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.
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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.
