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@@ -2,7 +2,8 @@
 Joseph Corneli, Raymond Puzio, and Cameron Ray Smith
 
 [[!template id=vid src="https://mirror.csclub.uwaterloo.ca/emacsconf/2020/emacsconf-2020--13-experience-report-steps-to-emacs-hyper-notebooks--joseph-corneli-raymond-puzio-cameron-ray-smith.webm" subtitles="/2020/subtitles/emacsconf-2020--13-experience-report-steps-to-emacs-hyper-notebooks--joseph-corneli-raymond-puzio-cameron-ray-smith.vtt"]]  
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+[View transcript](#transcript)
 
 We present a short experience report from the perspective of two
 long-time Emacs users and one relative newcomer.  Our motivations
@@ -52,3 +53,379 @@ I think he used org-tree-slides, like some earlier presentations.
 
 # Notes
 - <https://github.com/exp2exp/ob-servant>
+
+<a name="transcript"></a>
+# Transcripts
+
+00:00:00.320 --> 00:00:30.800
+Joe: Hi, I'm Joe Corneli. This is work I
+did with Ray Puzio and Cameron Smith.
+They're the main protagonists in this
+story. They are researchers who've been
+working on theoretical biology. In a
+typical project, they may use Maxima and
+Julia. Their work combines biology,
+physics and computer science. The latest
+work-in-progress is on branching
+processes for cancer modeling.
+
+00:00:30.800 --> 00:00:48.640
+How can Emacs possibly help? Let's have
+a look. Moving code and data between
+these different programs by hand is
+annoying. Separate workflows for writing
+up notes and preparing publications is
+perhaps even more annoying. All of it is
+time consuming and error-prone.
+
+00:00:48.640 --> 00:01:10.057
+So what about maybe using Jupyter? We
+found something called Script of
+Scripts. It solves some of those
+problems because you can use Maxima and
+Julia together, but we were quite happy
+to explore Emacs-based solutions, being
+Emacs enthusiasts. We even got Cameron to
+be enthusiastic about doing Emacs, so
+that went nice.
+
+00:01:10.057 --> 00:02:05.657
+Here's a little feature grid of Emacs +
+Org versus your generic tools that are
+in a different, more general ecosystem.
+As you can see, it's quite
+feature-complete. You've got your
+maxima-mode, julia-mode. You can use
+both of them inside of org-mode. You can
+present things with org-tree-slide. You
+can set up a wiki inside of org-roam.
+This is one I found rather recently. You
+can even use compatibly with org-roam,
+something called logseq, which is in the
+browser, so that's nice. You can do
+real-time collaborative editing, either
+in a kind of pairing style or in a more
+Etherpad style. Obviously, you can
+manage your references. You can typeset
+whatever you want. You can publish work
+in progress on a blog. Firn is another
+one of these external Org Mode tools.
+It's not actually in Emacs, but works
+with Org Mode stuff. And, you know... So
+we're good to go with all of that.
+
+00:02:05.657 --> 00:02:13.890
+So what does that look like? Well,
+here's a little example from before they
+were doing... before we started really
+thinking seriously about this stuff.
+
+00:02:13.890 --> 00:02:45.280
+So this is just Maxima. Well, Maxima
+doesn't have a long running process by
+default. If you've ever used Python, you
+have something called sessions. They
+don't have that for Maxima, at least not
+by default. So how... What was the
+workaround? There's this thing called
+solve-for-u here that shows up down
+below again in these angle brackets,
+which you've seen maybe in someone
+else's talk, which means go to the
+previous thing that was named
+solve-for-u and do that all over again,
+so they do that over again.
+
+00:02:45.280 --> 00:03:00.640
+Here's the little Maxima code for
+defining usol, so you've now defined
+usol, and then you can use it in the
+next expression. You get out a nice
+juicy zero at the end. It's a little bit
+like a partridge in a pear tree to have
+to redefine everything every time.
+
+00:03:00.640 --> 00:03:22.590
+So this is clearly at the level of
+work-around. Maybe just one more time
+looking through that stuff. Sorry. So,
+looking through that stuff, this is...
+We're going to need something like that,
+probably, for stitching Maxima and Julia
+together. so it's good to look a little
+bit about how that might work.
