path: root/2020/subtitles/emacsconf-2020--17-org-mode-and-org-roam-for-scholars-and-researchers--noorah-alhasan-autogen.sbv

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good afternoon or good evening everyone

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uh

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today my talk is going to be on org mode

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and or group for skulls and researchers

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leo has talked about like the overall

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picture of orgrim and or

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uh bibtex or groundbreak tech I will be

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talking more about

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the research process itself using these

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tools

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all right so just to introduce that the

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research process is really messy

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um you're always working in like

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piecemeal tasks and things move around

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all the time and so

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there needs to be a system where you can

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organize all these tasks

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all these ideas in a way that is

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flexible and effective

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so my motivation is that research is

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hard and

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writing about it is even more difficult

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and my goal is to add some structure to

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this whole madness

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so here's a list of some of the stuff

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that I've been using since I first

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learned about Emacs in 2019

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and what I've what I've found useful um

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during my res uh like um

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within my research process all right so

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I've organized org mode for researchers

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and scholars within the writing process

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into three modules first there's like

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the planning aspect of it

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then you've got the writing and the

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reference management which I will join

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together

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by looking at the example of doing your

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literature review

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all right so when we're talking about

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planning we're talking about either task

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management or

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time management with task management

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you've got

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org modes to do's and tags and

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categories these are really powerful

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tools that you could use

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um in your org files to just um

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uh like organize your tasks and

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your appointments so there are different

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types of to-do's that you can either set

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globally in your init file or they can

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be file buffer specific

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so that means based on context based on

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the type of

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manuscript you're working on whether

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it's like a literate programming

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report or your actual thesis slash

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dissertation

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um also these to-do's are either created

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as a set tree like think of them as

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headings and sections if you use latex

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or inline text which are like org inline

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tasks I

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like organ line tasks because like I can

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add

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to do's between two paragraphs and that

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way it doesn't show up

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in the table of contents when I export

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into pdf or html or

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anything else all right so this is an

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example of buffer specific to do's

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and and this is example of like a little

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programming report that I was working on

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where I was like dealing with

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data and like analysis and all of that

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stuff and so

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I needed um context specific to do's to

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use them within this buffer

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um and that's how I would organize it

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and there's also also another example

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of an org inline task where you could

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see it

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in the middle between the two headings

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that way it wouldn't show up in the

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table of contents and it would look like

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nature within the

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text when you export it

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oh but I also added a tag of no export

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so it won't show up at all

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when I export it into like either pdf

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which I use all the time all right so

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another useful tool

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um for the research and just like

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general planning

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is the org capture um when I first

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started with Emacs

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actually it was for org agenda and I

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went crazy with my capture template I

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created a template for

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everything um because I was just so

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excited

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but with time I was using less and less

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of them so I kept taking them out

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and now this is my simplified um

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capture templates that I use either for

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a general to do

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um for a regular appointment a fleeting

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note research tasks because like those

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are what I focus on

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like my bread and butter and then

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finally with meetings which I find

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sometimes I don't use it as much because

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I would just like

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have the org file ready instead of

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needing to capture

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you know open a capture template

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right or agenda um that's how I got into

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Emacs

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I needed to um organize my life and I

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found Emacs and

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it's been great ever since um it

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populates all your to-do's and

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appointments into a singular view so the

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default view I think it's a weak view

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however I use org super agenda love this

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um package and I set up my agenda as a

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daily view with just appointments

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deadlines and a habit tracker um and

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a side note you guys I'm still

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struggling with organizing the perfect

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agenda so it's a process

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and take it easy all right

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so this is just an overview of my daily

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agenda as you can see they're just like

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appointments that I import from gmail

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using org gcal

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a simple habit tracker of like daily

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free writing

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as you can see there are a lot of times

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where I'm skipping and the asterisk is

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the one where I've completed that day

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so you know it's a process and then just

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like regular deadlines

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so what happens is that I have other

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to-do's that I have

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not scheduled or not added a deadline

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but they're just

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tasks that keep piling up when I first

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started with Emacs and org agenda

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I had everything in there and it got

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overwhelming and then I decided no

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I'm not gonna even let them show up so

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what I would do

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at the beginning of each week or the

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night before

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um I would sit down look at all my to

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to-do's that I have

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not assigned yet to a deadline or a

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schedule or just a simple

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timestamp um and I would organize them

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throughout the week

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so here's an example of what I did

