Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

Course preparation

Before you meet up on the first day of the course, you will have to be able to start a terminal in a unix environment, and to edit files in the same environment with a text editor. Here is how and what you should do on various Operation Systems (OS). Anything mentioned here is free software. Some can be upgraded (for money) to more functionality, but it is not necessary.

Mac

A Mac has a BSD unix underneath all the fancy graphics. This means you are ready for the course once you figure out how to use it. There are several nice text editors for Macs; Komodo, TextWrangler, Sublime Text 2, jedit, gedit, etc. Some videos have been prepared for you, demonstrating what to do.
Mette Beck shows how to open a terminal and install and use Komodo text editor
Edita Karosiene shows how to install/use X11 and connect to a remote server with SSH
Finally a link to other resources about unix on Mac.

Windows

Windows is clearly the worst/weakest OS for interacting with unix (that was a hint). None the less there exists one good tool and several put-together solutions. The good tool is MobaXterm, that can be downloaded here at Mobatek. Choose the installer (or the portable, if you know what you are doing), and now that you are at it, also download NEdit and Perl under the plugins. If I get the time, I will make a video of this. Install MobaXterm - it will put itself in the windows program folder. This location differs depending on the version of windows you have, but it is "findable". Some places would be: Computer -> C: -> Programs -> Mobatek -> MobaXterm Home Edition. Instead of Programs it could be; Programmer, Programs (x86) or other. The point of knowing this location is that you should drag and drop (move) the plugins you downloaded to this folder from your download folder. That act will make the plugin available. Windows will ask if you want to do this - yes, you do. Windows Firewall will block some features of MobaXterm and ask if they should be allowed. Just block - it does not matter for what we do.
Here is a short downloadable instruction video for installing and using MobaXterm made by Daniel Edward Perez from Michigan State University.

The adventure: In the end MobaXterm is just a pale imitation of how unix works. I will recommend for all to use linux. This can be achieved without disturbing your windows installation, but it is not "easy and short". Install Virtualbox and create a virtual machine running Ubuntu linux. How to do this? Do a search on google for "installing ubuntu on virtualbox". Here is a youtube video demonstrating the procedure. If you succeed, you have full immersion in the unix environment and two computers running on the same machine simultaneously (max coolness factor), and if you fail you have not lost anything not even disk space if you clean up after yourself.

Linux, any flavour

You are already set and ready for the course. You should be able to find the terminal; Term, Xterm, Console, as this is a basic integrated part of linux. Perl is also built in. There are many editors you can use; gedit, jedit, nedit, emacs, vim and a dozen more.