Update docs

README.ISB401.md

+# Environmental Cheminformatics Educational Platform: Plan B
+
+This repository contains a collection of ansible scripts which can be
+used to provision an Ubuntu/Debian based virtual machine in a public
+cloud. The scripts have been written for a specific Digital Ocean
+_droplet_, but can easily be adapted for something else. And, indeed,
+they are now adapted to automate configuration of ECI workstations.
+
+
+## Access
+
+The desktop environment on the compute node *alien-one* is accessible
+through VNC protocol. Any VNC viewer can be used. If in doubt, try the
+cross-platform TigerVNC viewer [available from here for
+Windows](https://bintray.com/tigervnc/stable/download_file?file_path=vncviewer-1.11.0.exe),
+or as a package from your GNU/Linux distribution. 
+For Mac users, 
+[here is the Java version of the viewer](https://bintray.com/tigervnc/stable/download_file?file_path=VncViewer-1.11.0.jar).
+If you are on Big Sur [try this direct download](http://tigervnc.bphinz.com/nightly/osx/TigerVNC-1.11.80.dmg). 
+If you are on Catalina [try this direct download](https://bintray.com/tigervnc/beta/download_file?file_path=TigerVNC-1.10.90.dmg).
+If you are on El Capitan [try this direct download](https://bintray.com/tigervnc/stable/download_file?file_path=TigerVNC-1.8.0.dmg)
+
+
+
+**Before** connecting, you need: 
+	- A X509 certificate file (`*.pem`).
+	- The IP address of the server.
+	- Your username and password.
+
+### Connection instructions
+
+1. Open the VNC viewer.
+2. Click `Options`.
+3. Switch to `Security` tab.
+4. Make sure that at least `TLS with X509 certificates` is checked.
+5. Make sure that at least `None` is checked in the `Authentication` section.
+6. Set the `Path to X509 certificate` to the location of the X509
+   certificate file.
+7. Now, click `OK` to accept changes and close the `Options` tab.
+8. Fill in the IP address of the server in field `VNC server` and
+   append `:5950` to it. So, the `VNC server` entry should look like
+   `XXX.XXX.XXX.XXX:5950`, or `example.somewhere.biz`.
+9. Click `Connect`.
+10. **When at the login screen, ensure you are using the `Xfce Session` (settings wheel, bottom right) before entering your password**.
+11. Pro-tip: User experience may be better in fullscreen (`F8` and select `fullscreen`)
+
+## Using Environmental Cheminformatics programs
+
+### Getting started with Shinyscreen
+
+Shinyscreen is ECI's mass spectrum inspection program. It was written
+in R and exists as a R package. In order to run it, it is necessary to
+start a R session. 
+
+While most students get to know R through R Studio, this development
+environment (DE) is by no means the only one that can run R (indeed,
+you do not even need a DE to run R: try it yourself, start a command
+console and type `R` in there). The default choice of R DE on
+`alien-one` currently is GNU Emacs with its *Emacs Speaks Statistics
+(ESS)* mode.
+
+Steps:
+
+1. Fire up emacs
+2. `Alt-x` (`Cmd-x` for Mac) and `R` gets you an R session
+3. If asked, set your start working directory, e.g. 
+`setwd('/mnt/scratch/user/')` 
+(where `user` is an alias for your username)
+4. Enter `library(shinyscreen)`
+5. Enter `options(browser="chromium")`
+6. Enter `launch()` 
+
+To create subdirectories for different Shinyscreen calculations, 
+use `dir.create()` and `setwd()` to create and set new working 
+directories, respectively. This is highly recommended otherwise 
+you will auto-detect and/or overwrite previous results. 
+
+
+Alternatively, there there are two icons on your desktop that will
+start Shinyscreen immediately without a R session. One starts the
+~~stable~~outdated version of Shinyscreen. The other runs a
+development version (~~you can try it out if you feel
+adventurous~~recommended).
+
+
+
+### Material needed for the practical
+
+The *mzML* data files are in `/mnt/exchange` directory.
+
+#### Just in case
+1. Raw files `*.mzML` can be downloaded from [here](https://zenodo.org/record/3666069) 
+2. Input files for Shinyscreen from [here](https://git-r3lab.uni.lu/eci/isb401/-/tree/master/shinyscreen_files)
+
+
+### Some emacs tips
+To execute a script in Emacs Ess, you have different shortcuts:
+
+1. `Ctrl alt x`: runs a Paragraph
+2. `Ctrl enter`: similar, but closer to Rstudio in how it 
+treats collections of sratements
+3. `Ctrl j`: runs a single line
+
+The above commands are used when you have a separate R script that is 
+being evaluated in the session. In the session itself, it's just enter
+
+### Converting Shinyscreen MS2 files to MetFrag compatible format
+
+Assuming `AAs` is the Shinyscreen project folder, to create files 
+compatible with MetFrag input format follow these steps:
+
+1. Navigate to `AAs` folder using `Thunar` file browser.
+2. Right-click somewhere on the white space in the  view showing files and click on `Open Terminal Here`.
+3. In the terminal, type `ls`. Is there a `MS2` folder in there? If yes, then proceed.
+4. Type `ss2mf`. This command will create a `MS2_forMF` folder containing the MetFrag compatible input files.
+
+