+
+00:03:22.590 --> 00:03:46.923
+First of all, you can cache results, so
+if you wanted to save the date out of
+block one at a certain time and then use
+it again later... At the time when I ran
+this code, you can see I've got two
+slightly different time stamps down
+below. One's the cached result, and the
+other was the result of reevaluating the
+block. So you can move things around.
+That's going to be useful. But you know,
+that's not really the main problem.
+
+00:03:46.923 --> 00:04:11.760
+The main problem is making Maxima
+long-running. The core of this talk is a
+new observant facility, which is a
+general purpose way to do that kind of
+thing, which involves a very simple
+change to ob-core. We'll give a quick
+overview of that and show an example. So
+here's the example, a very simple sort
+of silly example.
+
+00:04:11.760 --> 00:04:30.240
+What does it mean to have a long-running
+process? Here, I've set this display2d
+to be false, which just means that
+things are going to come come across in
+1d. Then I ask it to expand something. I
+get LaTeX by default. So that's what it
+means. It's that I've sent something in
+and it's going to come across in one
+view, which is great.
+
+00:04:30.240 --> 00:04:40.320
+Maybe you'll also notice that there's no
+semicolon, if you're a Maxima fan, and
+things are coming across as TeX. So
+those were some little bonus features.
+I'll show you how that works later.
+
+00:04:41.040 --> 00:05:13.759
+The change to ob-core is as follows.
+Actually, this should say... Instead of
+stream here, it should say servant.
+Sorry. We tried an experimental version
+which was called stream, so now it's
+called servant. But all it does is it
+overrides org-babel-execute lang for
+arbitrary lang if you have a servant in
+your params. So that's the change that
+hasn't been pushed out or sent as a
+patch to anybody, but it's a pretty
+minor change.
+
+00:05:13.759 --> 00:05:30.720
+Here's an overview without the code.
+Just a high level overview of
+observant.el. It stores information
+about these processes in a hash table.
+It can do pre-processing and
+post-processing. It does all these
+things. It stores the output.
+
+00:05:30.720 --> 00:05:40.639
+I mentioned here that, in principle, we
+could store lots of output and have a
+kind of browsable history, although we
+don't do that presently. But that's what
+observant does. It does what you might
+expect.
+
+00:05:41.440 --> 00:06:16.960
+Here's the Maxima on-ramp to get Maxima
+brought in. You have to obviously have a
+Maxima process you can call. puthash...
+this is the preprocessing thing I
+mentioned, adding in some Tex and adding
+in-- or deleting, rather--a substring.
+Here is why you delete the substring.
+It's because Maxima thinks it's a good
+idea to tell you false once you run
+check on things. You've got to delete
+that back out to get something coherent
+out of it. So this is how to set up
+Maxima.
+
+00:06:16.960 --> 00:06:25.440
+That's enough, really, of the demo. It's
+not really a demo for show and tell, but
+as this is an experience report, I
+wanted to talk about the experience of
+doing this.
+
+00:06:25.440 --> 00:06:42.880
+Some negatives, like we tried to get
+Emacs Jupyter working prior to working
+on observant. We couldn't get it doing
+everything we wanted, despite a bit of
+heavy lifting and debugging and stuff.
+So that's not finished. That was a bit
+difficult.
+
+00:06:42.880 --> 00:07:11.695
+On the other hand, working on observant
+was fun, pretty lightweight, and easy.
+We got some experience co-editing things
+with these real-time tools. Obviously,
+the stack is somewhat work in progress.
+I just wanted to give a shout out to
+crdt which was really fun, and Qiantan
+was making bug fixes for that as we go.
+Similarly, for firn and logseq, the
+maintainers were really responsive, so
+that was nice.
+
+00:07:11.695 --> 00:07:27.120
+We did try to get Emacs running in the
+browser, thinking it would be really
+nice for people who didn't want to
+install it to get a chance to just try
+it, but actually, browsers capture
+things like C-n, so that was a bit
+annoying.
+
+00:07:27.120 --> 00:07:33.759
+But we did get lots of great feedback
+and interaction with people, including
+around this conference. Thank you to
+those who we've had discussions with.
+
+00:07:35.599 --> 00:08:19.120
+So, future work. Okay, so... Maybe you
+remember, I gave a talk a few years back
+on Arxana. What might this have to do
+with Org Mode? That's always the
+question one asks about Arxana.
