Posts Tagged ‘computers’

Books for Bioinformatics Beginners

Wednesday, August 19th, 2009

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?

Saturday, June 13th, 2009

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

Thursday, March 12th, 2009

ResearchBlogging.org

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

Tuesday, March 10th, 2009

ResearchBlogging.org

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

Saturday, January 31st, 2009

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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