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@@ -3,6 +3,7 @@ Noorah Alhasan
 
 [[!template id=vid src="https://mirror.csclub.uwaterloo.ca/emacsconf/2020/emacsconf-2020--17-org-mode-and-org-roam-for-scholars-and-researchers--noorah-alhasan.webm" subtitles="/2020/subtitles/emacsconf-2020--17-org-mode-and-org-roam-for-scholars-and-researchers--noorah-alhasan.vtt"]]  
 [Download compressed .webm video (22.2M)](https://mirror.csclub.uwaterloo.ca/emacsconf/2020/smaller/emacsconf-2020--17-org-mode-and-org-roam-for-scholars-and-researchers--noorah-alhasan--vp9-q56-video-original-audio.webm)
+[View transcript](#transcript)
 
 Org-mode improved so much over the years, and the use-cases in org-mode are
 vast and highly technical. There is something for everyone in org-mode, and
@@ -79,3 +80,317 @@ Definitely interested, but there is no place (yet!).
   show (parts of) other files inline and allow editing in a separate
   mini-buffer.
 - There is a Slack channel for org-roam link/backlink pls?
+
+
+<!-- transcript: 2020/subtitles/emacsconf-2020--17-org-mode-and-org-roam-for-scholars-and-researchers--noorah-alhasan.vtt -->
+
+<a name="transcript"></a>
+# Transcript
+
+Good afternoon or good evening, everyone. Today, my talk is going to
+be on Org Mode and org-roam for scholars and researchers. Leo has
+talked about the overall picture of org-roam and org-roam-bibtex. I
+will be talking more about the research process itself using these
+tools.
+
+(00:00:20) All right. So, just to introduce that the research process
+is really messy. You're always working in piecemeal tasks and things
+move around all the time. There needs to be a system where you can
+organize all these tasks, all these ideas in a way that is flexible
+and effective. So my motivation is that research is hard and writing
+about it is even more difficult. My goal is to add some structure to
+this whole madness.
+
+(00:00:51) Here's a list of some of the stuff that I've been using
+since I first learned about Emacs in 2019 and what I've found useful
+within my research process. I've organized Org Mode for Researchers
+and Scholars Within the Writing Process into three modules. First,
+there's the planning aspect of it, then you've got the writing and the
+reference management, which I will join together by looking at the
+example of doing your literature review.
+
+(00:01:21) When we're talking about planning, we're talking about
+either task management or time management with task management. You've
+got Org Mode's TODOs, tags, and categories. These are really powerful
+tools that you could use in your Org files to organize your tasks and
+your appointments. There are different types of TODOs that you can
+either set globally in your init file or they can be
+file-/buffer-specific. That means, based on context, based on the type
+of manuscript you're working on, whether it's a literate programming
+report or your actual thesis/dissertation.
+
+(00:02:03) Also, these TODOs are either created as a subtree, like
+think of them as headings and sections if you use LaTeX, or inline
+tasks, which are like Org inline tasks. I like Org inline tasks
+because I can add TODOs between two paragraphs. That way, it doesn't
+show up in the table of contents when I export into PDF, HTML, or
+anything else. So this is an example of buffer-specific TODOs, and
+this is an example of a little programming report that I was working
+on where I was dealing with data and analysis and all of that stuff. I
+needed context-specific TODOs to use them within this buffer. That's
+how I would organize it. There's also another example of an Org inline
+task where you could see it in the middle between the two headings.
+That way, it wouldn't show up in the table of contents, and it would
+look neater within the text when you export it. I also added a tag of
+:noexport: so it won't show up at all when I export it into either
+PDF, which I use all the time.
+
+(00:03:19) Another useful tool for the research and just general
+planning is the org-capture. When I first started with Emacs,
+actually, it was for org-agenda. I went crazy with my capture
+template. I created a template for everything because I was just so
+excited. But with time, I was using less and less of them, so I kept
+taking them out. Now this is my simplified capture templates that I
+use, either for a general TODO, for a regular appointment, a fleeting
+note, research tasks (because those are what I focus on, like my bread
+and butter), and then finally with meetings, which I find sometimes I
+don't use it as much because I would just have the Org file ready
+instead of needing to capture, you know, open a capture template.
