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diff --git a/2020/info/17.md b/2020/info/17.md index 937ba159..37a07710 100644 --- a/2020/info/17.md +++ b/2020/info/17.md @@ -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.) |