path: root/2022/captions/emacsconf-2022-science--writing-and-organizing-literature-notes-for-scientific-writing--vidianos--main.vtt

WEBVTT captioned by hannah

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Hello everyone, I'm Vidianos.

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Today I'm going to show you

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how I write and organize

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my literature notes using Emacs.

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I take my notes using Zettelkasten,

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which you may or may not have heard.

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It is about taking small atomic notes

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and linking them one another

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to create your so-called second brain.

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Here is mine.

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This is a graph of all the notes

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I have accumulated the last few years.

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It has various types of notes,

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but we're mainly going to focus on

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literature notes today.

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Here are the contents of my talk.

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We're going to start

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with bibliography management,

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which is how I take bibliography

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from the web and import it to Emacs.

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Then we're going to talk about

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how I create literature notes

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using a custom org-roam-bibtex template I have.

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And after talking about that,

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we can talk about how I write literature notes,

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which is through annotating an article

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using org-noter. Org-noter is a package

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that allows you to annotate PDFs

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using the Org format

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and creates a supplementary Org file to your PDF.

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Then we're going to talk about

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adding the literature to your Zettelkasten,

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which is a simple but important topic,

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and how you can write permanent notes

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based on the info you obtain from this literature.

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Lastly, we're going to focus on

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the organization problem

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one might find when having a lot of literature

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for an assignment or an article or something,

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and how I have tried to solve this

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with my package Zetteldesk.

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This isn't the perfect solution,

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but it is what I have, and I really like it.

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Finally, we're going to talk about

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how to compose the final article

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that you want to produce

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using this literature

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with the technique described

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in the rest of this talk.

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So let's begin the talk

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with bibliography management.

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Zotero is the bibliography manager I use.

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It is very simple to store articles with it,

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and it exports to .bib,

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integrating with packages

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such as org-roam-bibtex and ivy-bibtex.

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When researching, I typically find

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a long list of articles from a search engine.

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I open the titles which have interesting titles

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through their abstracts

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and save to Zotero those whose abstracts

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are the most relevant to what I want.

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From these articles,

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I typically won't read all of them

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because they're a lot,

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but I will select a few,

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once I have collected as many as I want.

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Zotero acts as a way to store everything

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that might be interesting,

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while Emacs and my Zettelkasten

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stores everything that is definitely interesting,

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and I have read it already.

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And then we can move to

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how I create literature notes.

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I set the default action of ivy-bibtex

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to ivy-bibtex-edit-notes,

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which will prompt-- which

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with org-roam-bibtex-mode active,

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prompts you for an org-capture template

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when selecting something

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if the node doesn't exist,

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or takes you to the existing node.

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And obviously you need to have this here,

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to set the default action

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that was already there

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to a letter.

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Then we can move to my org-roam reference template,

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using org-roam-bibtex.

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This isn't so complicated,

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but it has some important stuff

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I want to highlight.

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Save it to the ref directory,

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so I can remember where it is,

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and it's classified as a literature note.

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The file name is the cite key,

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which is easy and small,

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but the title is the actual article's title.

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Give it a tag of the entry-type;

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this is typically "article,"

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but it's easy to sort things this way

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because not all literature notes are articles.

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And then give the keywords

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that are given by Zotero, because why not?

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Tags here are tags from Zettelkasten.

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These are the links to

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other files which are relevant,

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but its initialization is empty, obviously.

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And then this heading is where

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all the magic happens.

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The name is just not really so relevant;

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I just needed something that made sense.

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The properties are what matters,

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and mainly this one here.

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The ${file} attribute finds

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the file of this specific literature

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and makes sure that org-noter works

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by default here.

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As I'm going to show you in a moment,

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this way [of] initializing the literature note,

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org-noter works by default.

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That's all, basically, for the template.

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This is the point of the talk

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where we reach the first demo.

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This is about opening ivy-bibtex,

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selecting an article I want to annotate,

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initializing the literature note.

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We can see that everything

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is inserted in for me,

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and if I open org-noter on this heading,

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it opens the article, as expected.

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I can read the article,

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I can say I want to

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annotate something here.

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Obviously, annotation is not that simple as here,

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but I don't really have the time

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to actually annotate an article live.

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But you can keep going, and it's a good setup.

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Then close org-noter,

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and let's go presentation again.

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Moving on, this section is some stuff

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about my annotation process.

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As I said, there is not enough time for me

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to actually annotate an article live,

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but here are some things about it.

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First, is that I annotate with org-noter,

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which I absolutely love.

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It is great for annotations

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because you do them in org,

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which is an amazing format

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and gives you a lot of flexibility,

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such as adding to the Zettelkasten,

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being initialized by a capture template,

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and other things.

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But also, you don't need to look for

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the notes inside the PDF,

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which is a problem you can have

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if you annotate on the PDF,

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and it is very annoying in my opinion.

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So I prefer having these notes,

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and I can only focus on them,

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but I can also see where they refer.

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The other scenarios are not so good.

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Annotating on the PDF,

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you search for it,

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and if you don't know which section it refers to,

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then you need to look about it,

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and that is very tiring.

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Also, I am always annotating in English.

