path: root/2025/info/reference-after.md

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<div class="transcript transcript-mainVideo"><a name="reference-mainVideo-transcript"></a><h1>Transcript</h1>


<div class="transcript-heading">[[!template new="1" text="""Introduction""" start="00:00:00.820" video="mainVideo-reference" id="subtitle"]]</div>[[!template text="""So, hello everyone, welcome to EmacsConf.""" start="00:00:00.820" video="mainVideo-reference" id="subtitle"]]
[[!template text="""My name is Vidianos, and I'm a PhD student in KU Leuven,""" start="00:00:03.080" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and today I'm going to be showing you""" start="00:00:06.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""how I managed to use Emacs as a reference manager,""" start="00:00:08.280" video="mainVideo-reference" id="subtitle"]]
[[!template text="""replacing what was for me Zotero,""" start="00:00:12.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""to a fully fledged approach inside Emacs.""" start="00:00:17.220" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So, what is my typical reference workflow?""" start="00:00:24.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""First I need to find literature,""" start="00:00:26.640" video="mainVideo-reference" id="subtitle"]]
[[!template text="""then I need to collect and organize it,""" start="00:00:28.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which I originally did with Zotero,""" start="00:00:30.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but now with Emacs centered tools""" start="00:00:32.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""such as zotra and ebib.""" start="00:00:36.612" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Then I create a reading list.""" start="00:00:39.880" video="mainVideo-reference" id="subtitle"]]
[[!template text="""This is a new addition to my workflow""" start="00:00:41.280" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I started doing after moving this approach to Emacs""" start="00:00:43.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because now everything is well integrated.""" start="00:00:47.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I have made a very nice reading list implementation""" start="00:00:50.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""inside org-roam which I am going to be showing today.""" start="00:00:53.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Then obviously I need to read the literature, take notes,""" start="00:00:57.760" video="mainVideo-reference" id="subtitle"]]
[[!template text="""organize the notes, and ensure I am actually learning""" start="00:01:01.200" video="mainVideo-reference" id="subtitle"]]
[[!template text="""from what I am reading. This is then done through packages""" start="00:01:04.240" video="mainVideo-reference" id="subtitle"]]
[[!template text="""such as org-noter and org-roam""" start="00:01:06.540" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and is not going to be the focus of this talk.""" start="00:01:09.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I already gave a talk about this part of my workflow,""" start="00:01:11.360" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which I've been doing for many years now.""" start="00:01:14.240" video="mainVideo-reference" id="subtitle"]]
[[!template text="""You can find that""" start="00:01:17.960" video="mainVideo-reference" id="subtitle"]]
[[!template text="""or you can find many other people's approaches""" start="00:01:20.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""to reading literature and taking notes""" start="00:01:23.240" video="mainVideo-reference" id="subtitle"]]
[[!template text="""as it is quite a popular topic in the Emacs community.""" start="00:01:26.000" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Lastly, I will have a short section""" start="00:01:31.040" video="mainVideo-reference" id="subtitle"]]
[[!template text="""about how I ensure that I can recall the knowledge""" start="00:01:32.760" video="mainVideo-reference" id="subtitle"]]
[[!template text="""from this literature very easily""" start="00:01:37.040" video="mainVideo-reference" id="subtitle"]]
[[!template text="""through this reference management system.""" start="00:01:39.680" video="mainVideo-reference" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Capture""" start="00:01:43.600" video="mainVideo-reference" id="subtitle"]]</div>[[!template text="""So, how can we capture an article in Emacs?""" start="00:01:43.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""One of the most commonly known packages is doi-utils""" start="00:01:48.200" video="mainVideo-reference" id="subtitle"]]
[[!template text="""where doi-utils has a lot of useful things to do""" start="00:01:52.100" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and one of them is to capture a paper,""" start="00:01:58.880" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but you need a DOI, and for me, that is a bit inconvenient,""" start="00:02:03.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because what I want to do is that""" start="00:02:06.460" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I have a URL here of a paper,""" start="00:02:08.880" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I want to just copy this URL, not copy the DOI,""" start="00:02:12.000" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and be able to save it immediately to my bib file.""" start="00:02:16.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And that can now be done""" start="00:02:23.200" video="mainVideo-reference" id="subtitle"]]
[[!template text="""through this function zotra-add-entry.""" start="00:02:24.312" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And as you can see here,""" start="00:02:27.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""there is also a zotra-download-attachment""" start="00:02:28.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that sometimes works, but not always.""" start="00:02:31.080" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I don't personally recommend it.""" start="00:02:34.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""But the problem is that due to articles being""" start="00:02:35.880" video="mainVideo-reference" id="subtitle"]]
