Getting side-tracked I'm going to start a Bio-Linux install whilst you read this

Introducing Linux

• Dan Swan, Linux Developer
• EGTDC, CEH Oxford

Getting side-tracked

• I'm going to start a Bio-Linux install whilst you read this.

• We will come back to the installation process later.

• We need to start the install now, otherwise I will get stuck with nothing to say whilst we are waiting for it to finish when get to the end of this talk, and you don't really want to hear about Plymouth Argyle losing this weekend.

• Installing Bio-Linux is easy. One CD-ROM, one floppy diskette, one computer, one power cycle.

What is Linux?

• Linux is a clone of the UNIX operating system originally started by Linus Torvalds, and now maintained by a group of thousands of volounteers worldwide.

• It runs on just about any hardware platform you care to name from mainframes to desktops to PDA's.

• Linux is distributed under a special licence - the GPL. Which basically means that you may freely copy, change, and distribute it, but you may not impose any restrictions on further distribution, and you must make the source code available.

What is Linux? (2)

• Consequently Linux is often said to be 'Free' software. This not only means free (as in free beer) but also free as in freedom. Authors maintain copyright, but the redistribution clause means this is often called 'copyleft'.

• Linux is a mature operating system - it has been in development since 1991. It is now a viable alternative to Microsoft Windows on the desktop, and UNIX variants in the server market.

Linux distributions

• Linux comes in many flavours. Some aim for the desktop market, some for the server market. They are all effectively built on the same underlying code.

• You may hear about the following:

• SuSE.
• Mandrake.
• RedHat.
• Gentoo.
• Debian.

Why are the EGTDC so excited about Linux?

• It is not because we are a bunch of geeks who like making life difficult for ourselves. Linux is userfriendly.

• Linux is a true multitasking, multiuser operating system. You can run multiple programs without your system grinding to a complete halt.

• Linux is fast, and reliable.

• 90% of scientific software is developed for Unix/Linux.

• It's simple to install - even simpler when provided by the EGTDC.

• It's simple to learn.

• It allows us the freedom to do what we want!

Linux vs Windows

• There is obviously the cost issue.

• Similar in operation when you are using a windowing interface.

• You can read every single line of code that makes up Linux, and none of Windows (unless you are the US government).

• Thousands of people scour Linux for bugs, and can fix them and contribute back to the process. Windows doesn't have the same development route therefore bug fixes and security fixes can take a long time to come through to the user.

• The command line, whilst occasionally mysterious is the most powerful aspect of Linux. It is hidden away in Windows!

So there's more?

• Linux is much more configurable than Windows. If you don't like how its set up - you can change any aspect of it!

• Vast, vast choice of software. There are many different text editors, word processors, spreadsheets, PIM's, email clients, groupware, IM clients etc. This talk was made in OpenOffice a Microsoft Office compatible office productivity suite.

Bio-Linux

• Linux with Biology in IT

What is Bio-Linux?

• We hope you are convinced that Linux is now 'a good thing'.

• We would like to see it being used more and more in the lab environment.

• Bio-Linux is an effort to take a Linux distribution and populate it with bioinformatics software tools to aid your research.

• EG PI's and co-I's are to get a dedicated Bio-Linux workstation.

• Bio-Linux is an ongoing project. As users we would greatly appreciate your feedback when you are using it.

Who develops Bio-Linux?

• Bio-Linux is a project of the EGTDC.

• The majority of Bio-Linux development has been done by Milo Thurston.

• As of February 2003 maintenance of Bio-Linux v1.0 and development of Bio-Linux v2.0 has been taken over by Dan Swan.

• Bio-Linux is a collaborative effort, we welcome input, suggestions and development help from others.

The technical bit

• Bio-Linux v1.1 is based on RedHat Linux 7.3.

• RedHat is the established market leader in the Linux world for distribution penetrance and is considered to be userfriendly for people migrating from other desktop platforms.

• It is not a distribution, it is a system image. This means that you will need to run it on very similar hardware to that it was developed on. This is because certain aspects of the software are configured for the hardware in the machine (eg ethernet cards, video cards etc.).

