path: root/2022/info/jupyter-after.md

<!-- Automatically generated by emacsconf-publish-after-page -->


<a name="jupyter-mainVideo-transcript"></a>
# Transcript

[[!template new="1" text="""Hi, my name is Blaine Mooers.""" start="00:00:00.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I'm an associate professor of biochemistry""" start="00:00:03.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""at the University of Oklahoma Health Sciences Center""" start="00:00:05.400" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""in Oklahoma City.""" start="00:00:08.200" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I'm going to talk about the use of Emacs""" start="00:00:09.760" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""to edit live Jupyter notebook cells""" start="00:00:12.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""as well as text areas on web pages.""" start="00:00:16.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So like a lot of technical workers,""" start="00:00:20.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I find myself having to write prose""" start="00:00:22.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""in text areas on web pages,""" start="00:00:24.880" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""as well as working with code""" start="00:00:28.680" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""in Jupyter notebooks and Colab notebooks,""" start="00:00:31.720" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and often I have wished for""" start="00:00:37.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""the full power of Emacs while doing so.""" start="00:00:39.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Well, now that is possible.""" start="00:00:43.480" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Actually, there are several solutions""" start="00:00:45.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""that have been available for some time.""" start="00:00:46.800" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I'm going to talk about one solution""" start="00:00:49.040" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""that I'm familiar with and has worked out for me.""" start="00:00:50.400" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""So this requires the use of two software packages,""" start="00:00:55.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""GhostText and Atomic Chrome.""" start="00:00:58.120" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""GhostText is an extension for the web browser,""" start="00:01:01.600" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""whereas Atomic Chrome is a package for Emacs.""" start="00:01:04.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""You have to have both of these.""" start="00:01:07.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So Chrome is for the editor side""" start="00:01:10.880" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and GhostText handles the browser side.""" start="00:01:13.400" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""The GhostText extension is available""" start="00:01:18.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""in the Chrome web store.""" start="00:01:22.480" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And GhostText is represented by this icon,""" start="00:01:26.800" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""which has a ghost in front of the capital letter T.""" start="00:01:29.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""It is being developed by Federico Brigante.""" start="00:01:31.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""He is a very prolific JavaScript developer.""" start="00:01:36.400" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""He has a web page committed to GhostText,""" start="00:01:41.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""as well as a GitHub site.""" start="00:01:44.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So here's an example of GhostText.""" start="00:01:47.200" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""This is a snapshot from a session""" start="00:01:50.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""that I had while editing LaTeX on the Overleaf website.""" start="00:01:54.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Overleaf is this web service""" start="00:02:01.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""that empowers the editing of LaTeX documents on the web.""" start="00:02:03.760" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So I have clicked on this GhostText icon in the toolbar.""" start="00:02:09.720" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I had already opened up Emacs,""" start="00:02:14.040" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and I had the Atomic Chrome server running.""" start="00:02:17.040" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So a connection was established,""" start="00:02:19.880" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""as indicated by this blue border around this text area.""" start="00:02:21.800" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And as soon as that appeared,""" start="00:02:28.600" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""the text appeared in a buffer inside of Emacs.""" start="00:02:30.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So I have overlaid the area where normally the compiled PDF""" start="00:02:35.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""would appear in an Overleaf session.""" start="00:02:40.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So I'm using a configuration for LaTeX that I developed,""" start="00:02:43.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""which is available through the MooersLab GitHub site.""" start="00:02:47.680" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I also gave a talk about how I use LaTeX in Emacs""" start="00:02:52.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""at the Berlin Emacs meetup in August.""" start="00:02:55.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""This talk was not recorded,""" start="00:02:58.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""but the slides are available on this website.""" start="00:03:00.040" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So I would like to now switch to a little live coding""" start="00:03:05.120" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""to make this a little more interesting.""" start="00:03:09.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So I start my day at this other website called 750Words.""" start="00:03:12.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""This site just takes plain text,""" start="00:03:22.440" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""but I like to write in LaTeX.""" start="00:03:25.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So GhostText came to my rescue""" start="00:03:28.560" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""when I started using this everyday last May.""" start="00:03:31.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So I clicked on the GhostText icon.""" start="00:03:34.480" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""It highlighted that area in blue.""" start="00:03:37.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""There's some boilerplate""" start="00:03:39.760" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""that I like to start my day with.""" start="00:03:41.