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so on that wednesday from my gmail I had

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all these appointments but

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one of them is I have a writing group

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session

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and so I looked at my tasks and I

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thought okay then I will just

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assign um like for example my emac

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slides

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or the framework diagram into that

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writing session

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and all I did was just add an active

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timestamp

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that is all I needed to do and it went

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straight into my

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appointment now if I miss that

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it won't show up on the next day so if

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you put in a deadline

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it will show up as an overdue but if you

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have no deadline or schedule it will not

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show up in your daily org agenda

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so just a star

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all right another way of accessing your

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to do's is that if it's

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um file specific org file specific

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buffer specific

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and so like when we talked about like

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whether to have a big ass org file or

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like tiny files

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it all depends and this isn't the the

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um you know the way this depends

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because if you're working on like a

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dissertation um it's a huge manuscript

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you need to like work

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on that org file all the time um

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then yes it might do should be in that

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file specifically because every time if

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I'm

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if I'm visiting this org file all the

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time I should be able to just look at my

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tasks from uh within that buffer

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and so I use org sidebar to

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keep all these specific uh to do's

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within that org file

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I find it helpful okay

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now that we're going into the writing

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and reference management

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we'll call it a literature review um

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and this is something I've built as a

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schema

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I think that it works for now

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um and it requires one outside pack

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of outside software which is zotero what

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I use it's an open source reference

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management

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software um it's great

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but the things to keep in mind is that I

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use two um

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plugins that is really needed for when

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we work with orgrim bibtex and orgrim

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and org mode um and the zap file so

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better bibtex organizes your reference

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keys

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um in um in a way like in a fashion that

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works for you so for me all my reference

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keys are like

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last author and gear um and with zap

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file I um I let it like rename all the

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pdf files

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the same way that I have for my bit of

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my bib keys which is like

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last name of author and year all right

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once you export your entire

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library as a bib file then you can work

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on it within org mode and Emacs

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using um the following packages

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all right so with orgrim bibtex it

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creates an org file for each bib entry

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and you have the option of like

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templating and doing other stuff with it

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and then finally there's like this orb

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pdf scraper

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I've used it briefly but I think the

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potential

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with or pdf scraper is if you're gonna

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do a bibliometric study or like a

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systematic literature view there's

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something there but I have to look

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through it

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anyway so once you create your you know

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your reference file of reference x and

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you're writing your notes

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you can either go like with going

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through org mode you're writing

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your ideas you're writing your notes

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you're assigning tasks

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and then there's org transclusion which

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I will mention briefly at the end

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and ways to extract if you're going to

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go through the orgrom

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things that you're going to use within

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orgrom it's a great way to build your

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database you start making the

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connections and you can visualize your

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notes and like how these references are

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linked to each other

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through the organ server or or ground

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graph

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all right this is just notes for later

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okay

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so this is an example of like an orgram

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file that I have

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for example if I'm working on adaptation

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policy I have these hyperlinks that are

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linked to other

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concepts and ideas such as either

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climate security

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um changing global environment so on and

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so forth and the backlinks

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are other references that talk about

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this specific concept

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so this is really helpful and then when

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you visualize it the picture on the left

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which I'm sure looks really small

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um you can see the connections that it's

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making with other

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references so of course this is just

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like a buffer

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network when you look at the entire

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database network it's it's

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it's growing okay

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so going into organ bidtech

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so it utilizes a combination of the or

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graph package helmbik tech candidate

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completion

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and it works with orgrom functionalities

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and

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other good stuff this is an example

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of my orgrim bibtex file all right so

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I've created

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um the template which I pretty much use

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what leo

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has uh produced like in his um

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tutorial so I think it's it's great it

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works well for me

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um and what it does is that it works

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with your bib file

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so if you're in your bib file you have a

0:11:17.519,0:11:21.040
sub entry that's called keywords and

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usually that's within

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a journal article the author would

0:11:23.120,0:11:27.519
specify these

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keywords um when it gets imported into

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zotero

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it extracts those keywords and then it