[[!template text="""locked behind paywalls in many cases,""" start="00:02:39.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""downloading attachments doesn't work""" start="00:02:42.640" video="mainVideo-reference" id="subtitle"]]
[[!template text="""through Emacs. Sometimes it doesn't work""" start="00:02:45.640" video="mainVideo-reference" id="subtitle"]]
[[!template text="""through Zotero. Sometimes you just need to go to the browser,""" start="00:02:47.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""say download PDF, and that's the only solution""" start="00:02:51.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that will properly work.""" start="00:02:54.260" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So how do I then add this to the paper?""" start="00:02:58.400" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I need to find this paper that is here""" start="00:03:01.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""through ivy-bibtex.""" start="00:03:04.712" video="mainVideo-reference" id="subtitle"]]
[[!template text="""This is the bib file manager I use.""" start="00:03:05.880" video="mainVideo-reference" id="subtitle"]]
[[!template text="""There is also others like citar.""" start="00:03:10.240" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I think citar has much better coding and integration""" start="00:03:11.760" video="mainVideo-reference" id="subtitle"]]
[[!template text="""with other packages, but I haven't really bothered""" start="00:03:15.560" video="mainVideo-reference" id="subtitle"]]
[[!template text="""to move from ivy-bibtex""" start="00:03:18.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because it does basically everything I want perfectly.""" start="00:03:19.640" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So I go here, say add pdf to library.""" start="00:03:24.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I find where I saved it,""" start="00:03:28.280" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and it will suggest to automatically name it something""" start="00:03:31.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which is in full integration""" start="00:03:35.400" video="mainVideo-reference" id="subtitle"]]
[[!template text="""with the rest of my Emacs packages,""" start="00:03:37.446" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and all the literature management stuff""" start="00:03:40.920" video="mainVideo-reference" id="subtitle"]]
[[!template text="""knows to find it with this exact name.""" start="00:03:43.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So it iss saved and now""" start="00:03:46.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""when I try to create a file from this,""" start="00:03:49.046" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which I will show later,""" start="00:03:53.320" video="mainVideo-reference" id="subtitle"]]
[[!template text="""you will see that the file will already appear there.""" start="00:03:55.200" video="mainVideo-reference" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Organizing""" start="00:04:00.920" video="mainVideo-reference" id="subtitle"]]</div>[[!template text="""So now let's go to organizing.""" start="00:04:00.920" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Organizing in Zotero is typically done through a""" start="00:04:06.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""hierarchical folder structure.""" start="00:04:09.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""This is very familiar to most people and generally works,""" start="00:04:10.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but being someone that takes notes using the Zettelkasten method,""" start="00:04:15.000" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which has a fully flat hierarchy, nothing goes in folders,""" start="00:04:19.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""everything is in the same folder,""" start="00:04:24.320" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and you find everything because it's connected to other things.""" start="00:04:27.960" video="mainVideo-reference" id="subtitle"]]
[[!template text="""We have some basic indexes,""" start="00:04:31.960" video="mainVideo-reference" id="subtitle"]]
[[!template text="""from where you can jump to different points.""" start="00:04:34.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I love this structure, so I also wanted to include it""" start="00:04:37.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""in my bibliography management,""" start="00:04:41.360" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because with folders you have problems like,""" start="00:04:42.920" video="mainVideo-reference" id="subtitle"]]
[[!template text="""this article can go in that folder, can go in that folder,""" start="00:04:45.580" video="mainVideo-reference" id="subtitle"]]
[[!template text="""can go in that folder. Where do I actually put it?""" start="00:04:48.360" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Do I put copies of it in different folders?""" start="00:04:51.080" video="mainVideo-reference" id="subtitle"]]
[[!template text="""It's just confusing and not really practical in my opinion.""" start="00:04:54.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So I tried to do this approach inside Emacs.""" start="00:04:59.280" video="mainVideo-reference" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Ebib""" start="00:05:03.479" video="mainVideo-reference" id="subtitle"]]</div>[[!template text="""And how? With Ebib.""" start="00:05:03.479" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Ebib is an amazing software built inside Emacs.""" start="00:05:08.240" video="mainVideo-reference" id="subtitle"]]