+
+(00:04:07) Right. Org Agenda. That's how I got into Emacs. I needed to
+organize my life. I found Emacs and it's been great ever since. It
+populates all your TODOs and appointments into a singular view. So the
+default view, I think, is a week view. However, I use
+org-super-agenda. Love this package. I set up my agenda as a daily
+view with appointments, deadlines, and a habit tracker. A side note,
+you guys: I'm still struggling with organizing the perfect agenda, so
+it's a process. Take it easy, all right? So this is just an overview
+of my daily agenda. As you can see they're just appointments that I
+import from Gmail using org-gcal; a simple habit tracker of daily free
+writing-- as you can see, there are a lot of times where I'm skipping,
+and the asterisk is the one where I've completed that day, so, you
+know, it's a process--and then regular deadlines. So what happens is
+that I have other TODOs that I have not scheduled or not added a
+deadline but they're just tasks that keep piling up.
+
+(00:05:19) When I first started with Emacs and org-agenda, I had
+everything in there, and it got overwhelming. Then I decided, no, I'm
+not gonna even let them show up. So what I would do at the beginning
+of each week or the night before, I would sit down, look at all my
+TODOs that I have not assigned yet to a deadline or a schedule or just
+a simple timestamp, and I would organize them throughout the week. So,
+here's an example of what I did. On that Wednesday, from my Gmail, I
+had all these appointments, but one of them is I have a writing group
+session. So I looked at my tasks and I thought, okay, then I will just
+assign, for example, my Emacs slides or the framework diagram into
+that writing session. All I did was just add an active timestamp. That
+is all I needed to do, and it went straight into my appointment. Now,
+if I miss that, it won't show up on the next day. So if you put in a
+deadline, it will show up as an overdue, but if you have no deadline
+or schedule, it will not show up in your daily org agenda. So, just a
+star.
+
+(00:06:32) All right. Another way of accessing your TODOs is that if
+it's Org file-specific, buffer-specific, and so... Like when we talked
+about like whether to have a big-ass Org file or like tiny files, it
+all depends. This isn't the... you know, the way this depends, because
+if you're working on a dissertation, it's a huge manuscript. You need
+to work on that Org file all the time. Then yes, my TODOs should be in
+that file specifically, because every time, if I'm visiting this Org
+file all the time, I should be able to just look at my tasks from
+within that buffer. And so I use org-sidebar to keep all these
+specific TODOs within that Org file. I find it helpful. Okay.
+
+(00:07:26) Now that we're going into the writing and reference
+management... We'll call it a literature review. This is something
+I've built as a schema. I think that it works for now. It requires one
+outside software, which is Zotero, what I use. It's an open source
+reference management software. It's great. But the thing to keep in
+mind is that I use two plugins that are really needed for when we work
+with org-roam-bibtex, org-roam, Org Mode, and the ZotFile. Better
+BibTeX organizes your reference keys in a way, in a fashion that works
+for you. For me, all my reference keys are last author and year. With
+ZotFile, I let it rename all the PDF files the same way that I have
+for my Bib keys, which is last name of author and year. All right.
+Once you export your entire library as a Bib file, then you can work
+on it within Org Mode and Emacs using the following packages. So with
+org-roam-bibtex, it creates an Org file for each Bib entry. You have
+the option of templating and doing other stuff with it.
+
+(00:08:52) Then finally, there's this orb-pdf-scrapper. I've used it
+briefly but I think the potential with orb-pdf-scrapper is if you're
+going to do a bibliometric study or a systematic literature review,
+there's something there, but I have to look through it. Anyway, so
+once you create your reference file of reference X and you're writing
+your notes, you can either go... Like, with going through Org Mode,
+you're writing your ideas, you're writing your notes, you're assigning
+tasks, and then there's org-transclusion, which I will mention briefly
+at the end, and ways to extract. If you're going to go through the
+org-roam... Things that you're going to use within org-roam... It's a
+great way to build your database. You start making the connections.
+You can visualize your notes and how these references are linked to
+each other through the org-roam server or org-roam graph. All right.
+This is just notes for later.
+
+(00:09:53) So this is an example of an org-roam file that I have. For
+example, if I'm working on adaptation policy, I have these hyperlinks
+that are linked to other concepts and ideas such as either climate
+security, changing global environment, so on and so forth. The
+backlinks are other references that talk about this specific concept.
