Setup#
VPN#
In order to access the resources for the Bioinformatics Concepts Course, you need to be connected to the ETH network. This can be achieved either by connecting to the ETH WiFi or through a Virtual Private Network (VPN).
If you have not yet used a VPN to connect to the ETH network, then you can find instructions on how to do so here.
Command line interface#
Although software exists which allows you to access a server just as if you were logging into a normal computer - with a graphical user interface (GUI) and everything - many will only provide a command line interface. This is a text-based method of communication that almost all computers have, though it is typically hidden out of sight for most users.
The terminal functions like an old fashioned text adventure game, or a voice-activated assistant that requires you to type in your commands.
Accessing the command line interface on your own computer depends on your system:
Windows#
In the taskbar menu type ‘command’ and Command Prompt should appear for you to launch
Alternatively press Windows Key + r and type ‘cmd’ into the box and Command Prompt should launch
Mac#
Click the launchpad icon in the dock, type ‘Terminal’ into the search field and launch from there
Alternatively in the Finder, navigate to /Applications/Utilities folder and launch Terminal from there
Mobaxterm#
Frequent users often use a software called Mobaxterm to connect to the command line. If you are interested in using this software instead of your local terminal:
Find the free version of Mobaxterm here and either download and execute the Portable edition or install the Installer edition
Connecting to Cousteau#
Your local computer is often not capable of doing bioinformatic work within a reasonable time. Therefore, for this course we are going to use a remote server called “Cousteau”. In order to work on a server, you have to connect to it using a protocol called Secure Shell or ssh. The ssh structure usually is <your-ID>@<server-address> (Note: < and > are not part of the command) in case of Cousteau this is <yourETH-ID>@cousteau.ethz.ch, so the command to connect to Cousteau is:
# Command to connect to cousteau
ssh <your ETH-ID>@cousteau.ethz.ch
#Your command could f.ex. look like this
ssh fieldc@cousteau.ethz.ch
After entering the command to connect to the remote server Cousteau, enter your password upon request (please note that no characters (even asterixes) will appear while you enter your password)
Exercise 0.1
Try to connect to Cousteau yourself
First, you have to open the command line interface on you computer For Windows: Type “command” into the taskbar menu For Mac: Click onto the launchpad icon in the dock and type “Terminal” into the search field
Second, connect to Cousteau with the ssh command. You need your user ID and your nethz password in order to connect to the serve. The command to connect to the Cousteau is:
ssh <your ETH-ID>@cousteau.ethz.ch
Disconnecting from Cousteau#
After you are done with your bioinformatic work on a server, you want to disconnect from the server. You can do this by using the command exit.
# Command to disconnect from server
exit
Exercise 0.2
Try to disconnect from Cousteau yourself
After connecting to Cousteau with the ssh command, disconnect from Cousteau with the exit command. The command to disconnect from Cousteau is:
exit
R-Studio#
Various parts of the Bioinformatics Concepts Course will be based in R-Studio. Instead of relying on a local installation on your computer, we have made R-Studio easily accessible to you on our server. This R-Studio has already been set up with all the necessary packages that you will need during the course. Click on the link below to load R-Studio in your browser:
R-Studio: http://cousteau-rstudio.ethz.ch/
Note
You need to use the web-based R-Studio on our server - your local version may not have the correct packages or set up for the course.
After clicking on the link, a login screen should appear (picture below). You can use your normal ethz-login, which will then provide you access to the R-Studio.
Note
Due to technical reasons, it is possible that you have to login twice when you first try to connect to R-Studio on our server.
After successfully logging in, you will be presented with the standard R-Studio interface (picture 1 below). Hopefully, you are familiar with this interface. As a brief reminder, there are three main sections (picture 2 below), which correspond to:
The red frame shows the R console. Here, you can write and run R code and see the results.
The blue frame shows the environment. Here, you will find all of the variables that you have created and any datasets that you have loaded.
The yellow frame shows your home folder on our server by default. However, you can toggle across the different tabs to view the ‘packages’ that you have loaded, or the ‘plots’ that you have created in your current R session.
To complete the set-up and begin working on course material, you will need to create a new R-script (Picture 3 below): Click on File -> New File -> R Script (or use the shortcut with key combination Ctrl + Alt + Shift + N) as you can see in picture 3.
Following this, you should have four panels in your R-Studio interface (picture 4 below), at which point the set-up is complete!
Jupyter#
In addition to R-Studio, Python will also be used for parts of the course. To make this programming language easily accessible to, we have set up Jupyter (with Python) on our servers. You can access Jupyter via the following link:
Jupyter: http://cousteau-jupyter.ethz.ch/
Note
You need to use Jupyter on over server through the link. Your local version may not work due to technical issues.
When you click on the link, a login screen should appear (picture below). You can use your normal ethz-login, which will then provide you access to Jupyter.
Once you are logged in, you should see the Jupyter interface (picture below). For those of you that are unfamiliar with this interface, there are two main sections:
In the middle (blue frame) you have the ‘launcher’. This is the area from which you can launch a notebook, console or terminal etc.
On the left-hand side, you have your file structure from your home folder on our server (orange), the menu bar (yellow) and the options bar (green). The options bar allows you to start a new launcher, to create new folders and to upload files to the server from your local machine.