0:11:30.399,0:11:34.959
gets populated as an org file

0:11:32.399,0:11:36.959
with orgrim bibtex so I always start

0:11:34.959,0:11:38.560
with the meta information first and then

0:11:36.959,0:11:42.480
I would write my notes

0:11:38.560,0:11:45.760
after that this is an example though

0:11:42.480,0:11:49.120
for reference of a physical book so

0:11:45.760,0:11:51.519
I don't have a pdf file for it um

0:11:49.120,0:11:53.920
so what I've figured out like a new idea

0:11:51.519,0:11:55.760
for it so if I'm writing notes on it

0:11:53.920,0:11:57.279
I would create a property that says

0:11:55.760,0:11:58.959
pages um

0:11:57.279,0:12:00.639
that way it's easier for you when you go

0:11:58.959,0:12:02.720
back to citing

0:12:00.639,0:12:04.720
um certain ideas or something that you

0:12:02.720,0:12:07.839
have the pages prepared there

0:12:04.720,0:12:11.279
it's easier that way okay

0:12:07.839,0:12:13.040
org noter which is something I

0:12:11.279,0:12:14.880
use a lot especially with journal

0:12:13.040,0:12:15.600
articles that have pdfs and stuff like

0:12:14.880,0:12:19.120
that

0:12:15.600,0:12:22.720
they're really helpful if you are gonna

0:12:19.120,0:12:23.760
if you've just started using um Emacs

0:12:22.720,0:12:26.959
and orgrim

0:12:23.760,0:12:29.519
and you have all these pdfs that have

0:12:26.959,0:12:30.079
all the annotations and highlighting and

0:12:29.519,0:12:32.639
the

0:12:30.079,0:12:33.200
all that stuff with org noter you can

0:12:32.639,0:12:36.720
just

0:12:33.200,0:12:39.519
use the org note or create skeleton

0:12:36.720,0:12:41.200
uh command and it will populate all your

0:12:39.519,0:12:43.760
notes that have already been

0:12:41.200,0:12:44.800
um entered within the pdf file if you're

0:12:43.760,0:12:48.160
using an outside

0:12:44.800,0:12:52.560
software and creates them like as a neat

0:12:48.160,0:12:55.920
org file I I highly recommend

0:12:52.560,0:12:57.920
finally org transclusion um

0:12:55.920,0:13:01.040
I think this is still in its beta phase

0:12:57.920,0:13:02.720
but I've been enjoying it so far

0:13:01.040,0:13:04.800
um I'm guessing people know what

0:13:02.720,0:13:06.480
translation mean which is sort of like

0:13:04.800,0:13:09.600
copy pasting text from

0:13:06.480,0:13:11.839
one org file to another this is helpful

0:13:09.600,0:13:12.959
I I think I I peeked at a question that

0:13:11.839,0:13:16.320
was talking about like

0:13:12.959,0:13:18.320
you know linking um to other org files

0:13:16.320,0:13:20.320
I think org transclusion could really

0:13:18.320,0:13:24.399
work okay it's

0:13:20.320,0:13:27.760
equivalent to the include

0:13:24.399,0:13:29.519
function within org mode um but I think

0:13:27.760,0:13:32.560
so like if you have other files

0:13:29.519,0:13:34.800
that you know which region that you

0:13:32.560,0:13:36.079
need in another file you could use the

0:13:34.800,0:13:38.160
include but with

0:13:36.079,0:13:39.440
org transclusion it's great I mean you

0:13:38.160,0:13:42.720
just have

0:13:39.440,0:13:43.360
um you're just linking one part to the

0:13:42.720,0:13:45.760
other

0:13:43.360,0:13:47.760
sort of like not refiling but you know

0:13:45.760,0:13:49.680
hyperlinking

0:13:47.760,0:13:51.120
so this is an example of what org

0:13:49.680,0:13:53.680
transclusion looks like

0:13:51.120,0:13:54.720
um so the highlighted problem statement

0:13:53.680,0:13:57.760
is from another

0:13:54.720,0:13:58.240
org file and then what I would do is

0:13:57.760,0:13:59.760
just like

0:13:58.240,0:14:01.440
link it to there and there was like a

0:13:59.760,0:14:05.440
transclusion command

0:14:01.440,0:14:08.399
I wish I made another screenshot of it

0:14:05.440,0:14:09.120
and so when you invoke org transclusion

0:14:08.399,0:14:12.079
mode

0:14:09.120,0:14:12.480