+This is really helpful. Then, when you visualize it, the picture on
+the left (which I'm sure looks really small), you can see the
+connections that it's making with other references. Of course, this is
+just like a buffer network. When you look at the entire database
+network... It's growing. Okay.
+
+(00:10:38) So going into org-roam-bibtex... It utilizes a combination
+of the org-ref package, helm-bibtex, bibtex-completion. It works with
+org-roam functionalities and other good stuff. This is an example of
+my org-roam-bibtex file. All right. So I've created the template which
+I pretty much use, what Leo has produced in his tutorial. I think it's
+great. It works well for me. What it does is that it works with your
+bib file. So if you're in your bib file, you have a sub entry that's
+called keywords, and usually that's within a journal article. The
+author would specify these keywords. When it gets imported into
+Zotero, it extracts those keywords and then it gets populated as an
+Org file with org-roam-bibtex. I always start with the meta
+information first, and then I would write my notes after that. This is
+an example, though, for reference of a physical book, so I don't have
+a pdf file for it. So when I've figured out a new idea for it, if I'm
+writing notes on it, I would create a property that says pages. That
+way, it's easier for you when you go back to citing certain ideas or
+something, that you have the pages prepared there. It's easier that
+way. Okay.
+
+(00:12:07) org-noter which is something I use a lot, especially with
+journal articles that have PDFs and stuff like that. They're really
+helpful if you are going to... If you've just started using Emacs and
+org-roam, and you have all these PDFs that have all the annotations
+and highlighting and all that stuff, with org-noter you can just use
+the org-noter-create-skeleton command and it will populate all your
+notes that have already been entered within the PDF file if you're
+using an outside software, and creates them as a neat Org file. I
+highly recommend.
+
+(00:12:52) Finally, org-transclusion. I think this is still in its
+beta phase, but I've been enjoying it so far. I'm guessing people know
+what transclusion means, which is like copy-pasting text from one Org
+file to another. This is helpful. I think I peeked at a question that
+was talking about linking to other Org files. I think org-transclusion
+could really work. It's equivalent to the include function within Org
+Mode, but I think... So if you have other files that you know which
+region that you need in another file, you could use the #+INCLUDE, but
+with org-transclusion... It's great. I mean you just have... you're
+just linking one part to the other. Sort of... Like, not refiling, but
+you know hyperlinking. So this is an example of what org-transclusion
+looks like. The highlighted problem statement is from another Org
+file. Then what I would do is just link it to there, and there was a
+transclusion command. I wish I made another screenshot of it. When you
+invoke org-transclusion-mode, it turns... It prints it out like that.
+It's in view mode. Then when you want to edit, it will take you back
+to that buffer and you can edit the text however you want. All right.
+So, thank you so much.
+
+(00:14:22) I wanted to leave room for questions, but special thanks to
+all the folks that work on org-roam, org-roam-bibtex, org-roam-server,
+org-transclusion, and of course alphapapa on org-super-agenda and
+org-sidebar. That's how I got into Emacs. Thank you.
+
+(00:14:43) (Leo: All right. Well, thank you. So yeah, this time I'll
+be the one asking the question and not Amin. I'm filling big shoes
+right now, so you'll have to bear with me folks. So thank you so much,
+Noorah, for your presentation that is incredibly interesting. Would
+you mind if I fed you questions from the charts?)
+
+(00:15:00) Noorah: Go ahead. (Leo: Okay. so the first one I've picked
+on my end was "Did you try using ebib instead of Zotero, and if so, is
+it better than Zotero in some ways?) Noorah: No, I have not used Ebib.
+I've only used Mendeley and then they got bought by Elsevier, and so I
+was, like, okay I'm done, I'm going to Zotero. There are a lot of
+plugins with Zotero that you can play around with. I can't speak for
+Ebib, but definitely Zotero has been a good experience so far. (Leo:
+Yes, same. I also do research on the side; as I told you, English
+major, and yeah I also do Zotero. Some people have been using uh a
+connector between Zotero and Emacs which has... they've had great
+success with them but personally I haven't touched it already, so
+yeah. Oh, go ahead. Sorry.) Noorah: All right. So far, I don't have
+any problems with Zotero, but maybe if I run into something, I might
+check out Ebib in the future. (Leo: yeah, definitely. I think zotero
+is a very solid project. You know, the fact that it's being used by
+people outside of Emacs also ensures that there's quite a lot of
+backing behind the software, which is reassuring when your livelihood
+depends on your research.) Noorah: Right. And then I think one more
+thing with Zotero is that you can create groups, so if you're in a
+collaborative project, you can create a reference, a library just for
+your group, and I think that could help. I'm going to be in a project
+next semester that requires that.