[[!template text="""It's a reference manager and it works absolutely amazing""" start="00:05:11.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""if you configure it to your liking.""" start="00:05:15.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So let's open ebib first.""" start="00:05:18.200" video="mainVideo-reference" id="subtitle"]]
[[!template text="""This is the interface you will see when opening.""" start="00:05:21.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Actually, by default you will not see anything,""" start="00:05:23.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but I have open three bib files.""" start="00:05:27.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""These are opened by default on boot of ebib for me.""" start="00:05:30.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""These are my three main master bib files.""" start="00:05:36.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""This is the Zotero master bib file,""" start="00:05:39.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which only Zotero can touch. If I change it,""" start="00:05:41.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""it will be overwritten. This is my new master bib,""" start="00:05:44.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""where I save all the files that I have now started using""" start="00:05:47.960" video="mainVideo-reference" id="subtitle"]]
[[!template text="""after switching to this approach.""" start="00:05:53.760" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And then this is the master bib file""" start="00:05:55.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""for literature related to my PhD""" start="00:05:59.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and things that I have already read.""" start="00:06:02.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""It's a very convenient interface.""" start="00:06:07.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""There is also search. There is one searching tool,""" start="00:06:09.760" video="mainVideo-reference" id="subtitle"]]
[[!template text="""the jump to entry, ebib-jump-to-entry,""" start="00:06:14.141" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which searches through all open bib files for the title.""" start="00:06:16.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So for example, I can search for membrane fabrication,""" start="00:06:23.040" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because that's something I am currently doing,""" start="00:06:29.320" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and go to this. There is another searching tool,""" start="00:06:35.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""the ebib-search, which searches through the database""" start="00:06:41.920" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that you're on right now""" start="00:06:45.640" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and it does a full text search,""" start="00:06:48.360" video="mainVideo-reference" id="subtitle"]]
[[!template text="""not only in the titles, but everywhere.""" start="00:06:50.400" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So, for example, I see that in this paper""" start="00:06:53.460" video="mainVideo-reference" id="subtitle"]]
[[!template text="""if I go to the abstract and search for the word FTIR,""" start="00:06:57.040" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which is a chemical analysis,""" start="00:07:04.760" video="mainVideo-reference" id="subtitle"]]
[[!template text="""it will tell me that it's here.""" start="00:07:06.880" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Can it find it anywhere else? It cannot. That's okay.""" start="00:07:09.880" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Let's search for something""" start="00:07:16.540" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that we'll be able to find more easily,""" start="00:07:18.112" video="mainVideo-reference" id="subtitle"]]
[[!template text="""like, for example, membrane crystallization""" start="00:07:21.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which is a main focus of my PhD.""" start="00:07:24.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Then it will be able to find it many times,""" start="00:07:27.540" video="mainVideo-reference" id="subtitle"]]
[[!template text="""many, many times.""" start="00:07:30.320" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I can also search on the next database""" start="00:07:35.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""or on this database and see where is everything that I want.""" start="00:07:40.300" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So this is different searching tools which are very useful.""" start="00:07:49.480" video="mainVideo-reference" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Filters""" start="00:07:55.480" video="mainVideo-reference" id="subtitle"]]</div>[[!template text="""Then there's also another tool, that is, filters.""" start="00:07:55.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So I can filter on any field.""" start="00:08:01.701" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Like, for example, let's say on any field,""" start="00:08:06.200" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and let's say I'm looking now again""" start="00:08:09.740" video="mainVideo-reference" id="subtitle"]]
[[!template text="""for membrane crystallization.""" start="00:08:13.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""This will now filter to all entries.""" start="00:08:16.280" video="mainVideo-reference" id="subtitle"]]
[[!template text="""You can see right now there's 18 entries here""" start="00:08:19.880" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that mention these two words together in any field.""" start="00:08:22.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Sometimes this is easier, because this is permanent.""" start="00:08:28.020" video="mainVideo-reference" id="subtitle"]]