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I like to get a list of my deadlines""" start="00:03:45.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""that are coming up, as shown here,""" start="00:03:50.600" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""for the next several months.""" start="00:03:54.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And then I have landed at this tab stop.""" start="00:03:55.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And so I had issued a tab trigger""" start="00:03:59.400" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""which inserted this almost 50 lines of text""" start="00:04:04.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""from a snippet through Yasnippet.""" start="00:04:09.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And then I'll change this text to whatever.""" start="00:04:13.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And then I can hit TAB to move to the next site.""" start="00:04:17.480" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I was dead tired last night, so I fell asleep at my desk,""" start="00:04:29.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and whatever. So I just keep on going""" start="00:04:38.440" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and then hit TAB again and enter my &quot;To Be Done&quot; items.""" start="00:04:42.440" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And then what I love about Emacs is that""" start="00:04:47.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""you can hit C-c C-j to insert a new item and so forth,""" start="00:04:50.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""so you can extend the list.""" start="00:04:56.120" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Initially, I just have 10 items.""" start="00:05:03.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I'm going to have more. And on I go,""" start="00:05:05.080" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""using the full power of LaTeX.""" start="00:05:08.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So I have configured Atomic Chrome""" start="00:05:12.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""so it will recognize this website as a –""" start="00:05:16.120" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""it will open up this website –""" start="00:05:20.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""the connection to this website with this buffer""" start="00:05:21.400" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""in the LaTeX major mode. To turn this off,""" start="00:05:26.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""we can close – simply just close the buffer""" start="00:05:36.560" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and that will shut things down.""" start="00:05:40.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""On the browser side, you can right-click on the icon""" start="00:05:42.960" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and disconnect GhostText on this page.""" start="00:05:46.400" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Okay, let's go to a different situation.""" start="00:05:49.040" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""This is not a feature that's advertised by the developer,""" start="00:05:53.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""but I discovered that you can edit code cells""" start="00:05:57.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""(or any kind of cell for that matter)""" start="00:06:00.120" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""in a Jupyter Notebook.""" start="00:06:02.800" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""However, we have a challenge here.""" start="00:06:04.440" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""We have three text areas open – three code cells.""" start="00:06:05.720" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So if we click on the GhostText icon,""" start="00:06:09.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""these three areas will show up in green""" start="00:06:14.760" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and we'll be prompted to select the one""" start="00:06:17.480" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""that we want to activate.""" start="00:06:19.120" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""We want to activate the one with text.""" start="00:06:20.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So then we can go in here and make edits, of course,""" start="00:06:22.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and you can do this in Emacs""" start="00:06:31.400" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""or we can do it in the browser. It doesn't matter.""" start="00:06:33.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""You saw me editing in Emacs,""" start="00:06:35.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""but we can also make the edits""" start="00:06:38.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""in the text area of the browser""" start="00:06:40.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and they will show up immediately in Emacs.""" start="00:06:44.880" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So we could change the case of that M and that's going to –""" start="00:06:47.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""shows up over here. Okay, we can run this code.""" start="00:06:54.440" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So this is R, one of the three major""" start="00:06:59.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""programming languages for data science.""" start="00:07:03.440" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""At least, Jupyter is supposed to be""" start="00:07:05.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""a combination of Julia, Python, and R.""" start="00:07:07.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So we're running mcmc to get the posterior distribution""" start="00:07:13.480" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and we're going to plot those out with this pyplots package,""" start="00:07:17.560" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and we have these beautiful plots showing the median""" start="00:07:21.120" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""of the posterior distribution for four variables in –""" start="00:07:24.080" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""four parameters in the CARS data set,""" start="00:07:27.040" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""which is available – built into the R package.""" start="00:07:31.560" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And then these shaded areas are the 80% interval.""" start="00:07:38.040" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Okay. Oops.""" start="00:07:45.560" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So now for the Python side,""" start="00:07:49.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""here's an example in which I'm going to actually""" start="00:08:07.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""insert a snippet of that cell""" start="00:08:13.