Genetic Inference » computers

ASHG: Chatting with the Sequencing People

Luke — Thu, 22 Oct 2009 22:37:27 +0000

While I am here, I though I’d take the chance to chat to the people at the booths for the three major Second Gen sequencing platforms (Illumina, SOLiD and 454). It was surprisingly fun, the guys I talked to all seemed enthusiastic, and it was nice to find out where the scientists in the companies think the technology is going.

In the interests of openness: the 454 booth gave me a cool T-shirt and poster, so this may well have biased my opinion of them

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Scientia Pro Publica #14

Luke — Mon, 19 Oct 2009 13:00:56 +0000

Welcome to the 14th Edition of Scientia Pro Publica (Science For The People). This blog carnival collects together the best non-technical science writing that has appeared around the blogosphere in the last few months, to promote and celebrate science, nature or medicine blogs written for the public.

In this edition, we have a glut of posts related to climate change, and an equally large group of posts about the interaction of science and society. Along the way, we will also cover some basic science posts from physics and biology.

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On Revisionism

Luke — Thu, 17 Sep 2009 10:23:16 +0000

Today, I attempted to log into the Sanger computing cluster, and was presented with the following error message:

> ssh farm2-login
You don’t exist, go away!

I was somewhat taken aback by the snappy tone from a usually jovial machine. As much to reassure myself as anything, I enquire who the computer thinks I am.

> whoami
whoami: cannot find name for user ID 12722

I see, so the computer is claiming to not know who I am; that to it, I have ceased to exist, or have never existed. Given that I was in work yesterday, it is unfortunate that the computer would forget about me so rapidly.

I attempted to reassert my existence, and was met with this:

> su lj4
Sorry.

The resigned sadness of this message is haunting. The computer would be refusing to meet my eye, if it was able to do so in the first place.

I cannot help but feel that my machine has done something terrible, something that fills it with guilt and shame, something that it knows I cannot forgive. It greets me with shock and anger, then with denial, and then finally with a guilt-weary apology. What has happened? Should I be reassuring my machine? Growing angry with it? Or panicking blindly as the sense of unease and mounting horror rises sharply in my breast?

In the end, I go with turning it off and then on again.

Books for Bioinformatics Beginners

Luke — Wed, 19 Aug 2009 10:58:59 +0000

Olaf left a comment asking about what books a mathematically competent and generally informed non-geneticist can read to learn about modern genetics. As he notes there tends to be a bit of a lack of books that assume you are know the basics, but does not assume you have an undergrad degree. You tend to find things that are either of the form “this is Mr Gene, he makes proteins!”, or of the form “a non-Bayesian could infer with certainty an inversion-deletion event had caused this ribosomal disruption, so attached are they to their bootstrapped pseudo-statistics!”.

This sort of request also tends to come from the very large number of undergrads trained in genetics in some classical sense (a mixture of population and functional genetics) who want to get a general understanding of this whole Modern Genomics phenomenon that basically all of genetics is at least partly involved in these days.

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The Genome Campus is a Mac?

admin — Sat, 13 Jun 2009 10:06:29 +0000

Catching up on my RSS feeds, I came across a post at PolITiGenomics, about the European Bioinformatics Institute’s Paul Flicek taking part in one of those ‘I am a person of significance, I use a Mac’ videos:

First the most important bits. At 0:06, THAT’S MY COLLEGE! And at 0:25, THAT’S THE BUILDING I WORK IN! And at 2:24, I EAT THERE! How exciting.

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On The Digital Embryo and Some Very Cool Videos

Luke — Thu, 12 Mar 2009 10:46:54 +0000

Reader, I have a bit of a visual treat for you today. A group at the Heidelberg branch of the European Molecular Biology Lab (EMBL) published a paper in Science a few months ago, detailing a full microscopic scan of the first 24 hours in the development of the zebrafish embryo, from a handful of cells to when the first structuring starts to occur. And, in doing so, they produced some startlingly beautiful videos of the first moments of life.

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On Excel-Damaged Genes

Luke — Tue, 10 Mar 2009 15:14:58 +0000

Hello again, it has been a while. In the half an hour I have before an afternoon seminar, I thought I’d share an interesting and amusing paper that came out a few years back. It is entitled Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics. It is available for free on PubMed Central (three cheers for Open Access!).

The paper is about a distressing clash between the sublime and the mundane. The first element of the two is the DNA microarray, a technology that allows you to measure the expression of a very large number of genes (a technology that is now reaching the end of it’s lifespan, a point that I may discuss another day). The output of these experiments tends to be large text tables, in which rows correspond to genes and columns correspond to different individuals, which each entry giving an indicated of the level of gene expression. Often, this data will be processed and analysed with a variety of high tech algorithms to discover genes that differ among classes of people (say diseased and healthy), or to model the expression mathematically, or to reconstruct the networks that underly expression.

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On Phoenix

admin — Sat, 31 Jan 2009 17:25:57 +0000

Hello again, patient reader; I apologise for my long absence, I have had a pretty busy couple of weeks, what with the Amsterdam trip being added to my otherwise hectic life. If you have been pinning for information on how it all went, I can finally reveal that it went very well, thanks for asking. In addition, I went to Artis (Amsterdam Zoo) as part of my continued quest to visit all the science museums in Europe (the zoo contains their equivalent of a Natural History Museum); perhaps in the future I will write something about this. I will have to synthesise everything I remember about all the museums into a Coherent Whole though, so you will have to be patient.

Anyway, today I went on what you could describe as a Journey into the Past, if you were feeling grandiose. It started when I had a free hour due to one of my students being taken ill, so I decided to look up a question that I have been meaning to find the answer to for a long time. I must warn, this post gets a little sentimental, and if you find such things irritating, I apologise.

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