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This is not my mother tongue,

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but it helps me avoid

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the necessary mental overhead

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of translating while reading.

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I want to pay attention to what I read

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and not to translate stuff.

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I will translate later.

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And when finishing an article,

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I write a mini-abstract myself,

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which contains what I think about the article.

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It doesn't need to be much,

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it's usually like 3 or 4 paragraphs,

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and it shows things that are useful in the article,

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and what is mentioned that matters to me.

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So I can look back at it,

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and it is very easy for me to find

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what I got from this article,

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so where I will cite it on my actual project.

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Then last thing you need to do

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is add a note to your Zettelkasten.

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This is very easy due to it being in an org format.

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You can just have it in the org-roam directory,

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which it automatically goes to,

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and link it to other relevant notes,

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which is its index

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because everything in my Zettelkasten

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(at least) has an index,

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but also every other permanent note

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whose contents are in one way or another

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mentioned inside the article.

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This way the article is in a network with notes

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that are similar to it.

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Then we move on to the second demo,

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which is about a full-fledged literature note.

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We can go on org-roam-node-find,

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search for references,

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go to this, and you can see

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it is linked to other notes.

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And here is the mini-abstract,

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and here are my notes on it.

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The last thing you need to do

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when creating a literature note,

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is obviously create permanent notes

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based on what you read.

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If you never create these literature notes,

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you will never get new information.

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So for your Zettelkasten to grow,

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you need to create such notes.

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This means that the subject you are researching

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is not just literature notes

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but has well-structured permanent notes,

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which is what you will actually read.

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You typically only read literature notes

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to see what gets cited where.

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What you will mostly read

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is these permanent notes

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that you create from this knowledge.

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So finally we are at the last part of the talk,

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which is about organizing literature notes.

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And this is in my opinion

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the most interesting part

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because it is very unique.

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It uses a package I wrote myself,

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and it doesn't have as much usage

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as the rest of the things I described so far.

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So what is the problem you might find?

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Indeed, if you read a lot of things,

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you have a large collection of notes,

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and it's not the only thing you will think about.

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However, you do need to

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justify everything with citations,

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so you need to remember everything

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you read in these notes.

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You have done a lot of work,

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but there is still a lot for you

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to reach your final manuscript.

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Except if there was a handy little way

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to combine everything

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and sort it in a very easy way.

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Well, there is,

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and I think it came out pretty well.

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It's zetteldesk.el.

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It was inspired by this quote here

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from How to Take Smart Notes.

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Sönke Ahrens here talked about a desktop,

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which you have all the literature

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you want in that desktop,

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and you try to bring it in order.

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And by doing that,

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you can improve your ideas

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and have a structure

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so that your manuscript will then be

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very, very easy to write.

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And as I say here, in trying to do this,

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I made something much more general

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than it needed to be, so yeah,

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you can use it for many other things.

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But before I show you some things about it,

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I want to introduce you to what a desktop is.

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It's essentially a collection of the knowledge

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you want to be able to see.

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You add things to your Zetteldesk,

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and using filter functions,

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you only see these notes and nothing else,

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which in my opinion is very handy.

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So having said that,

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we can see these things in action

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for the final demo of the talk.

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This is the third one.

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I will go to an index file of mine.

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This is 3D printing,

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an assignment I had last semester.

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And this has 28 backlinks,

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so a lot of things that I looked at

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for this assignment.

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I can say I want to add

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the current note's backlinks to the Zetteldesk,

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and now I have a filtered version

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of org-roam-node-find defined,

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which only lists these 29 notes.

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Very nice, right?

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I can also filter just the literature notes,

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which can also use other UIs beside org-roam,

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such as, for example,

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one I use a lot is the ivy-bibtex command.

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This takes a lot of time,

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much longer than the org-roam one,

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but has them in this UI,

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which in a lot of cases is more useful for me.

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The other very important thing is inserting these.

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For example, say I want to insert a permanent note,

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such as this.

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Its title will become a top-level heading,

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and everything else will be inserted as expected.

00:12:29.320 --> 00:12:35.399
But the most important thing for us

00:12:35.400 --> 00:12:37.159
is inserting literature, right?

00:12:37.160 --> 00:12:39.519
This is done with this command,

00:12:39.520 --> 00:12:42.719
and let's say I want to insert this.

00:12:42.720 --> 00:12:48.239
The title again becomes a heading,

00:12:48.240 --> 00:12:50.839
and this is the article title also.

00:12:50.840 --> 00:12:53.039
I store the cite key here,

00:12:53.040 --> 00:12:56.319
and everything else about it is also here.

00:12:56.320 --> 00:12:58.239
And I can add others,

00:12:58.240 --> 00:13:01.199
for example, this and this.

00:13:01.200 --> 00:13:09.039
And we have all of them here.

00:13:09.040 --> 00:13:11.279
I see it says this is the basic,

00:13:11.280 --> 00:13:12.799
so let's put it at the top.

00:13:12.800 --> 00:13:18.839
And then maybe I want to put this last.