it turns um it prints it out like that

0:14:12.079,0:14:15.120
so

0:14:12.480,0:14:16.560
it's in view mode and then when you want

0:14:15.120,0:14:18.480
to edit it will take you back to that

0:14:16.560,0:14:21.839
buffer and you can edit the text

0:14:18.480,0:14:22.720
however you want all right so thank you

0:14:21.839,0:14:26.000
so much

0:14:22.720,0:14:29.120
um I wanted to leave room for questions

0:14:26.000,0:14:32.560
but special thanks to all the folks that

0:14:29.120,0:14:33.440
work on orgrom or ground bibtex orgrim

0:14:32.560,0:14:36.320
server or

0:14:33.440,0:14:38.240
transclusion and of course alpha papo on

0:14:36.320,0:14:42.560
or super agenda and org sidebar

0:14:38.240,0:14:42.560
that's how I got into Emacs thank you

0:14:43.440,0:14:47.120
all right and uh well thank you so yeah

0:14:45.600,0:14:49.120
this time I'll be the one asking the

0:14:47.120,0:14:51.360
question and not I'm in so

0:14:49.120,0:14:53.120
I'm feeling filling big shoes right now

0:14:51.360,0:14:54.880
so you'll have to bear with me folks

0:14:53.120,0:14:56.240
so thank you so much noora for your

0:14:54.880,0:14:57.279
presentation that is incredibly

0:14:56.240,0:14:58.959
interesting

0:14:57.279,0:15:00.800
so would you mind if I fed you questions

0:14:58.959,0:15:04.000
from the charts yeah

0:15:00.800,0:15:06.160
go ahead okay so the first one I I've

0:15:04.000,0:15:07.920
picked on my end was did you try using

0:15:06.160,0:15:10.560
ebib instead of zotero

0:15:07.920,0:15:12.079
and if so is it better than zotero in

0:15:10.560,0:15:14.880
some ways

0:15:12.079,0:15:15.680
I no I have not used eb I've only used

0:15:14.880,0:15:18.560
mendeley

0:15:15.680,0:15:20.320
and then they got bought by el savior

0:15:18.560,0:15:23.040
and so like I was like okay I'm done

0:15:20.320,0:15:25.120
I'm going to zotero um there are a lot

0:15:23.040,0:15:26.240
of plugins with zotero that you can play

0:15:25.120,0:15:28.320
around with

0:15:26.240,0:15:30.480
so I can't speak for ebit but definitely

0:15:28.320,0:15:32.079
zotero it's been a good experience so

0:15:30.480,0:15:34.880
far

0:15:32.079,0:15:35.360
yes same I also I also do research on

0:15:34.880,0:15:38.079
the site

0:15:35.360,0:15:39.360
as I told you english major and yeah I

0:15:38.079,0:15:41.839
also do zotero

0:15:39.360,0:15:43.759
some people have been using uh a

0:15:41.839,0:15:44.160
connector between zotero and Emacs which

0:15:43.759,0:15:46.000
has

0:15:44.160,0:15:47.360
they've had great success with them but

0:15:46.000,0:15:50.480
personally I haven't touched

0:15:47.360,0:15:52.240
touched it already so yeah

0:15:50.480,0:15:53.920
oh go ahead sorry all right so far I

0:15:52.240,0:15:54.880
don't have any problems with zotero but

0:15:53.920,0:15:56.320
maybe if I

0:15:54.880,0:15:58.320
run into something I might check out

0:15:56.320,0:16:00.240
ebay in the future

0:15:58.320,0:16:01.680
yeah definitely I think zotero is a very

0:16:00.240,0:16:02.560
solid project and you know the fact that

0:16:01.680,0:16:04.959
it's being used

0:16:02.560,0:16:06.560
by people outside of Emacs also ensures

0:16:04.959,0:16:07.680
that there's quite a lot of packing

0:16:06.560,0:16:09.759
behind the software

0:16:07.680,0:16:11.759
which is reassuring when your livelihood

0:16:09.759,0:16:13.519
depends on your research

0:16:11.759,0:16:15.600
right and then I think one more thing

0:16:13.519,0:16:17.519
with zotero is that you can create

0:16:15.600,0:16:18.079
groups so if you're in a collaborative

0:16:17.519,0:16:20.160
project

0:16:18.079,0:16:22.320
you can create a reference you know a

0:16:20.160,0:16:23.759
library just for your group and I think

0:16:22.320,0:16:25.279
that could help because like I

0:16:23.759,0:16:27.600
I'm going to be in a project next

0:16:25.279,0:16:29.839