[[!template text="""It's not like the search that we find one""" start="00:08:31.760" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and then if you move, you've lost it,""" start="00:08:33.700" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and you need to find it again.""" start="00:08:35.219" video="mainVideo-reference" id="subtitle"]]
[[!template text="""This is permanent until I say,""" start="00:08:37.886" video="mainVideo-reference" id="subtitle"]]
[[!template text="""okay, cancel the filter.""" start="00:08:39.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I mostly work with filters,""" start="00:08:41.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I think they're the most convenient.""" start="00:08:43.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Then there's also the ebib-list-recent""" start="00:08:47.060" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which is another very useful command.""" start="00:08:49.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""It asks you for a number of days""" start="00:08:51.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and it will show you the files that were added""" start="00:08:53.360" video="mainVideo-reference" id="subtitle"]]
[[!template text="""in the most recent.""" start="00:08:56.560" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So for example, show me the literature files""" start="00:08:58.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that were added to this bib file in the last month.""" start="00:09:02.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I will see five files in this case,""" start="00:09:05.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because in this bib file, I have mostly entries""" start="00:09:09.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that I have read, these are the files""" start="00:09:12.700" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I have most recently read and added here.""" start="00:09:15.240" video="mainVideo-reference" id="subtitle"]]
[[!template text="""While if I go for example here and say that,""" start="00:09:18.960" video="mainVideo-reference" id="subtitle"]]
[[!template text="""these are files that maybe I haven't read yet,""" start="00:09:21.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but I was planning to read. So this is something useful.""" start="00:09:25.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Although for things I'm planning to read,""" start="00:09:31.100" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I mostly use the reading list""" start="00:09:33.000" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that I'm going to show next.""" start="00:09:34.440" video="mainVideo-reference" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Dependent databases""" start="00:09:36.179" video="mainVideo-reference" id="subtitle"]]</div>[[!template text="""But before that,""" start="00:09:36.179" video="mainVideo-reference" id="subtitle"]]
[[!template text="""a few more neat things that you can do in Ebib.""" start="00:09:37.400" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So I have a list of dependent databases.""" start="00:09:41.760" video="mainVideo-reference" id="subtitle"]]
[[!template text="""For ease, I have already opened them here.""" start="00:09:45.020" video="mainVideo-reference" id="subtitle"]]
[[!template text="""These, as you can see, have two brackets here,""" start="00:09:48.820" video="mainVideo-reference" id="subtitle"]]
[[!template text="""indicating that they're dependent on phd_literature_1.bib,""" start="00:09:52.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and these, in my case, act as the sort of index file,""" start="00:09:59.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""where I am tagging things based on the structure""" start="00:10:06.379" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that I wanted to have for the organization.""" start="00:10:10.912" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So all the organization is flat,""" start="00:10:14.652" video="mainVideo-reference" id="subtitle"]]
[[!template text="""all the literature is in phd_literature_1,""" start="00:10:16.479" video="mainVideo-reference" id="subtitle"]]
[[!template text="""however, I have this file""" start="00:10:20.146" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that has 14 entries.""" start="00:10:23.420" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I have another file here that has 20 entries.""" start="00:10:25.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And these are smaller indexes""" start="00:10:32.900" video="mainVideo-reference" id="subtitle"]]
[[!template text="""where I can find things easier,""" start="00:10:35.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but things are not limited to one of these.""" start="00:10:38.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Things can be in all of these, or probably not all of these,""" start="00:10:41.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but can be in three or four of these very easily.""" start="00:10:45.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And how you add things is that I go here,""" start="00:10:50.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and I say not r, it's... M for the dependent databases,""" start="00:10:55.220" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and I add entry, and it will tell me""" start="00:11:00.080" video="mainVideo-reference" id="subtitle"]]
[[!template text="""&quot;Where do you want to add this?&quot;""" start="00:11:02.080" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So when I read a new paper,""" start="00:11:03.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I can say okay, this is related to these three tags,""" start="00:11:05.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and this is sort of like, again,""" start="00:11:09.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""it's tagging it and it's putting it""" start="00:11:11.240" video="mainVideo-reference" id="subtitle"]]
