good afternoon or good evening everyone
uh
today my talk is going to be on org mode
and or group for skulls and researchers
leo has talked about like the overall
picture of orgrim and or
uh bibtex or groundbreak tech I will be
talking more about
the research process itself using these
tools
all right so just to introduce that the
research process is really messy
um you're always working in like
piecemeal tasks and things move around
all the time and so
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
and my goal is to add some structure to
this whole madness
so 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 what I've found useful um
during my res uh like um
within my research process all right so
I've organized org mode for researchers
and scholars within the writing process
into three modules first there's like
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
all right so when we're talking about
planning we're talking about either task
management or
time management with task management
you've got
org modes to do's and tags and
categories these are really powerful
tools that you could use
um in your org files to just um
uh like organize your tasks and
your appointments so there are different
types of to-do's that you can either set
globally in your init file or they can
be file buffer specific
so that means based on context based on
the type of
manuscript you're working on whether
it's like a literate programming
report or your actual thesis slash
dissertation
um also these to-do's are either created
as a set tree like think of them as
headings and sections if you use latex
or inline text which are like org inline
tasks I
like organ line tasks because like I can
add
to do's between two paragraphs and that
way it doesn't show up
in the table of contents when I export
into pdf or html or
anything else all right so this is an
example of buffer specific to do's
and and this is example of like a little
programming report that I was working on
where I was like dealing with
data and like analysis and all of that
stuff and so
I needed um context specific to do's to
use them within this buffer
um and that's how I would organize it
and there's also 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 like
nature within the
text when you export it
oh but I also added a tag of no export
so it won't show up at all
when I export it into like either pdf
which I use all the time all right so
another useful tool
um for the research and just like
general planning
is the org capture um when I first
started with Emacs
actually it was for org agenda and I
went crazy with my capture template I
created a template for
everything um because I was just so
excited
but with time I was using less and less
of them so I kept taking them out
and now this is my simplified um
capture templates that I use either for
a general to do
um for a regular appointment a fleeting
note research tasks because like 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 like
have the org file ready instead of
needing to capture
you know open a capture template
right or agenda um that's how I got into
Emacs
I needed to um organize my life and I
found Emacs and
it's been great ever since um it
populates all your to-do's and
appointments into a singular view so the
default view I think it's a weak view
however I use org super agenda love this
um package and I set up my agenda as a
daily view with just appointments
deadlines and a habit tracker um and
a side note you guys I'm still
struggling with organizing the perfect
agenda so it's a process
and take it easy all right
so this is just an overview of my daily
agenda as you can see they're just like
appointments that I import from gmail
using org gcal
a simple habit tracker of like 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 just
like regular deadlines
so what happens is that I have other
to-do's that I have
not scheduled or not added a deadline
but they're just
tasks that keep piling up when I first
started with Emacs and org agenda
I had everything in there and it got
overwhelming and 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
um I would sit down look at all my to
to-do's that I have
not assigned yet to a deadline or a
schedule or just a simple
timestamp um and I would organize them
throughout the week
so here's an example of what I did
so on that wednesday from my gmail I had
all these appointments but
one of them is I have a writing group
session
and so I looked at my tasks and I
thought okay then I will just
assign um like for example my emac
slides
or the framework diagram into that
writing session
and 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
all right another way of accessing your
to do's is that if it's
um file specific 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 and this isn't the the
um you know the way this depends
because if you're working on like a
dissertation um it's a huge manuscript
you need to like work
on that org file all the time um
then yes it might do should be in that
file specifically because every time if
I'm
if I'm visiting this org file all the
time I should be able to just look at my
tasks from uh within that buffer
and so I use org sidebar to
keep all these specific uh to do's
within that org file
I find it helpful okay
now that we're going into the writing
and reference management
we'll call it a literature review um
and this is something I've built as a
schema
I think that it works for now
um and it requires one outside pack
of outside software which is zotero what
I use it's an open source reference
management
software um it's great
but the things to keep in mind is that I
use two um
plugins that is really needed for when
we work with orgrim bibtex and orgrim
and org mode um and the zap file so
better bibtex organizes your reference
keys
um in um in a way like in a fashion that
works for you so for me all my reference
keys are like
last author and gear um and with zap
file I um I let it like rename all the
pdf files
the same way that I have for my bit of
my bib keys which is like
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 um the following packages
all right so with orgrim bibtex it
creates an org file for each bib entry
and you have the option of like
templating and doing other stuff with it
and then finally there's like this orb
pdf scraper
I've used it briefly but I think the
potential
with or pdf scraper is if you're gonna
do a bibliometric study or like a
systematic literature view there's
something there but I have to look
through it
anyway so once you create your you know
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 orgrom
things that you're going to use within
orgrom it's a great way to build your
database you start making the
connections and you can visualize your
notes and like how these references are
linked to each other
through the organ server or or ground
graph
all right this is just notes for later
okay
so this is an example of like an orgram
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
um changing global environment so on and
so forth and the backlinks
are other references that talk about
this specific concept
so this is really helpful and then when
you visualize it the picture on the left
which I'm sure looks really small
um you can see the connections that it's
making with other
references so of course this is just
like a buffer
network when you look at the entire
database network it's it's
