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Environmental Cheminformatics
plan-b
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edd90686
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edd90686
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Feb 28, 2021
by
Todor Kondic
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@@ -38,20 +38,44 @@ or as a package from your GNU/Linux distribution.
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
## 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:
### Getting started
1.
Fire up emacs
2.
`Alt-x`
and
`R`
gets you an R session
3.
Enter
`library(shinyscreen)`
4.
Enter
`options(browser="chromium")`
5.
Enter
`launch()`
### JustInCase - Downloading instructions
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).
### 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
)
### The Rest
TODO
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