path: root/2020/subtitles/emacsconf-2020--13-experience-report-steps-to-emacs-hyper-notebooks--joseph-corneli-raymond-puzio-cameron-ray-smith-autogen.vtt

WEBVTT

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um so hi I'm joe corneli

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uh this is work I did with ray puzio and

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cameron smith

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um and they're the main protagonists in

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this story they

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are uh researchers who've been working

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on theoretical biology um so in a

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typical project they may use manxima

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and julia their work for biology physics

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and computer science

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computer science and the latest work in

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progress is on branching processes for

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cancer modeling so

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how can um Emacs possibly help

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let's let's have a look uh moving code

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and data between these different

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programs by hand is

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annoying on separate workflows for

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writing up notes and preparing

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publications

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is perhaps even more annoying all of

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it's time consuming and error-prone

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um so what about maybe using jupiter

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uh we found something called script of

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scripts and it solves some of those

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problems because you can use

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maximum and julia together but we were

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quite happy to explore emacs based

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solutions being emax enthusiasts and we

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even

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got cameron to be enthusiastic about

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doing emacs so that

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went nice so just here's a little

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feature grid

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of emacs org versus just sort of your

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generic

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um tools that are in a different more

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general ecosystem so as you can see it's

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quite

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feature complete you've got your maximo

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mode julia mode you can use both of them

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inside of org mode

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you can present things with word tree

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slide you can set up a

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wiki inside of orgrome this is one I

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found

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rather recently you can even use

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compatibly with orgrome something called

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log seek

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which is in the browser um so that's

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nice

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um you can do real-time collaborative

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editing um

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either in a kind of pairing style or in

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a more etherpad style

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obviously you can manage your references

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you can typeset whatever you want um you

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can publish work in progress on a blog

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and the fern is another one of these

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external

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org mode tools it's not actually any mac

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but works with

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org mode stuff and you know so we're

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good to go

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uh with all of that so what does that

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look like well here's

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a little example from before they were

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doing um

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before we started really thinking

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seriously about this stuff so this is

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just maxima

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well maximo doesn't have a long running

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process by default if you've ever used

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python

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uh you have something called sessions uh

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they don't have that for maxim at least

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not by default

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um so how what was the workaround

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there's this thing called uh

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solve for you here and um

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that shows up down below again in these

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angle brackets which you've seen maybe

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in someone else's talk

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uh which means go to the previous uh

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thing that was named soul for you

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and do that all over again so they do

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that over again

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and here's the little maxima code for

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defining you saw so you've now defined

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you saw

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and then you can use it in the next

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expression you get out a nice juicy

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zero at the end but it's a little bit a

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little bit

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like cartridge in a pear tree to have to

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redefine everything every time

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so this is clearly at the level of work

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around um maybe just

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one more time going looking through that

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um

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that stuff um

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sorry so uh looking through that stuff

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this is we're going to need something

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like that probably for stitching

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maxima and julie julia together so it's

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good to

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look a little bit about how that might

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work so first of all you can cache

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results so if you wanted to save the

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date

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out of block one at a certain time and

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then use

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use it again later so at the time when I

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ran this code

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you can see I've got two slightly

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different time stamps down below one's

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the cached result and the other was the

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result of reevaluating

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the block so you can move things around

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um and that's

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that's going to be useful but you know

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that's not really the main problem the

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main problem is

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making maxima long running so kind of

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the

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core of this talk is a new observant

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facility which is a general purpose

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way to do that kind of thing which

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involves a very simple

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change to obcor uh so we'll give a quick

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overview of that and show

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an example um so here's the example

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um a very simple sort of silly example

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uh what does it mean to have a long

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running process here I've set this

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display2d

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to be false um which just means that

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things are going to come

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come across in 1d and then I ask it to

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expand

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uh something and I get latex by default

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so so that's what it means is I've sent

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something in and it's going to come

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across in one view which is great

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um maybe you'll also notice that there's

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no semicolon if you're a maxima fan

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um and things are coming across as tech

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so those were some little bonus features

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and I'll show you how that works later

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so

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um the change to obcor is as follows uh

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um we uh actually this should say uh

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instead of stream here it should say um

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servant

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sorry uh we tried an experimental

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version what's called stream so now it's

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called servant but all it does is it

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overrides uh or babel execute laying for

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arbitrary laying

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if you have um a servant

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in your in your params so that's the

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change that hasn't been

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pushed out or sent as a patch to anybody

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but it's a pretty minor change

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um here's an overview without the code

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of just a high level overview of

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observant.el so

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it stores information about these

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processes in a hash table

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it can do pre-processing and

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post-processing

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um it does all these things it stores

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the output

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I mentioned here that in principle we

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could store lots of output and have a

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kind of browsable

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history although we don't do that

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presently um but that's what observant

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does is it does what you might expect