it's growing okay
so going into organ bidtech
so it utilizes a combination of the or
graph package helmbik tech candidate
completion
and it works with orgrom functionalities
and
other good stuff this is an example
of my orgrim bibtex file all right so
I've created
um the template which I pretty much use
what leo
has uh produced like in his um
tutorial so I think it's it's great it
works well for me
um and 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 um when it gets imported into
zotero
it extracts those keywords and then it
gets populated as an org file
with orgrim bibtex so 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 um
so what I've figured out like a new idea
for it so if I'm writing notes on it
I would create a property that says
pages um
that way it's easier for you when you go
back to citing
um certain ideas or something that you
have the pages prepared there
it's easier that way okay
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 gonna
if you've just started using um Emacs
and orgrim
and you have all these pdfs that have
all the annotations and highlighting and
the
all that stuff with org noter you can
just
use the org note or create skeleton
uh command and it will populate all your
notes that have already been
um entered within the pdf file if you're
using an outside
software and creates them like as a neat
org file I I highly recommend
finally org transclusion um
I think this is still in its beta phase
but I've been enjoying it so far
um I'm guessing people know what
translation mean which is sort of like
copy pasting text from
one org file to another this is helpful
I I think I I peeked at a question that
was talking about like
you know linking um to other org files
I think org transclusion could really
work okay it's
equivalent to the include
function within org mode um but I think
so like 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
um 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
um so the highlighted problem statement
is from another
org file and then what I would do is
just like
link it to there and there was like a
transclusion command
I wish I made another screenshot of it
and so when you invoke org transclusion
mode
it turns um it prints it out like that
so
it's in view mode and 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
um I wanted to leave room for questions
but special thanks to all the folks that
work on orgrom or ground bibtex orgrim
server or
transclusion and of course alpha papo on
or super agenda and org sidebar
that's how I got into Emacs thank you
all right and uh well thank you so yeah
this time I'll be the one asking the
question and not I'm in so
I'm feeling filling big shoes right now
so you'll have to bear with me folks
so thank you so much noora for your
presentation that is incredibly
interesting
so would you mind if I fed you questions
from the charts yeah
go ahead okay so the first one I 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
I no I have not used eb I've only used
mendeley
and then they got bought by el savior
and so like I was like okay I'm done
I'm going to zotero um there are a lot
of plugins with zotero that you can play
around with
so I can't speak for ebit but definitely
zotero it's been a good experience so
far
yes same I also I also do research on
the site
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
touched it already so yeah
oh go ahead sorry all right so far I
don't have any problems with zotero but
maybe if I
run into something I might check out
ebay in the future
yeah definitely I think zotero is a very
solid project and you know the fact that
it's being used
by people outside of Emacs also ensures
that there's quite a lot of packing
behind the software
which is reassuring when your livelihood
depends on your research
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 you know a
library just for your group and I think
that could help because like I
I'm going to be in a project next
semester that requires that
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 the questions do you
have any suggestion on what subjects or
things should be tags or separate organ
files for cross-linking
right um so so far now like I'm having
trouble with like should I be combining
certain concepts together as one like
this is
where the the thought process you know
starts coming to fruit is that when you
start you know 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 like so far I've been using
the orgrum
you know the default way which is like
many small
um files and then just
linking them to my like either if I have
a report to write or if I have a like
you know
essay to write
I think you're muted
q and I just I did two stupid things the
first one
was filling up my water the second one
was peeking without actually turning on
my microphone
so let's just hope that nothing is going
to fry in the near vicinity of me right
now
but uh 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
um 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
well you do have a a pretty good
candidate in front of you if I
should say so myself I'm incredibly
interested about
um the ability to do research in Emacs
and about the ability to
um 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
but yeah I believe I believe some work
could be done and if people are
interested in the chat right now
I mean do get in touch with us both
neuron and I
are on our slack channel yes I know
slack
the corporate hive mind that it's like
but we've decided with orgrim to use
slack
but you can find us very easily and uh
if you want to talk about these topics
yes
by all means do and we'll be very
interested to answer your questions
so I have a question here says like how
does the view for time blocking works
um I use org super agenda so
um what happens is that my active
timestamps are
only in my gmail or file
so if you use org gcal you have to
specify
a certain org file and when it you know
imports them it imports them as like
active
timestamps and I make sure whenever I
create a to-do or even a research task
that it doesn't have a time stamp on it
because what I want to do is go back
and then move around um these tags
according to my you know either weekly
schedule or monthly or however long you
want to do it
um so yeah only active timestamps or
deadlines um appear in your time grid
so that could work um that's very good
just just to uh interject for a second
about this
you know with orgrim right now we're
mostly uh focused on optimization
but we're hoping to move on to ux very
soon so all those matters about
you know having to do's in your files it
is something that we've been thinking
about with jethro kwan who is my main
commentator
or grow and we'll be working on this in
the coming months so don't worry too
much about it and stay tuned
yeah um so I've got the ebib
and what else um what subjects I think
okay
what is this question have you seen the
project papi's
I'm not sure what oh it's a zotero
alternative okay
I'll look into it thank you I don't know
I don't know about it either so
please look into it and let me know yeah
um have we covered all the questions
I believe we have and 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 and good luck everyone
well thank you and thank you so much for
coming and uh doing allowing me not to
be the only one
talking about all room today sounds good
all right thank you both very much
yes