[[!template text="""there, there, and there.""" start="00:11:13.186" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And then this creates a flat structure""" start="00:11:15.060" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that however has a great organization,""" start="00:11:17.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""similar to how Zettelkasten works""" start="00:11:21.620" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and I really like working with something like this,""" start="00:11:23.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""with dependent databases.""" start="00:11:27.880" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Another feature that I really like,""" start="00:11:33.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""another feature that exists by default... But if I tag,""" start="00:11:36.540" video="mainVideo-reference" id="subtitle"]]
[[!template text="""this tagging is done through &quot;m&quot;,""" start="00:11:41.920" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and then I can tag different files here,""" start="00:11:45.280" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and this is to do different actions with these together,""" start="00:11:49.020" video="mainVideo-reference" id="subtitle"]]
[[!template text="""such as, for example,""" start="00:11:52.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""copy them to a different file,""" start="00:11:53.586" video="mainVideo-reference" id="subtitle"]]
[[!template text="""with &quot;x&quot; I can export the entries somewhere else,""" start="00:11:55.586" video="mainVideo-reference" id="subtitle"]]
[[!template text="""there are many things that you can do""" start="00:11:59.460" video="mainVideo-reference" id="subtitle"]]
[[!template text="""when you mark them.""" start="00:12:00.686" video="mainVideo-reference" id="subtitle"]]
[[!template text="""By the way, one of them is this function,""" start="00:12:01.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which sees everything that I have marked""" start="00:12:05.320" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and shows me an org-roam-node-find entry""" start="00:12:08.940" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that is filtered to just these files.""" start="00:12:14.786" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I can select one and it will take me""" start="00:12:18.053" video="mainVideo-reference" id="subtitle"]]
[[!template text="""to my notes on this specific paper.""" start="00:12:20.886" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I find this very useful,""" start="00:12:24.400" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because I can be looking for something""" start="00:12:25.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and I can say, okay I remember,""" start="00:12:27.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""or I did some filtering,""" start="00:12:30.019" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and I know it's in one of these files""" start="00:12:31.400" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and now I want to see my in-depth notes on each one""" start="00:12:34.100" video="mainVideo-reference" id="subtitle"]]
[[!template text="""to remember where exactly I found it.""" start="00:12:37.240" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So I find this kind of filtering,""" start="00:12:41.080" video="mainVideo-reference" id="subtitle"]]
[[!template text="""this org-roam related filtering, to be also very effective.""" start="00:12:43.420" video="mainVideo-reference" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Reading lists""" start="00:12:50.540" video="mainVideo-reference" id="subtitle"]]</div>[[!template text="""So now let's finally move to reading list.""" start="00:12:50.540" video="mainVideo-reference" id="subtitle"]]
[[!template text="""The reading list in ebib""" start="00:12:54.080" video="mainVideo-reference" id="subtitle"]]
[[!template text="""reminds me a lot of the philosophy that Emacs uses.""" start="00:12:55.400" video="mainVideo-reference" id="subtitle"]]
[[!template text="""By default, it is extremely bare bones, not very usable,""" start="00:13:00.260" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but it is so customizable, to where you can do""" start="00:13:05.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""anything that you can imagine through it""" start="00:13:10.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because the limit truly is your imagination.""" start="00:13:13.020" video="mainVideo-reference" id="subtitle"]]
[[!template text="""It's how much you can code into this""" start="00:13:16.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that actually makes sense""" start="00:13:21.040" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and you can actually imagine it working.""" start="00:13:22.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Besides that, you can do anything really.""" start="00:13:25.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So we can open ebib and try to find this paper""" start="00:13:31.700" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that I just added here.""" start="00:13:36.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Then we can create a reading list entry from it.""" start="00:13:42.700" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Here, my reading list prompts me""" start="00:13:48.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""for a priority for this.""" start="00:13:52.000" video="mainVideo-reference" id="subtitle"]]
[[!template text="""How urgent it is for me to read this.""" start="00:13:53.419" video="mainVideo-reference" id="subtitle"]]