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and here's the

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here's the maxima kind of um

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on-ramp uh to get maxima brought in so

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you have to obviously have a maximum

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process you can call

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um put hash uh this is the preprocessing

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thing I mentioned adding in some tech um

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and adding in

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uh or deleting rather a substring and

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here here is why you delete the

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substring

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is because um maxima thinks it's a good

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idea to tell you false

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once you once you run check on things

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you've got to delete that back out to

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get something kind of coherent out of it

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but so this is how to set up maximal um

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that's enough really of the demo is not

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really a demos for

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show and tell but uh this is an

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experience report I wanted to talk about

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the experience of doing this

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so some some negatives like we tried to

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get emacs jupiter working

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prior to prior to working on the um

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observant and we couldn't get it doing

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everything we wanted despite a bit of

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heavy lifting and debugging and stuff so

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that's not not finished that was a bit

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difficult

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um on the other hand working on

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observing was fun and pretty lightweight

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and easy

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um we got some experience co-editing

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things with these real-time tools

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obviously the stack is somewhat work in

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progress um

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so I just wanted to give a shout out to

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crdt which was really fun

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and champion was making bug fiction

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bug fixes for that as we go similarly

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for fern and log seek the maintainers

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were really responsive

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um and so that was nice we did try to

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get emacs running in the browser

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thinking it would be really nice for

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people who

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um didn't want to install it to get a

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chance to just try it

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uh but actually browsers capture things

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like uh control n

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and so that's that was a bit annoying

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but we did get lots of great feedback

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and interaction with people including

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around this conference so thank you

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to those who we've had discussions with

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um

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so future work okay so maybe you

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remember I didn't

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give a talk a few years back on arcana

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so what what

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might this have to do with org mode and

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that's always the question one asks

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about arcata

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well so arcana one of the things it does

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is transclusions and so that could be

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actually very helpful

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in connection with this combined notes

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and write-up workflow so you might have

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a

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forward mode uh and some of these

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results we got back as raw results

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could go right into your write up in a

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kind of

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convenient way at a level above um

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transparently a level above the notebook

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so you'd have the notebook alongside the

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write-up in that case

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which is a sort of variation on the

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literate programming

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workflow this is speculative who knows

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the other thought is

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it just relates to the idea of network

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programming so we can imagine these

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networks of

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computational nodes maybe sitting inside

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of orgrome calling each other

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um and you would want to maintain some

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kind of model of that

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process and a sort of general question

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is how do we have a remote control for

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long-running processes you could do that

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in lisp or closure but

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maybe we could have something a little

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bit like that here

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um so conclusions what have we actually

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addressed well uh we addressed uh

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accessing any long-running process with

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a simple or mode interface

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obviously we're not the only people to

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think about notebooks but we think that

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emacs has some advantages

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related to reproducible research and

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interdisciplinary collaboration so let's

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just

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say that we think something is

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reproducible if it's actually teachable

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to someone new and they can do it

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org mode seems very useful for that many

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of the other talks have touched on this

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interdisciplinary collaboration is great

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this was an interdisciplinary

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collaboration on some level but

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what about you know future work for

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bringing in scenario planners simulation

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scientists

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and local farmers and building something

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that they can all

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use that's more than the sum of the

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parts so a little

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future work for everybody else here so

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we think science should be widely

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teachable

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shareable semi-automated

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transdisciplinary and real time

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like EmacsConf so you can get in touch

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uh via these methods and the code which

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is very much early stage work in

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progress

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as this was meant to be an experience

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report not a it's all done here it is

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polished report

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um it's also online if you'd like to

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have a look so that's the end of the

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talk and I don't know if there's time

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for questions

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or not but um I'm at your disposal now

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thank you you are now unmuted

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um many thanks for the tough job

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uh let's see we have about I think four

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minutes four questions

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um and we have a couple of questions on

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the pad would you like to read them

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yourself or should I read them to you

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uh just for sake of easy management why

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don't you read them out if that's okay

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yeah sure uh so they ask have you looked

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into trying

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sage math I've long uh long wanted

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nothing org files

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right and I and I wrote the answer that

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we should be possible because one can

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call it from a command

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okay

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and I see there's another sagemath

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question that you seem to have answered

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as well so I guess I won't repeat that

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[Music]

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there's let's not forget about embedded

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calc in emacs

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so so the first demos actually were with

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calc so that's that's

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useful uh although I think it was a

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different kind of a different command

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line

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well that was the next calc yeah

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so sure there is there is calc so that

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would be calculus and

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calc is already in org mode yeah

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yeah yeah

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um still looking for questions

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okay I think that's about it I don't see

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any questions on the ether pad

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and let's see

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anything on irc

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um nothing but phrases and everyone

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thanking you

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thank you all right you're welcome

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thanks a lot uh

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we'll see you guys around then cheers

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and see you around