CSC8306 -- Systems Administration

Introduction

In the good old days (that's around 1993), installing linux used to be a right-of-passage. Many years ago, it used to come on floppy disks. Slackware, which is about the oldest distribution still out there, used to come on "Series A" and "Series B" floppies; the operating system came on A, and the basic applications came on B. Hard-Core linux people used to sit in pubs and tell war stories about their attempts to install linux; most of them revolved around one of the floppies not working properly.

The hardest task of all was installing a dual-boot machine; having linux and windows (3.1 at the time). Anyone who had actually managed to achieve this was revered. Anyone who had managed to achieve this while only having one physical hard drive in their machine raised to almost god-like status. Anyone who managed to do this without reinstalling windows was...well, no one had ever achieved this, so we don't know how they would have been received.

In this practical, we will dual-boot your machine without having to touch windows at all.

Dual Boot

What is dual-booting? How is it different from a virtual machine? Why would you choose to use a virtual machine? Why a dual boot?

There are quite a few different ways of dual-booting. Although, it is a little easier than it used to be, it's still very possible to make your machine unusable while doing this. This includes windows. If you have files which exist only on your hard drive, you should back them up. You may lose them.

We're are going to use Wubi because it's the most straightforward system I have found for doing this.

Download Wubi. Install it.

What is Wubi? Describe briefly how it works. What version of Ubuntu have you installed?

Welcome to Wubi

You will have discovered one the of disadvantages of a dual boot machine; you can't get to your windows OS at the same time. If you have not followed the previous practical about getting access to the outside world, now would be a good time.

So, what can you do with Wubi that you can't with a Virtual Machine. One of the main advantages is that you have direct access to the physical hardware of the machine. By now you may or may not have received information about "Restricted Drivers" — you should install these as suggested. Make sure that you update your system also.

So, what can we do with restricted drivers.

Using the Graphics Card

Ubuntu now has a full range of interesting desktop effects.

System —> Preferences —> Appearances Visual Effects —> Extra

What differences do you see? There are quite a few different effects. Find out and describe how to get the "Advanced Desktop Effects" dialog. Try a few out — describe their effects.

Working faster

One of the advantages of using a dual boot rather than a virtual machine is that things generally run faster. Lets try this out.

Install the clustalx onto your machine. You should be able to work out how to do this by now. This does multiple sequence alignment which is quite demanding. So next we need some sequences to align. Interpro provides lists of files. Try the GPCR Kinase entry; there is an accession list link somewhere down the page. You can get all the sequences in fasta format from Uniprot. Use the "retrieve panel". Cut and paste the sequences in. Load them into clustalx, and run the alignment. It will store an elapsed time. Once you have finished, try repeating the same experiment on your virtual machine. Probably (but not necessarily!) the dual boot will be faster.

Tidying up

Congratulations; you have finished the module. By now you will have used up quite a chunk of your hard drive installing various machines. So you may want to clean up afterwards. Please don't feel obligated; you can keep them if you feel that they will be useful.

To uninstall Wubi, Reboot into windows. Start -> Control Panel -> Add/Remove Programs -> Ubuntu. For VMWare, leave the VMserver alone — it's not very big and it's installed by your friendly local support staff. Find the virtual machine that you installed on the hard drive. Delete it.

Afterword

Hopefully, during this course, you will have been shown the most common tasks of system administration. As a bioinformatician, you do not need enormously in-depth admin skills, but having some will make you much more efficient. Alternatively, system admins with some biological/bioinformatics skills are highly prized within research as they have a good knowledge of what their users are trying to achieve.

In practice, there is a lot more to being a good system administrator, but a surprisingly large amount of it is variations-on-the-theme of what you are have learnt — installation, scripting, data security and safety, networking and upgrading. The key skills are being careful and precise with what you are doing, and gaining as much background knowledge as you can from all the information sources you have available. Hopefully, the course will have helped you to learn this.