INF-BIOX121 H14 RStudio IPython

Using the IPython Notebook

• login as usual, with X forwarding on tjhe course server
• start a so-called virtual Python environment (virtualenv):

source /opt/ipytest/bin/activate

• this changes your promt, don't worry.
• move (cd) to a folder if needed, for example where the data is you want to analyse
• launch iPython notebook

ipython notebook

• check where it says "The IPython Notebook is running at: http://127.0.0.1:8888/" and note the last four digits ('8888' in this case)
• MAC/Linux
  • start another terminal session and you create a so-called SSH tunnel, make sure to use the same four digits in the middle

ssh -L 30000:127.0.0.1:8888 username@bioinfcourse.hpc.uio.no

• leave both terminal windows open
  Windows users: see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ on how to set up your tunnel
  • source port: 30000
  • destination: 127.0.0.1:8888 (use those same four digits as you noted down above)
  • on the classroom PC, open a webbrowser (e.g. firefox)
  • point the browser to 127.0.0.1:30000

  Using Rstudio

  2)To use that instance, it is essential that you use SSH tunneling for security purposes. From a Linux or Mac workstation/laptop, you can type something like the one below:

  ssh -L 20000:localhost:8787 username@bioinfcourse.hpc.uio.no

  
  

  (The port number on the left (20000) is an example. Choose any large port number > 20000. The one on the right should *always* be 8787)

  
  

  Once you type the above command, login with your SSH username and password, like you normally do.  Once you are in, you can THEN point your LOCAL workstation/laptop browser to the URL: localhost:20000, to access the RStudio server login screen. You can then type your username and password to login and access your R environment from your web browser.

  
  

  3)For Windows users, you should use an SSH client like PuTTY. You can then establish a tunnel in a similar way as step 2) above by using this document as a guide:

  http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/

  
  

  For any issues/help, feel free to communicate with me directly.