INF-BIOX121 H14 RStudio IPython

Using the IPython Notebook

• login as usual, with X forwarding on the 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

• ​Windows
  • see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ on how to set up your tunnel
  • source port: 30000
  • destination: http://127.0.0.1:8888 (use those same four digits as you noted down above)

• All
  • on the classroom PC, open a webbrowser (e.g. firefox)
  • point the browser to 127.0.0.1:30000

Using Rstudio

• Linux or Mac
  • open a terminal and write

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.  

• ​Windows
  • see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/on how to set up your tunnel
  • source port: 20000 (choose any large port number > 20000)
  • destination: localhost:8787 (dont change this number)
• All
  • on the classroom PC, open a webbrowser (e.g. firefox)
  • point the browser to 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