README.md

-# Environmental Cheminformatics Educational Platform: Plan B
+# Environmental Cheminformatics Platform: Plan B
 
 This repository contains a collection of ansible scripts which can be
 used to provision an Ubuntu/Debian based virtual machine in a public
 cloud. The scripts have been written for a specific Digital Ocean
-_droplet_, but can easily be adapted for something else.
+_droplet_, but can easily be adapted for something else. Indeed,
+they are now adapted to automate configuration of ECI workstations.
 
 
 ## Access
@@ -38,7 +39,7 @@ If you are on El Capitan [try this direct download](https://bintray.com/tigervnc
 7. Now, click `OK` to accept changes and close the `Options` tab.
 8. Fill in the IP address of the server in field `VNC server` and
    append `:5950` to it. So, the `VNC server` entry should look like
-   this `XXX.XXX.XXX.XXX:5950`.
+   `XXX.XXX.XXX.XXX:5950`, or `example.somewhere.biz`.
 9. Click `Connect`.
 10. **When at the login screen, ensure you are using the `Xfce Session` (settings wheel, bottom right) before entering your password**.
 11. Pro-tip: User experience may be better in fullscreen (`F8` and select `fullscreen`)
@@ -77,19 +78,9 @@ you will auto-detect and/or overwrite previous results.
 
 Alternatively, there there are two icons on your desktop that will
 start Shinyscreen immediately without a R session. One starts the
-stable version of Shinyscreen (used in this course). The other runs a
-development version (you can try it out if you feel adventurous).
-If you choose this path you are at the mercy of the default file path.
-
-
-### Material needed for the practical
-
-The *mzML* data files are in `/mnt/exchange` directory.
-
-#### Just in case
-1. Raw files `*.mzML` can be downloaded from [here](https://zenodo.org/record/3666069) 
-2. Input files for Shinyscreen from [here](https://git-r3lab.uni.lu/eci/isb401/-/tree/master/shinyscreen_files)
-
+~~stable~~outdated version of Shinyscreen. The other runs a
+development version (~~you can try it out if you feel
+adventurous~~recommended).
 
 ### Some emacs tips
 To execute a script in Emacs Ess, you have different shortcuts:
@@ -100,16 +91,21 @@ treats collections of sratements
 3. `Ctrl j`: runs a single line
 
 The above commands are used when you have a separate R script that is 
-being evaluated in the session. In the session itself, it's just enter
-
-### Converting Shinyscreen MS2 files to MetFrag compatible format
-
-Assuming `AAs` is the Shinyscreen project folder, to create files 
-compatible with MetFrag input format follow these steps:
-
-1. Navigate to `AAs` folder using `Thunar` file browser.
-2. Right-click somewhere on the white space in the  view showing files and click on `Open Terminal Here`.
-3. In the terminal, type `ls`. Is there a `MS2` folder in there? If yes, then proceed.
-4. Type `ss2mf`. This command will create a `MS2_forMF` folder containing the MetFrag compatible input files.
-
+being evaluated in the session. In the session itself, it's just enter.
+
+Some venerable Emacs personalities suggest window-based organisation
+of Emacs workflow:
+
+1. Start Emacs.
+2. Resize it to a strip at the bottom of the screen (the *session*
+   window), then `Alt-x R`.
+3. C-x 5 2 to open a new window (connected to the same session).
+4. Open an existing R script, or start writing a new one.
+5. Commands from above will work and be displayed in the session window.
+6. Switch between the windows with `C-x 5 o`.
+7. You can also split windows in panes with `C-x 2`,`C-x 3`, hide all
+   but one with `C-x 1`, hide this one `C-x 0`, ...
+8. Reading the `Emacs Tutorial` is not a bad place to start if you
+   want to delve deeper [note that ECI's Emacs is heavily customised,
+   so it might not behave as you'd expect].