00:13:18.840 --> 00:13:24.159
And this way, you can sort things,

00:13:24.160 --> 00:13:26.319
and typically, on the other side,

00:13:26.320 --> 00:13:27.719
I have a manuscript,

00:13:27.720 --> 00:13:29.999
and I look at what order

00:13:30.000 --> 00:13:31.159
I want to have things in

00:13:31.160 --> 00:13:34.799
and sort the articles and the permanent notes

00:13:34.800 --> 00:13:38.359
in a way so that each section can have

00:13:38.360 --> 00:13:41.799
its own citations and its own notes,

00:13:41.800 --> 00:13:46.199
which makes writing, again, very easy, in my opinion.

00:13:46.200 --> 00:13:53.719
Finally, let's go to composing the final article.

00:13:53.720 --> 00:13:57.279
This is our goal: we wrote and organized

00:13:57.280 --> 00:13:58.359
all these literature notes

00:13:58.360 --> 00:14:00.399
to put them in your final project.

00:14:00.400 --> 00:14:01.879
This might be an assignment

00:14:01.880 --> 00:14:04.439
or an actual scientific article.

00:14:04.440 --> 00:14:07.479
It is apparent that you have done

00:14:07.480 --> 00:14:09.079
a lot of work for this so far,

00:14:09.080 --> 00:14:12.279
but you don't need to do a lot more.

00:14:12.280 --> 00:14:14.079
In my opinion, this is the easiest part

00:14:14.080 --> 00:14:15.519
of the whole workflow.

00:14:15.520 --> 00:14:19.279
People consider final article composition hard,

00:14:19.280 --> 00:14:21.239
but if you've done all these steps,

00:14:21.240 --> 00:14:23.439
you already have everything you want

00:14:23.440 --> 00:14:25.639
to add in the article from your notes.

00:14:25.640 --> 00:14:27.719
It's already there,

00:14:27.720 --> 00:14:30.759
a lot of things are copy-pasted,

00:14:30.760 --> 00:14:34.039
it's all in a coherent order,

00:14:34.040 --> 00:14:38.439
connections are to an extent already there,

00:14:38.440 --> 00:14:41.599
and you know what citation goes where,

00:14:41.600 --> 00:14:44.199
so you can justify everything you write.

00:14:44.200 --> 00:14:46.799
The actual draft isn't there,

00:14:46.800 --> 00:14:48.519
but it is very easy

00:14:48.520 --> 00:14:52.599
because now you just write things as you see them

00:14:52.600 --> 00:14:54.439
in your desktop and connect them.

00:14:54.440 --> 00:14:56.959
Connections are basic--

00:14:56.960 --> 00:14:59.439
connections and making the article good, obviously,

00:14:59.440 --> 00:15:02.399
are basically the only thing you need to worry,

00:15:02.400 --> 00:15:05.919
but those are very important

00:15:05.920 --> 00:15:09.039
because others will only see the final manuscript,

00:15:09.040 --> 00:15:11.079
so if that's not good,

00:15:11.080 --> 00:15:14.079
then the whole assignment is not good, obviously.

00:15:14.080 --> 00:15:17.519
So it's not like your work is done,

00:15:17.520 --> 00:15:19.159
it's just very easy.

00:15:19.160 --> 00:15:23.279
And with that, I hope you liked my talk

00:15:23.280 --> 00:15:25.519
because it is coming to an end now.

00:15:25.520 --> 00:15:27.919
I want to thank you for your time;

00:15:27.920 --> 00:15:29.679
I hope you enjoyed it.

00:15:29.680 --> 00:15:32.519
You can feel free to email me at this address;

00:15:32.520 --> 00:15:35.639
it has also been on every slide since the beginning.

00:15:35.640 --> 00:15:40.239
I also have the GitHub for zetteldesk.el here,

00:15:40.240 --> 00:15:42.519
and I will be available for questions.

00:15:42.520 --> 00:15:44.999
I will be viewing both the pad and the IRC

00:15:45.000 --> 00:15:49.159
and will do a live Q&A after this. See you.

00:15:49.160 --> 00:15:51.279
Actually, before I go,

00:15:51.280 --> 00:15:54.199
let's show you the GitHub for zetteldesk.el.

00:15:54.200 --> 00:15:57.119
Here's the README; if you're interested on it,

00:15:57.120 --> 00:15:58.519
you can see more about it,

00:15:58.520 --> 00:16:02.559
and also I have a very in-depth wiki about it

00:16:02.560 --> 00:16:06.519
with 11 pages, and talking about everything

00:16:06.520 --> 00:16:08.079
that happens here.

00:16:08.080 --> 00:16:11.759
A lot of what we discussed is in this section

00:16:11.760 --> 00:16:12.919
about literature notes.

00:16:12.920 --> 00:16:17.199
These documents go a lot more in-depth

00:16:17.200 --> 00:16:22.799
in how Zetteldesk works, and also how to use it,

00:16:22.800 --> 00:16:27.719
so if you're interested, feel free to read them,

00:16:27.720 --> 00:16:30.239
and if you have any problems,

00:16:30.240 --> 00:16:31.839
you can open an issue about it;

00:16:31.840 --> 00:16:44.480
I will be very active. Thank you.