• It is pre-configured. All you need to do to install it is to pop in a CD-ROM, floppy diskette and turn the machine on.

Why do we image machines?

• It allows Bio-Linux to be rolled out very quickly across multiple machines.

• Whilst Linux is relatively easy to install, esoteric hardware configurations can cause trouble. A system image takes away the problems that can arise during an installation.

• It makes it easier for us to customise heavily before release.

• We get to standardise our support (we are only a small team!).

• You get a tried and tested installation.

Bio-Linux - future directions.

• We will move towards a RedHat 8.0 base. This is more up to date.

• More bioinformatics tools!

• As we switch the standard hardware, we will have an SMP kernel (use two processors at once!).

• Implementation of GRID software to create a 'virtual' supercomputer.

• Hardware independent distribution (at some point).

• Many more things - based on user input.

• Do you want more programs in? Just ask us to add them.
• Do you not like the windows interface? Ask us how we can change it to make it more useful.
• Finding something awkward? Tell us, so we can document it for you and help people in future releases.

Getting Bio-Linux

• From our server to your lab

How is the install going?

• Just checking. Hopefully by now a lot of text should be scrolling rapidly up the screen.

• This means the installation is in progress. Files are being transferred to the machine.

Hardware considerations

• As discussed earlier the Bio-Linux system image is hardware dependent to a certain extent.

• This does not mean it cannot be installed on other hardware, but we encourage you to match the specifications of our development machines. We will not be able to support non-standard machines, nor offer upgrades.

• Bio-Linux v1.1 requires either a Dell Optiplex GX240 or GX260 (Pentium 4 machines).

• If you're waiting for a machine you are likely to get Bio-Linux v2.0. We don't know yet what the hardware will be, but it is likely to be Dell Precision 650 dual-Xeon machines. Your friends will be very jealous.

Requesting Bio-Linux

• Assuming you have not already requested a Bio-Linux install you will need to pay a visit to the EGTDC website and download an application form.

• All the latest Bio-Linux information can be found at:

• http://envgen.nox.ac.uk/biolinux.html

• The technical information on the application form is very important!

• Please liase with your IT department on filling this out.
• Do not make educated guesses!
• If its not correct, the install will fail!
• If your IT department don't like the idea of you running Linux, or have concerns about the security of the machine, please put them directly in contact with us. We are used to dealing with IT departments and know how to keep them happy.

What happens next?

• We will send you a CD-ROM and a floppy disk.

• The CD-ROM contains a minature Linux install which will boot your machine into Linux for the first time and prepare the system for installation.

• The floppy contains configuration files so when your machine is installed it will be online and ready for use. It also contains your GeneSpring Licence.

• When you have arranged a time for the installation with the EGTDC - we will be ready to install.

Installation

• Check the BIOS of the machine is set to boot from the CD-ROM (we can help you with this).

• Insert the CD-ROM and floppy into the drives and turn the machine on.

• The CD-ROM will load a Linux image into memory and partition your drives.

• The floppy is read, and when the drives are ready your machine contacts the EGTDC and requests a download.

Installation (2)

• The EGTDC machine will download the image to your machine, replicating our 'gold' server.

• When the install is finished - the computer will beep repeatedly to let you know its done, and prompt you by text to reboot.

• Remove the CD-ROM before rebooting!

• When the machine is rebooted, you will be presented with a standard Linux login prompt. Do not panic.

Installation (3)

• At this point you will need to login as 'manager'. There will be more on the accounts later.

• The manager password will be supplied to you on the install day. We highly recommend you change it at the earliest possible convenience.

• When you login you will be at the command line.

• Type 'sudo setup.perl'.

• Press 'enter' when prompted.

• The script will tell you when it is finished.

• Type 'sudo /sbin/telinit 5'.

• When the screen settles, you will be at a graphical login prompt. You are now ready to use Bio-Linux and the machine is online!

• By the time you get your machine, we will have simplified this process even further.

Congratulations!

• You are now ready to log-in.
• Thank you for choosing Bio-Linux.
• Its never too early to teach good practice - the first thing to do is change the passwords!