+
+(00:16:27) (Leo: Yeah, definitely. I believe the ability to have
+folders inside Zotero makes it incredibly useful to manage your
+different projects, concurrent projects. So moving on to other
+questions, do you have any suggestion on what subjects or things
+should be tags or separate org-roam files for cross-linking?)
+
+(00:16:46) Right. So far, now, I'm having trouble with "should I be
+combining certain concepts together as one?" This is where the thought
+process starts coming to fruit, is that when you start combining ideas
+together so you won't need a specific tag and another one that are
+like similar in ideas... I'm not sure if that answers the question,
+but so far I've been using the org-roam the default way, which is many
+small files and then just linking them to my... Like, either if I have
+a report to write, or if I have an essay to write... I think you're
+muted.
+
+(00:17:35) (Leo: I did two stupid things. The first one was spilling
+out my water. The second one was speaking without actually turning on
+my microphone. Let's just hope that nothing is going to fry in the
+near vicinity of me right now. But yeah, I believe you've answered the
+question, so don't worry about it. I'm slightly wet right now, which
+is not a very agreeable feeling, but we'll have to carry on, I
+suppose. Another question: "is there a place where people are
+collaborating on research about Emacs?" So do you want to try to take
+this one?)
+
+(00:18:06) Noorah: I don't know, but I'm definitely interested in the
+user experience of Emacs, so if anyone wants to work on that, I'm
+happy.
+
+(00:18:16) (Leo: Well you do have a a pretty good candidate in front
+of you, if I should say so myself. I'm incredibly interested about the
+ability to do research in Emacs and about the ability to preach the
+FLOSS way to academia and to the academe, especially because I believe
+there's really something great to be done. Sorry, I'm just looking at
+the puddle of water on the side which is slightly oozing my way, which
+is not a very good feeling, really. I believe some work could be done,
+and if people are interested in the chat right now, do get in touch
+with us. Both Noorah and I are on our Slack channel. Yes, I know,
+Slack, the corporate hive mind that is Slack. But we've decided with
+org-roam to use Slack. You can find us very easily. If you want to
+talk about these topics, by all means, do, and we'll be very
+interested to answer your questions.)
+
+(00:19:10) Noorah: I have a question here that says, "How does the
+view for time blocking works?"
+
+(00:19:15) I use org-super-agenda, so what happens is that my active
+timestamps are only in my Gmail Org file. If you use org-gcal, you
+have to specify a certain Org file. When it imports them, it imports
+them as active timestamps. I make sure whenever I create a TODO or
+even a research task that it doesn't have a timestamp on it, because
+what I want to do is go back and then move around these tasks
+according to my either weekly schedule, or monthly, or however long
+you want to do it. So yeah, only active timestamps or deadline um
+appear in your time grid. So that could work. (Leo: That's very good.
+Just to interject for a second about this, you know with org-roam
+right now, we're mostly focused on optimization, but we're hoping to
+move on to UX very soon. So all those matters about having TODOs in
+your files, it is something that we've been thinking about with Jethro
+Kuan, who is my main co-maintainer for org-roam. We'll be working on
+this in the coming months, so don't worry too much about it and stay
+tuned.)
+
+(00:20:26) Noorah: Yeah. So I've got the ebib and what else... What
+subjects... I think... Okay! What is this question? "Have you seen the
+project Papis?"
+
+(00:20:37) I'm not sure what... oh it's a Zotero alternative. Okay.
+I'll look into it. Thank you. (Leo: I don't know about it either, so
+please look into it and let me know.) Have we covered all the
+questions?
+
+(00:20:53) (Leo: I believe we have. We have about two-minute leeway
+for me to move into the next talk, so we're right on time.) All right.
+Thank you so much. Really appreciate it. Good luck everyone! (Leo:
+well thank you, and thank you so much for coming, and allowing me not
+to be the only one talking about org-roam today.) Noorah: Sounds good.
+All right. (Amin: Thank you both very much.)