+Arxana... One of the things it does is
+transclusions, and so that could be
+actually very helpful in connection with
+this "combined notes and write-up"
+workflow. So you might have an Org Mode.
+Some of these results we got back as raw
+results could go right into your
+write-up in a convenient way, at a level
+above-- transparently, a level above the
+notebook. So you'd have the notebook
+alongside the write-up in that case,
+which is a variation on the literate
+programming workflow. This is
+speculative. Who knows?
+
+00:08:19.120 --> 00:08:33.357
+The other thought is,
+it just relates to the idea of network
+programming. So we can imagine these
+networks of computational nodes
+sitting inside of org-roam,
+calling each other.
+You would want to maintain some
+kind of model of that process.
+
+00:08:33.357 --> 00:09:11.680
+A general question is: how do we have a
+remote control for long-running
+processes? You could do that in Lisp or
+Clojure, but maybe we could have
+something a little bit like that here.
+Conclusions: what have we actually
+addressed? Well, we addressed accessing
+any long-running process with a simple
+Org Mode interface. Obviously, we're not
+the only people to think about
+notebooks, but we think that Emacs has
+some advantages related to reproducible
+research and interdisciplinary
+collaboration. Let's just say that we
+think something is reproducible if it's
+actually teachable to someone new and
+they can do it. Org Mode seems very
+useful for that. Many of the other talks
+have touched on this.
+
+00:09:11.680 --> 00:09:27.857
+Interdisciplinary collaboration is
+great. This was an interdisciplinary
+collaboration on some level, but what
+about future work for bringing in
+scenario planners, simulation
+scientists, and local farmers, and
+building something that they can all use
+that's more than the sum of the parts?
+
+00:09:27.857 --> 00:09:38.135
+So a little future work for everybody
+else here. We think science should be
+widely teachable, shareable,
+semi-automated, transdisciplinary, and
+real-time like EmacsConf.
+
+00:09:38.135 --> 00:10:00.240
+So you can get in touch via these
+methods. The code--which is very much
+early stage work in progress, as this
+was meant to be an experience report,
+not a "it's all done, here, it is
+polished" report-- it's also online if
+you'd like to have a look. That's the
+end of the talk. I don't know if there's
+time for questions or not, but um I'm at
+your disposal now. Thank you.
+
+00:10:00.240 --> 00:10:14.240
+(Amin: Many thanks for the tough job.
+Let's see. We have about I think four
+minutes for questions, and we have a
+couple of questions on the pad. Would
+you like to read them yourself or should
+I read them to you?)
+
+00:10:14.240 --> 00:10:18.079
+Just for the sake of easy management why
+don't you read them out, if that's okay?
+
+00:10:18.079 --> 00:10:33.760
+(Amin: yeah, sure. They ask, "Have you
+looked into trying Sage Math? I've long
+wanted to use Sage Math in Org files.")
+
+00:10:33.760 --> 00:10:44.839
+Ray: Right. I wrote the answer that it
+should be possible because one can call
+it from a command.
+
+00:10:44.839 --> 00:11:00.640
+(Amin: okay, and I see there's another
+Sage Math question that you seem to have
+answered as well, so I guess I won't
+repeat that. There's... "Let's not
+forget about embedded Calc in Emacs.")
+
+00:11:00.640 --> 00:11:08.240
+Joe: So the first demos actually were
+with Calc. That's useful. Although I
+think it was a different--kind of a
+different command line.
+
+00:11:08.240 --> 00:11:11.839
+Ray: Well, that was UNIX Calc.
+
+00:11:11.839 --> 00:11:13.839
+Joe: So, sure, there is calc, so that...
+
+00:11:15.680 --> 00:11:19.120
+Ray: Calc is already in Org Mode.
+
+00:11:25.680 --> 00:11:57.290
+(Amin: Still looking for questions.
+Okay, I think that's about it. I don't
+see any questions on the Etherpad. And
+let's see... Anything on irc? Nothing
+but praises and everyone thanking you.
+Thank you.)
+
+00:11:57.290 --> 00:11:59.120
+Ray: all right, you're welcome.
+
+00:11:59.120 --> 00:12:01.923
+Joe: Thanks a lot!
+We'll see you guys around then.
+
+00:12:01.923 --> 00:12:06.800
+Amin: Cheers, and see you around!