:14:25.640" video="mainVideo-science" id="subtitle"]]
[[!template text="""a lot of things are copy-pasted,""" start="00:14:27.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""it's all in a coherent order,""" start="00:14:30.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""connections are to an extent already there,""" start="00:14:34.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""and you know what citation goes where,""" start="00:14:38.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""so you can justify everything you write.""" start="00:14:41.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""The actual draft isn't there,""" start="00:14:44.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""but it is very easy""" start="00:14:46.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""because now you just write things as you see them""" start="00:14:48.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""in your desktop and connect them.""" start="00:14:52.600" video="mainVideo-science" id="subtitle"]]
[[!template text="""Connections are basic--""" start="00:14:54.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""connections and making the article good, obviously,""" start="00:14:56.960" video="mainVideo-science" id="subtitle"]]
[[!template text="""are basically the only thing you need to worry,""" start="00:14:59.440" video="mainVideo-science" id="subtitle"]]
[[!template text="""but those are very important""" start="00:15:02.400" video="mainVideo-science" id="subtitle"]]
[[!template text="""because others will only see the final manuscript,""" start="00:15:05.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""so if that's not good,""" start="00:15:09.040" video="mainVideo-science" id="subtitle"]]
[[!template text="""then the whole assignment is not good, obviously.""" start="00:15:11.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""So it's not like your work is done,""" start="00:15:14.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""it's just very easy.""" start="00:15:17.520" video="mainVideo-science" id="subtitle"]]
[[!template new="1" text="""And with that, I hope you liked my talk""" start="00:15:19.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""because it is coming to an end now.""" start="00:15:23.280" video="mainVideo-science" id="subtitle"]]
[[!template text="""I want to thank you for your time;""" start="00:15:25.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""I hope you enjoyed it.""" start="00:15:27.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""You can feel free to email me at this address;""" start="00:15:29.680" video="mainVideo-science" id="subtitle"]]
[[!template text="""it has also been on every slide since the beginning.""" start="00:15:32.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""I also have the GitHub for zetteldesk.el here,""" start="00:15:35.640" video="mainVideo-science" id="subtitle"]]
[[!template text="""and I will be available for questions.""" start="00:15:40.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""I will be viewing both the pad and the IRC""" start="00:15:42.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""and will do a live Q&A after this. See you.""" start="00:15:45.000" video="mainVideo-science" id="subtitle"]]
[[!template text="""Actually, before I go,""" start="00:15:49.160" video="mainVideo-science" id="subtitle"]]
[[!template text="""let's show you the GitHub for zetteldesk.el.""" start="00:15:51.280" video="mainVideo-science" id="subtitle"]]
[[!template text="""Here's the README; if you're interested on it,""" start="00:15:54.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""you can see more about it,""" start="00:15:57.120" video="mainVideo-science" id="subtitle"]]
[[!template text="""and also I have a very in-depth wiki about it""" start="00:15:58.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""with 11 pages, and talking about everything""" start="00:16:02.560" video="mainVideo-science" id="subtitle"]]
[[!template text="""that happens here.""" start="00:16:06.520" video="mainVideo-science" id="subtitle"]]
[[!template text="""A lot of what we discussed is in this section""" start="00:16:08.080" video="mainVideo-science" id="subtitle"]]
[[!template text="""about literature notes.""" start="00:16:11.760" video="mainVideo-science" id="subtitle"]]
[[!template text="""These documents go a lot more in-depth""" start="00:16:12.920" video="mainVideo-science" id="subtitle"]]
[[!template text="""in how Zetteldesk works, and also how to use it,""" start="00:16:17.200" video="mainVideo-science" id="subtitle"]]
[[!template text="""so if you're interested, feel free to read them,""" start="00:16:22.800" video="mainVideo-science" id="subtitle"]]
[[!template text="""and if you have any problems,""" start="00:16:27.720" video="mainVideo-science" id="subtitle"]]
[[!template text="""you can open an issue about it;""" start="00:16:30.240" video="mainVideo-science" id="subtitle"]]
[[!template text="""I will be very active. Thank you.""" start="00:16:31.840" video="mainVideo-science" id="subtitle"]]



Captioner: hannah
Questions or comments? Please e-mail [vidianosgiannitsis@gmail.com](mailto:vidianosgiannitsis@gmail.com?subject=Comment%20for%20EmacsConf%202022%20science%3A%20Writing%20and%20organizing%20literature%20notes%20for%20scientific%20writing)


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