semester that requires that

0:16:27.600,0:16:31.600
yeah definitely I believe the ability to

0:16:29.839,0:16:33.839
have folders inside zotero

0:16:31.600,0:16:35.360
makes it incredibly useful to manage

0:16:33.839,0:16:37.440
your different projects concurrent

0:16:35.360,0:16:39.279
projects

0:16:37.440,0:16:41.279
so moving on to the questions do you

0:16:39.279,0:16:43.440
have any suggestion on what subjects or

0:16:41.279,0:16:46.560
things should be tags or separate organ

0:16:43.440,0:16:50.320
files for cross-linking

0:16:46.560,0:16:52.720
right um so so far now like I'm having

0:16:50.320,0:16:55.360
trouble with like should I be combining

0:16:52.720,0:16:55.839
certain concepts together as one like

0:16:55.360,0:16:59.360
this is

0:16:55.839,0:17:00.959
where the the thought process you know

0:16:59.360,0:17:02.959
starts coming to fruit is that when you

0:17:00.959,0:17:04.880
start you know combining

0:17:02.959,0:17:06.480
ideas together so you won't need a

0:17:04.880,0:17:09.199
specific tag

0:17:06.480,0:17:11.280
and another one that are like similar in

0:17:09.199,0:17:12.720
ideas

0:17:11.280,0:17:14.799
I'm not sure if that answers the

0:17:12.720,0:17:15.919
question but like so far I've been using

0:17:14.799,0:17:17.919
the orgrum

0:17:15.919,0:17:19.039
you know the default way which is like

0:17:17.919,0:17:22.160
many small

0:17:19.039,0:17:24.400
um files and then just

0:17:22.160,0:17:26.319
linking them to my like either if I have

0:17:24.400,0:17:26.959
a report to write or if I have a like

0:17:26.319,0:17:32.240
you know

0:17:26.959,0:17:35.360
essay to write

0:17:32.240,0:17:37.760
I think you're muted

0:17:35.360,0:17:38.400
q and I just I did two stupid things the

0:17:37.760,0:17:40.640
first one

0:17:38.400,0:17:42.320
was filling up my water the second one

0:17:40.640,0:17:43.760
was peeking without actually turning on

0:17:42.320,0:17:45.760
my microphone

0:17:43.760,0:17:47.760
so let's just hope that nothing is going

0:17:45.760,0:17:48.320
to fry in the near vicinity of me right

0:17:47.760,0:17:49.840
now

0:17:48.320,0:17:51.440
but uh yeah I believe you've answered

0:17:49.840,0:17:53.200
the question so don't worry about it I'm

0:17:51.440,0:17:55.280
slightly wet right now which is not a

0:17:53.200,0:17:57.280
very agreeable feeling but we'll have to

0:17:55.280,0:17:59.360
carry on I suppose

0:17:57.280,0:18:01.600
another question is there a place where

0:17:59.360,0:18:04.320
people are collaborating on research

0:18:01.600,0:18:06.160
about Emacs so do you want to try to

0:18:04.320,0:18:08.559
take this one

0:18:06.160,0:18:10.559
um I don't know but I'm definitely

0:18:08.559,0:18:12.480
interested in the user experience of

0:18:10.559,0:18:14.720
Emacs so

0:18:12.480,0:18:16.400
if anyone wants to work on that I'm

0:18:14.720,0:18:18.320
happy

0:18:16.400,0:18:19.760
well you do have a a pretty good

0:18:18.320,0:18:22.080
candidate in front of you if I

0:18:19.760,0:18:22.960
should say so myself I'm incredibly

0:18:22.080,0:18:25.039
interested about

0:18:22.960,0:18:26.960
um the ability to do research in Emacs

0:18:25.039,0:18:30.480
and about the ability to

0:18:26.960,0:18:32.480
um preach the floss way

0:18:30.480,0:18:34.080
to academia and to the academe

0:18:32.480,0:18:35.280
especially because I believe there's

0:18:34.080,0:18:38.240
really something

0:18:35.280,0:18:39.919
great to be done sorry I'm just looking

0:18:38.240,0:18:41.840
at the puddle of water on the side which

0:18:39.919,0:18:45.039
is slightly oozing my way

0:18:41.840,0:18:46.880
which is not a very good feeling really

0:18:45.039,0:18:48.320
but yeah I believe I believe some work

0:18:46.880,0:18:50.000
could be done and if people are

0:18:48.320,0:18:52.320
interested in the chat right now