[[!template text="""It adds a TO-READ, which is a todo entry,""" start="00:13:57.240" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which helps with organizing my reading list,""" start="00:14:02.220" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because as you may also be able to see, this has an ID,""" start="00:14:04.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because this is an org-roam node,""" start="00:14:08.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""so the TO-READ allows me to organize it inside org-roam.""" start="00:14:11.580" video="mainVideo-reference" id="subtitle"]]
[[!template text="""It saves the citekey, the link to the paper,""" start="00:14:16.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and also tags it with the parent file node""" start="00:14:21.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because I don't like having orphan nodes in my Zettelkasten.""" start="00:14:25.980" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I like everything to be linked to at least one thing.""" start="00:14:30.380" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So everything in the reading list""" start="00:14:33.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""is linked to the parent file.""" start="00:14:35.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And now I can find this in the org-roam-node-find menu,""" start="00:14:39.300" video="mainVideo-reference" id="subtitle"]]
[[!template text="""here. However, that's not very interesting.""" start="00:14:47.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""In practice, my typical org-roam-node-find""" start="00:14:53.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""does not even include these reading list files""" start="00:14:56.240" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because I don't really care to have them there.""" start="00:14:59.760" video="mainVideo-reference" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Special org-roam-node-find""" start="00:15:02.440" video="mainVideo-reference" id="subtitle"]]</div>[[!template text="""I have a special org-roam-node-find""" start="00:15:02.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that is designed to find these in particular.""" start="00:15:06.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And here these have 22. These are the amount of files""" start="00:15:13.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that are currently in my reading list.""" start="00:15:16.460" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So for example, let's try and press here.""" start="00:15:21.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And magically, this prompts me to select a capture template,""" start="00:15:29.900" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because what it's doing is that I selected this,""" start="00:15:33.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and because of the citekey, it knows""" start="00:15:39.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that it wants to create a new node for that.""" start="00:15:42.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So I select the capture template.""" start="00:15:46.540" video="mainVideo-reference" id="subtitle"]]
[[!template text="""It knows that it wants to create this new node for this.""" start="00:15:47.960" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And now, if I for a second close the reading list,""" start="00:15:56.100" video="mainVideo-reference" id="subtitle"]]
[[!template text="""now I can already go ahead and take notes on this.""" start="00:16:01.360" video="mainVideo-reference" id="subtitle"]]
[[!template text="""This is org-noter, in particular,""" start="00:16:07.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and it makes it all very easy""" start="00:16:09.760" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because it's all integrated in one place.""" start="00:16:11.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""If I then close this and open a new Emacs,""" start="00:16:15.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""we have this, and the reading list allows me to very quickly""" start="00:16:22.540" video="mainVideo-reference" id="subtitle"]]
[[!template text="""go from this being reading this item to initializing it.""" start="00:16:27.940" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Another thing that is very useful is that""" start="00:16:32.540" video="mainVideo-reference" id="subtitle"]]
[[!template text="""everything is sorted by priority.""" start="00:16:35.040" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So I need to increase the font size again""" start="00:16:38.740" video="mainVideo-reference" id="subtitle"]]
[[!template text="""because I closed the previous Emacs.""" start="00:16:41.360" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So here, I can select what is high priority,""" start="00:16:48.900" video="mainVideo-reference" id="subtitle"]]
[[!template text="""what is low priority. I can also change the priority""" start="00:16:52.320" video="mainVideo-reference" id="subtitle"]]
[[!template text="""without needing to be in this file.""" start="00:16:56.400" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Let's leave this file. I can say, okay, I decided""" start="00:16:58.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that this file is priority B. It needs to be A,""" start="00:17:05.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""which is more urgent.""" start="00:17:08.640" video="mainVideo-reference" id="subtitle"]]
[[!template text="""In my system, there's five different priority levels.""" start="00:17:11.900" video="mainVideo-reference" id="subtitle"]]
[[!template text="""You can get away with less""" start="00:17:16.080" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but I like to have the very much low ones""" start="00:17:18.000" video="mainVideo-reference" id="subtitle"]]
