Linux with Biology in IT

Transcription

1 Bio-Linux Linux with Biology in IT

2 What is Bio-Linux? Bio-Linux is a part of the EGTDC's solution to data management. For a biologist Bio-Linux gives access to many bioinformatics programs and packages, both standard favourites, and cutting edge tools, in a user-friendly computing environment. In addition, a high level of support and help is available from the EGTDC to enable researchers to quickly make the most of the capabilities of their Bio-Linux machine. From the computing side Bio-Linux makes it easy to get started working on the Linux platform by offering a custom designed version of Linux based on the stable and well developed RedHat distribution. Thus, in addition to the core set of bioinformatics tools available on Bio-Linux, it contains all the security features and a wide range of general development tools (programming languages, compilers, MySQL, Postgres, etc) common on Linux machines.

3 Who develops Bio-Linux? Bio-Linux is a project of the EGTDC. Bio-Linux development was started by Dr Milo Thurston. As of February 2003 development and roll out of Bio-Linux v2.0 has been taken over by Dr Dan Swan. We have partners who will supply us with an EST analysis pipelines and partners in Manchester who supply us with the transcriptomics package MaxD, as well as an agreement with Silicon Genetics to supply "GeneSpring" for microarray analysis. Bio-Linux is a collaborative effort, we welcome input, suggestions and development help from others.

4 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. Purists will tell you that Linux refers only to the 'kernel' the core part of the operating system that interfaces your software to your hardware but nowadays it refers to the whole package of programs that make up a fully functional computer system (GUI/tools/Office packages/games etc). 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 GNU GPL (General Public Licence). 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 for everyone to view. This is also known as the Open Source philosophy.

5 More on Linux 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 It is now a viable alternative to Microsoft Windows on the desktop, and UNIX variants in the server market. A quick note on pronunciation. Lee-nux or Lie-nux or Lyn-ux. Noone really cares. The former is the most correct and the least used!

6 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, clients, groupware, IM clients etc. This talk was made in OpenOffice a Microsoft Office compatible office productivity suite. The command line, whilst occasionally mysterious is the most powerful aspect of Linux. It is hidden away in Windows!

7 Linux distributions Linux comes in many flavours. Some aim for the desktop market, some for the server market. There are underlying similarities between them all, and some differences between them all. Standards for Linux are emerging. You may hear about the following: SuSE. Mandrake. RedHat (which we will mostly be talking about) Gentoo. Debian.

8 Bio-Linux foundations Bio-Linux v2.0 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. The desktop environment is Ximian Gnome, a set of extensions to the Gnome environment to make it more userfriendly and ease tasks like system updating.

9 Linux vs Windows There is obviously the cost issue - lower TCO of Linux. 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. 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.

10 Can I install Bio-Linux on different hardware? The short answer, if you are not experienced with Linux configuration, is no ;-) A fuller answer is yes, but there are some caveats. It would be best to approach me about this at a later date and we can talk about the issues involved.

11 Bio-Linux and..... data management

12 The rationale of Bio-Linux Bio-Linux is part of the EGTDCs strategy for data management. Designed to allow researchers to handle and store data locally but also feed data back to the EGTDC. Setting up of analysis pipelines. EST pipeline solution Microarray pipeline solution

13 The Bio-Linux install process From our server to your lab

14 The Bio-Linux install process Installing Bio-Linux is not like installing Linux! Bio-Linux is pre-configured, what you get is a system image. What you get is effectively a 'clone' of the hard drive of our 'gold' server. We use a program called systemimager. Every time we release a Bio-Linux version, we make a 'carbon copy' of the hard drive in our development machine and store it on a central server. This server then feeds out this 'carbon copy' to your machine during the install.

15 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.

16 What happens on installation? CD-ROM & floppy into drive. genomics pinged, rsync connection established The EGTDC machine will download the image to your machine, replicating our 'gold' server. This can take from 30 minutes to 2 hours+ depending on your network speed. You are then prompted to log-in and run a setup script which sets up various networking information and sets up your hard-drives. You are returned to a graphical menu log in and go!