Archive for the ‘material existence’ Category

Summer is coming …

Monday, April 13th, 2009

img_4579.jpg

It has been Easter weekend, and as a surprise in Finland we have even had some sunshine and temperatures in double positive figures! When presented with both sun and a little warmth then the bicycle must come out.

Many of the best things in life are associated with Italy; good food, good wine, great motorcycles and fantastic racing bicycles. (It’s just a shame that the Italians can’t make cars – just look at Fiat …) My own Italian bike is now out and we went for the first dash of the season – there is a great round tour of the island where I live and I had fun, some pain, aching lungs, tortured legs, and a rather pathetic time, but we are now into cycle season.

I sometimes wonder what other bioinformaticians do for escape? Bioinformaticians I very much hope are not the archetypal geeks – pale skin unexposed to the sun – flabby waists and oily skin … Yikes … I am a fan of the warm outdoors and like sailing, biking and hiking. I am now in summer mood and things feel really positive.

I have been clearly trees and bushes in the garden, have tidied parts of the estate and will soon start preparing the boat for the sailing season. Life feels great at the moment – I guess that chocolate really does help.

Posted in absolutely nothing at all to do with bioinformatics, life experience, material existence | No Comments »

biomedexperts – scientific social networking

Thursday, January 15th, 2009

europeisall.png

Googling for yourself is always an interesting way to waste some time! I was curious to see if the bioinformatics blog would be identified by a name search (not appears to be the answer). Amongst the surprising many people who share my name, are a few pages dedicated to just me within the sphere of social networking. Beyond the typical linkedin-type pages (and a remarkably untouched facebook page, was a resource that I hadn’t seen before – biomedexperts “your scientific match point”.

Pretty interesting stuff, a collation as to whom I have worked with, when and the scientific articles that have been published. It is very clear that the centre of my scientific network is based in Bavaria! Enough years in the wastelands of the Finnish periphery, and the network remains and is still stronger than anything that went before.

Have a look, and I guess that if you have a few articles published within a typical biomed indexed journal, your global scientist::scientist interactions will be intuitively plotted.

As a side note (or even grumble) I stumbled across the web pages for the national UK census of 1911. I was interested to check out the gossip of my great-great-grandparents who would I guess have been just a few years younger than I am now! I have found a few candidate names, registered (for free) to access the data, and am then asked to supply credit card details for more info …. Having wasted sufficient time in filling the abomination that is the census document, I feel that if in another 90 years time my great-great-grandchildren have to fork out cash to see just how unseriously I take such things, I’ll come back and haunt some tightassed civil servant!

OK another post that is full of waffle and guff, no bioinformatics (but cool networks that Ingenuity can’t yet plot ..) I’m still thinking about how and when to start making this site attractive (but waiting to get a threshold number of visitors per day first)

Posted in blah blah, material existence, public data | No Comments »

Who is reading BioinformaticsBlog.org?

Tuesday, January 6th, 2009

A view of the server logs for 2008

I am feeling quite into this New Years Resolution and am slowly beginning to feel comfortable with the process of writing a little drivel on this humble blog. The BioinformaticsBlog.org domain has been sitting here idle for the last couple of years, and for the first time I have collated some of the server logs. To my surprise, there has actually been some usage of the blog over this time! Whilst nothing has been posted or updated, there were 9140 hits to the blog in 2008, this involved the same 8626 pages within 5189 visits and from a non-specified but less than 1024 visitor count! Not bad for an idle domain!

I should really thank our main visitors, tech2.nature.com, Unknown robot (identified by ‘robot’) and Yahoo Slurp! Greetings, engines! Let’s see what we can do this year – and hopefully we can start getting a few real visitors over the next few weeks!

Posted in blah blah, material existence | No Comments »

self-learning in bioinformatics …

Tuesday, January 6th, 2009

Today is the 6th of January – and the 12th Night after Christmas. Superstition argues that it is today at the latest when the decorations from Christmas should be taken down and put away to avoid bad luck. With a corporate restructuring due to complete tomorrow, I need all of the good luck that I can get!

Whilst putting away the decorations I came across a pile of former playthings. The tools on which I learned very much of the bioinformatics tricks and techniques that I rely upon today! Amongst these toys I have an eclectic array of old SGI boxes (indy, indigo2 impact), Sun workstations (Sparc 10 pizza boxes and Sparc IPX lunch boxes galore) along with other slightly more bizarre hardware such as Sun Javastations and ancient RAID arrays.

Why do I have this junk? Back as a PostDoc I decided that there was more to bioinformatics and computing that the obligatory DEC alpha and the piece-of-$%&* Windows workstations available at the time. I spent a lot of time and money (ebay.de was my friend) buying end-of-life Unix hardware and running cool software (beyond NCBItools) such as openPBS to get complex genome analysi jobs running on machines that were rather fantastically expensive when they were new!

Those were pretty good times. Bioinformatics hardware is now kind of sucky. At home I have a couple of self-build linux servers and a Mac laptop. At work I have some pretty OK HP Xeon workstations, and at the University the group still runs some now rather dated Dell rack servers as a modest Beowulf. There isn’t really anything cool out there anymore is there.

My next goal for this year (sponsorship, career and readership allowing) is to start the process of buying some of the slightly more off-the-wall hardware to start seeing what the new boundaries of bioinformatics hardware could be? Are you interested?

Please post examples of great hardware that you are running bioinformatics on! Which ancient hardware do you still run?

Posted in gadgets, hardware, material existence | No Comments »

New wheels – ready for collection

Sunday, January 4th, 2009

If my bioinformatics career progresses beyond the current corporate restructuring a hot new Saab 9-3 Turbo will be mine! This car appeals to the family senses – it is safe, comfortable enough for the 5 of us, is rather understated (compared to other sets of wheels) and should faciliate the transformation from A to B (Turku to Espoo / Finland to UK etc) with a little fun and a lot of :-) What should bioinformaticians drive?

Posted by ShoZu

Posted in gadgets, material existence | No Comments »