[[!template text="""as this is not urgent at all""" start="00:17:20.960" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but I want to keep it somewhere. A is very urgent""" start="00:17:23.000" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and B is urgent but just below A.""" start="00:17:27.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And then the C in the middle is just""" start="00:17:31.780" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I will eventually read this""" start="00:17:34.620" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but not something I want to focus my attention on right now.""" start="00:17:36.000" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So this is mostly about reading list.""" start="00:17:41.920" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I can also show, for example,""" start="00:17:45.440" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I have this if I finalize something,""" start="00:17:46.640" video="mainVideo-reference" id="subtitle"]]
[[!template text="""if I read it. For example, I created a note for this new thing.""" start="00:17:50.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Let's say I finished reading it.""" start="00:17:56.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I want to remove from my reading list.""" start="00:17:59.080" video="mainVideo-reference" id="subtitle"]]
[[!template text="""It's also just one command and it's done.""" start="00:18:02.180" video="mainVideo-reference" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Annotations""" start="00:18:05.640" video="mainVideo-reference" id="subtitle"]]</div>[[!template text="""If we now return to the presentation,""" start="00:18:05.640" video="mainVideo-reference" id="subtitle"]]
[[!template text="""the last thing I want to show is annotations.""" start="00:18:08.740" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So for annotations, it's the idea that sometimes""" start="00:18:11.700" video="mainVideo-reference" id="subtitle"]]
[[!template text="""you just need to find something in Ebib quickly.""" start="00:18:17.120" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So I'm here and I'm looking for something.""" start="00:18:23.140" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I said I'm here and I'm looking for something.""" start="00:18:26.680" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And as you can see, there's the annote file everywhere,""" start="00:18:31.000" video="mainVideo-reference" id="subtitle"]]
[[!template text="""the annote entry, which is a very very small description""" start="00:18:35.200" video="mainVideo-reference" id="subtitle"]]
[[!template text="""of things that I want to remember for this paper.""" start="00:18:40.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""So I can be scrolling here or scrolling""" start="00:18:43.800" video="mainVideo-reference" id="subtitle"]]
[[!template text="""in one of the smaller files""" start="00:18:48.040" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and saying this was in this subsection,""" start="00:18:51.812" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and which paper was it, and I can scroll,""" start="00:18:56.860" video="mainVideo-reference" id="subtitle"]]
[[!template text="""read all these annotes.""" start="00:18:59.520" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Each annote takes like 15 seconds to read,""" start="00:19:01.712" video="mainVideo-reference" id="subtitle"]]
[[!template text="""and really decide, okay,""" start="00:19:04.920" video="mainVideo-reference" id="subtitle"]]
[[!template text="""it was this paper that I wanted, good.""" start="00:19:07.360" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Now I can open the note for it, go there, and it's very easy.""" start="00:19:09.800" video="mainVideo-reference" id="subtitle"]]

<div class="transcript-heading">[[!template new="1" text="""Wrapping up""" start="00:19:21.820" video="mainVideo-reference" id="subtitle"]]</div>[[!template text="""So I think that's all. I would like to thank you for your time.""" start="00:19:21.820" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I would love to see your questions either in IRC,""" start="00:19:25.720" video="mainVideo-reference" id="subtitle"]]
[[!template text="""I will be, maybe I've already answered""" start="00:19:29.320" video="mainVideo-reference" id="subtitle"]]
[[!template text="""some of your questions there in the Etherpad,""" start="00:19:32.200" video="mainVideo-reference" id="subtitle"]]
[[!template text="""or right now, we're going to the live Q&A""" start="00:19:35.040" video="mainVideo-reference" id="subtitle"]]
[[!template text="""where I'd love to interact with everyone and have a discussion.""" start="00:19:37.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""However, if you don't have any questions right now,""" start="00:19:42.160" video="mainVideo-reference" id="subtitle"]]
[[!template text="""but you have a question later on, feel free to send me an email.""" start="00:19:44.480" video="mainVideo-reference" id="subtitle"]]
[[!template text="""My mail is also on the site.""" start="00:19:48.560" video="mainVideo-reference" id="subtitle"]]
[[!template text="""And if you're curious how all this &quot;magic&quot; worked,""" start="00:19:51.740" video="mainVideo-reference" id="subtitle"]]
[[!template text="""feel free to go to my Github and see the ebib section""" start="00:19:54.600" video="mainVideo-reference" id="subtitle"]]
[[!template text="""here that will also be linked in the doc page,""" start="00:20:00.840" video="mainVideo-reference" id="subtitle"]]
[[!template text="""where you can see all the configuration""" start="00:20:04.040" video="mainVideo-reference" id="subtitle"]]
[[!template text="""that I have done in Ebib for everything to work.""" start="00:20:06.280" video="mainVideo-reference" id="subtitle"]]
[[!template text="""Thank you again and have a wonderful EmacsConf!""" start="00:20:10.920" video="mainVideo-reference" id="subtitle"]]

</div>Questions or comments? Please e-mail [vidianosgiannitsis@gmail.com](mailto:vidianosgiannitsis@gmail.com?subject=Comment%20for%20EmacsConf%202023%20reference%3A%20Emacs%20as%20a%20fully-fledged%20reference%20manager)


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