0:18:50.000,0:18:53.440
I mean do get in touch with us both

0:18:52.320,0:18:56.480
neuron and I

0:18:53.440,0:18:57.280
are on our slack channel yes I know

0:18:56.480,0:19:00.080
slack

0:18:57.280,0:19:01.919
the corporate hive mind that it's like

0:19:00.080,0:19:02.720
but we've decided with orgrim to use

0:19:01.919,0:19:05.520
slack

0:19:02.720,0:19:06.880
but you can find us very easily and uh

0:19:05.520,0:19:07.360
if you want to talk about these topics

0:19:06.880,0:19:08.720
yes

0:19:07.360,0:19:10.720
by all means do and we'll be very

0:19:08.720,0:19:12.640
interested to answer your questions

0:19:10.720,0:19:15.520
so I have a question here says like how

0:19:12.640,0:19:18.640
does the view for time blocking works

0:19:15.520,0:19:22.000
um I use org super agenda so

0:19:18.640,0:19:23.200
um what happens is that my active

0:19:22.000,0:19:26.960
timestamps are

0:19:23.200,0:19:29.200
only in my gmail or file

0:19:26.960,0:19:30.080
so if you use org gcal you have to

0:19:29.200,0:19:32.559
specify

0:19:30.080,0:19:34.320
a certain org file and when it you know

0:19:32.559,0:19:35.679
imports them it imports them as like

0:19:34.320,0:19:38.400
active

0:19:35.679,0:19:40.480
timestamps and I make sure whenever I

0:19:38.400,0:19:42.480
create a to-do or even a research task

0:19:40.480,0:19:45.039
that it doesn't have a time stamp on it

0:19:42.480,0:19:48.480
because what I want to do is go back

0:19:45.039,0:19:50.160
and then move around um these tags

0:19:48.480,0:19:51.919
according to my you know either weekly

0:19:50.160,0:19:52.960
schedule or monthly or however long you

0:19:51.919,0:19:56.480
want to do it

0:19:52.960,0:19:59.679
um so yeah only active timestamps or

0:19:56.480,0:20:03.280
deadlines um appear in your time grid

0:19:59.679,0:20:05.440
so that could work um that's very good

0:20:03.280,0:20:06.320
just just to uh interject for a second

0:20:05.440,0:20:07.840
about this

0:20:06.320,0:20:10.720
you know with orgrim right now we're

0:20:07.840,0:20:13.039
mostly uh focused on optimization

0:20:10.720,0:20:14.720
but we're hoping to move on to ux very

0:20:13.039,0:20:16.720
soon so all those matters about

0:20:14.720,0:20:18.159
you know having to do's in your files it

0:20:16.720,0:20:20.000
is something that we've been thinking

0:20:18.159,0:20:20.880
about with jethro kwan who is my main

0:20:20.000,0:20:23.280
commentator

0:20:20.880,0:20:24.480
or grow and we'll be working on this in

0:20:23.280,0:20:26.080
the coming months so don't worry too

0:20:24.480,0:20:29.760
much about it and stay tuned

0:20:26.080,0:20:33.200
yeah um so I've got the ebib

0:20:29.760,0:20:34.080
and what else um what subjects I think

0:20:33.200,0:20:35.919
okay

0:20:34.080,0:20:37.120
what is this question have you seen the

0:20:35.919,0:20:40.400
project papi's

0:20:37.120,0:20:41.280
I'm not sure what oh it's a zotero

0:20:40.400,0:20:43.840
alternative okay

0:20:41.280,0:20:45.919
I'll look into it thank you I don't know

0:20:43.840,0:20:49.600
I don't know about it either so

0:20:45.919,0:20:53.200
please look into it and let me know yeah

0:20:49.600,0:20:55.679
um have we covered all the questions

0:20:53.200,0:20:56.880
I believe we have and we have about

0:20:55.679,0:20:58.880
two-minute leeway

0:20:56.880,0:21:00.240
for me to move into the next talk so

0:20:58.880,0:21:01.760
we're right on time

0:21:00.240,0:21:04.159
all right thank you so much really

0:21:01.760,0:21:05.440
appreciate it and good luck everyone

0:21:04.159,0:21:07.600
well thank you and thank you so much for

0:21:05.440,0:21:08.400
coming and uh doing allowing me not to

0:21:07.600,0:21:11.440
be the only one

0:21:08.400,0:21:14.559
talking about all room today sounds good

0:21:11.440,0:21:16.799
all right thank you both very much

0:21:14.559,0:21:16.799
yes