Steve's Systems Biology blog » Linux

Jaunty Jackalope

Steve — Fri, 27 Mar 2009 15:10:38 +0000

Ubuntu 9.04 – Jaunty Jackalope beta has hit the Canonicle servers. Full release is due at the end of April. I’m going to give the 32bit desktop edition a run out on my laptop over the weekend.

9.04 promises Open Office 3.01 and the new ext4 filesystem which is reporting faster boot up times. No 2.6.29 kernel however as the development team will freeze the feature set before its release. 9.04 will ship with 2.6.28 stable. Ubuntu 9.10 will be shipping with 2.6.30 or 2.6.31… or neither if we’re all credit crunched to oblivion :p

LaTeX

Steve — Wed, 11 Jun 2008 19:14:05 +0000

I have been thinking for a while about the best tools to use when writing scientific reports throughout my PhD. Systems Biology combines mathematical modelling with wet lab experimentation. For me, writing equations alongside experimental data is a new experience and I was unsure how to insert this kind of information into an electronic document. There is always Microsoft equation editor, but this didn’t seem to produce the same quality of script as seen in scientific publications. I have recently favored the open source applicaton MathCast for creating equations as it outputs both as images and mathml which makes it quite versatile. I had been aware of LaTex for a few years but had many problems compiling something usable in Windows and had been too lazy to bother learning the LaTex coding to perform tasks that Office could do with a mouse click. I found it difficult to break into the LaTex scene and had rebounded back to Office and my toolbox of open source applications. Recently I have migrated over to Ubuntu and ventured into LaTex again using the synaptic package manager to compile the myriad dependencies for LaTex. This went ok and I got myself a working LaTex environment, however I still couldn’t be bothered to “code” my documents when I could just churn out an office document.

Today I stumbled on Lyx, a WYSIWYM LaTex editor. WYSIWYM is “what you see if what you mean” and utilizes a word processor style interface to plug into MikTex. For new people, idiots, and combinations of the 2 like myself, this enables the user to construct a LaTex document using a minimal understanding of the markup language but without losing any of the capabilities of LaTex.

A comprehensive review can be found here. I have to get my head around structuring a LaTex document, however Lyx provides the “leg up” to begin escaping the comfort blanket of Microsoft Office.

Ubuntu 8.04

Steve — Sat, 10 May 2008 23:31:13 +0000

No updates in a while due to work commitments. Just a quick post before bed to comment on the latest release of Ubuntu Linux. I have been tinkering with Ubuntu for a couple of years after brief forays into Mandrake, Peanut, and SUSE. I have had a few problems with driver and general compatibility issues between Linux and the rest of the world using MS Windows and stuck to XP. I tried out Ubuntu as it was the first distribution that moved away from supplying the user with 6 CDs containing a myriad of applications all doing the same thing, installing from a single 700mb CD with everything you needed. My course here at Manchester provided an Acer Travelmate 4230 laptop which we have been using for general report writing and more recently mathematical modelling with Mathematica and Copasi. I had a play with various versions of Ubuntu 6 and 7 but could never get it to recognise all the integrated hardware and ended up back with XP again.

Earlier this month I downloaded the latest Ubuntu 8.04 and gave their new Wubuntu windows installer a go as I could have a quick play and delete it without having to re-partition my hard disk. Ubuntu installed alongside XP with a smooth bootloader and ISO image instead of dual boot. I was stunned to find the operating system happily detecting all the integrated intel hardware on the laptop, the widescreen resolution, and even the integrated 3D graphics accelerator to provide the full bells and whistles Compiz Fusion desktop. A week later and I haven’t booted back into XP! The OS migrated all my user accounts automatically from XP and mapped the old partition as a drive within Ubuntu. I downloaded a couple of extra packages like Amorak and Thunderbird and I’m seriously considering waving goodbye to Microsoft for my future work. The speed gained from the Linux filesystem is considerable and the integrated synaptics package manager makes downloading additional software and updates simple.

I feel version 8.04 is a significant step forward for the Ubuntu community and a serious contended as a mainstream desktop operating system. I would seriously recommend anybody who is considering an expensive upgrade to Vista or Apple give it a try before shelling out.

The revolution is here