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and then I'm going to enter nvlig for nglview ligand,""" start="00:08:18.680" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and just hit enter. Oops. Hit TAB, excuse me,""" start="00:08:27.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and we don't need this line of code, so delete that.""" start="00:08:43.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Yep, we want to load up this pdb file""" start="00:08:48.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""that's in this subdirectory.""" start="00:08:52.200" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So the pdb file is a plain text file""" start="00:08:54.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""that contains atomic coordinates""" start="00:08:56.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""of protein crystal structure.""" start="00:08:58.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""This protein happens to be important in cancer""" start="00:09:00.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and we have – we screened by docking 55,000 compounds""" start="00:09:03.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""on a supercomputer""" start="00:09:09.080" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and then we did MD [molecular dynamics] simulations""" start="00:09:10.680" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""of the top 10 [actually 20] leads.""" start="00:09:12.744" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Twelve of them had the compound remain bound""" start="00:09:14.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""during the period of the simulation,""" start="00:09:18.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""so those have some potential for –""" start="00:09:19.680" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and require experimental validation.""" start="00:09:22.560" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So we'll run this chunk of code,""" start="00:09:25.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and this will give a view of the molecule""" start="00:09:28.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""that we can interact with by using the mouse.""" start="00:09:30.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""But I want to share this with my colleague.""" start="00:09:36.480" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""My colleague is not set up to use Jupyter,""" start="00:09:39.880" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""but instead we can write this out to a HTML file,""" start="00:09:42.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""which I have loaded up already.""" start="00:09:46.960" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And so we can actually – perhaps.""" start="00:09:48.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""We click on these two arrows pointing at each other,""" start="00:09:55.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and we can get a full screen view of this molecule""" start="00:10:01.680" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and he can identify each atom in this structure.""" start="00:10:05.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Over a thousand atoms present.""" start="00:10:10.440" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""We're just hovering over a specific atom.""" start="00:10:12.720" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So shown in gray is the ligand that is bound. Okay.""" start="00:10:14.960" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So we still have this box selected""" start="00:10:27.760" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and we still have these two different –""" start="00:10:32.080" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""so for each of the – our selected text areas""" start="00:10:36.560" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""we have a separate – we have a separate buffer open. Okay.""" start="00:10:40.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""To wrap things up here, here's an example of using –""" start="00:11:03.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""with evolving Julia code.""" start="00:11:06.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And so this Julia code in this cell is in a Emacs buffer.""" start="00:11:08.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""So you've got an idea now, I think.""" start="00:11:12.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So in terms of plain text areas like in Overleaf""" start="00:11:19.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and then these cells in Jupyter Notebooks,""" start="00:11:23.760" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""these are other areas that can be edited""" start="00:11:27.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""like in the text areas within Outlook Webmail and Gmail.""" start="00:11:30.960" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Instead of having to point with the mouse""" start="00:11:37.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""or click with the mouse,""" start="00:11:42.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""one can also use keybindings or keyboard shortcuts.""" start="00:11:43.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So here are the ones for three major operating systems.""" start="00:11:48.080" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So how does GhostText work?""" start="00:11:51.600" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Main thing is you have to open up Emacs""" start="00:11:54.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and get this Atomic Chrome server running.""" start="00:11:57.200" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""And then with it up and going,""" start="00:11:59.680" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""GhostText will be able to – has to be activated""" start="00:12:03.120" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and it will find the GhostText server""" start="00:12:06.680" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""through the localhost port 4001.""" start="00:12:09.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Put that into the web browser.""" start="00:12:15.080" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""If you navigate to that port,""" start="00:12:19.040" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""you'll get output that looks like this""" start="00:12:21.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""if everything's working well.""" start="00:12:23.720" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Otherwise, you'll get a error message""" start="00:12:25.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and it should have a port socket –""" start="00:12:27.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""a web socket port number.""" start="00:12:30.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""It will not be the same every time.""" start="00:12:34.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So these are the supported web browsers""" start="00:12:36.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""in addition to Chrome. These are supported""" start="00:12:42.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""and likewise anything in these –""" start="00:12:45.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""any browser related to these""" start="00:12:47.280" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""can probably use these extensions.""" start="00:12:49.880" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""For example, the Brave browser will use Chrome extension""" start="00:12:53.080" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and the Firefox browser extension works with WaterFox.""" start="00:12:56.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""These are the supported editors.""" start="00:13:01.680" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Each editor has its own extension""" start="00:13:05.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and this GhostText was initially developed for SublimeText.""" start="00:13:10.200" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So if you have SublimeText,""" start="00:13:15.720" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""then you can use its smooth operation as positive control""" start="00:13:17.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""when things go wrong with Emacs.""" start="00:13:21.960" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""This is Atomic. This is a GitHub site for Atomic Chrome.""" start="00:13:25.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Atomic Chrome is available for installation through Melpa.""" start="00:13:29.480" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""This is my configuration for Atomic Chrome.""" start="00:13:33.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So I have this setup so the server starts whenever I log in,""" start="00:13:40.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and I have it set up so that default major mode is Python""" start="00:13:45.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""to deal with the Jupyter notebooks and Colab notebooks.""" start="00:13:50.320" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And then I have major modes""" start="00:13:55.560" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""for these other websites defined below.""" start="00:13:57.720" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""This is a testing site so the developer has made""" start="00:13:59.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""to help with troubleshooting.""" start="00:14:06.080" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""He also has a protocol on his website""" start="00:14:08.120" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""to follow during troubleshooting.""" start="00:14:11.160" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So here are some precautions.""" start="00:14:13.560" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""You'll find that GhostText doesn't work with Pluto.""" start="00:14:16.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Pluto is a new computational notebook""" start="00:14:19.080" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""for working with Julia.""" start="00:14:21.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""My suggestion would be just to run IJulia in Jupyter.""" start="00:14:23.480" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""It also doesn't work, of course, with RStudio.""" start="00:14:27.040" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Even though RStudio sort of resembles""" start="00:14:32.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""a web page, web browser, it's not.""" start="00:14:35.200" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Of course, you can always run R,""" start="00:14:39.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""as you've just seen, using the IPy kernel.""" start="00:14:41.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I will also caution you that if you use the Emacs server,""" start="00:14:48.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""you may run into issues""" start="00:14:52.240" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""with the server competing with the port 4001.""" start="00:14:53.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So instead, you should probably configure the Emacs server""" start="00:14:58.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""to use a specific port.""" start="00:15:01.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So far – although I haven't done that myself –""" start="00:15:05.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""so far, I haven't found any conflicts""" start="00:15:07.640" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""with the Org Roam user interface.""" start="00:15:11.000" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So my conclusions are: GhostText allows you to edit prose""" start="00:15:13.480" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""with your favorite major mode""" start="00:15:20.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""in the text areas of web pages""" start="00:15:24.440" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and in the cells of Jupyter notebooks.""" start="00:15:28.120" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""This allows you to tap into snippets""" start="00:15:31.080" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and thereby save time as you have – probably have –""" start="00:15:34.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""hopefully got an idea of.""" start="00:15:37.520" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I'd like to thank my friends and mentors""" start="00:15:39.720" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""who've helped me out during my second year""" start="00:15:44.040" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""in my Emacs learning spiral.""" start="00:15:46.600" video="mainVideo-jupyter" id="subtitle"]]
[[!template new="1" text="""These include my local colleagues.""" start="00:15:49.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""We meet once a month in the Oklahoma Data Science Workshop.""" start="00:15:55.840" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Last July, I gave a presentation about GhostText.""" start="00:15:58.680" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""And then also my friends at Berlin and Austin Emacs meetups""" start="00:16:01.720" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""and in the UK research software engineer""" start="00:16:08.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Emacs research Slack channel.""" start="00:16:12.960" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""So I don't attend these every month,""" start="00:16:17.600" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""but I try to make the meetings as often as I can.""" start="00:16:18.920" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""Then I'm supported by the following grants,""" start="00:16:21.440" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""which allow me to spend""" start="00:16:25.400" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""at least some time each day in Emacs.""" start="00:16:28.360" video="mainVideo-jupyter" id="subtitle"]]
[[!template text="""I'll be happy to take any questions.""" start="00:16:30.680" video="mainVideo-jupyter" id="subtitle"]]



Captioner: sachac

Questions or comments? Please e-mail [Blaine-Mooers@ouhsc.edu](mailto:Blaine-Mooers@ouhsc.edu?subject=Comment%20for%20EmacsConf%202022%20jupyter%3A%20Edit%20live%20Jupyter%20notebook%20cells%20with%20Emacs)


<!-- End of emacsconf-publish-after-page -->