Archive April 2012

University of Otago campus loses power Grant Jacobs Apr 30


In local news, the main campus* of the University of Otago lost power this morning. According to reports on social media, the power outage is restricted to the campus area:

Paul Le Comte (@five15design)
Massive boom & the power has gone out to a big part of #Otago Uni Centre for Innovation is dark – home time via the wood & coal shop

Paul Le Comte (@five15design)
By all accounts St David St block, Centre for Innovation & all of Registry is without power

Tom Tremewan (@TomTremewan)
Complete power outage all over @otago campus right now.

Pippa Mackay (@pip_pip_pippy)
@BioinfoTools @five15design @otago power has just come back on in central library, unsure if it’s just back up or restored completely

Other self-reporting on social media indicate that surrounding suburbs were unaffected. There is no word from the University of Otago on social media at this time.

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New Zealand viewers: Hawking on Prime Grant Jacobs Apr 25


Just a quick heads-up for New Zealand readers, tonight at 8:30pm Prime will be showing the British drama Hawking, produced by the BBC, which covers cosmologist Stephen Hawking’s earlier years from the initial stages of his diagnosis of motor neurone disease. The production features Benedict Cumberbatch, who starred in Sherlock.

Hannah M’s review at Rotten Tomatoes reads

I first saw Benedict Cumberbatch in the BBC TV show “Sherlock” and decided to look up what else he’d done. In this made-for-TV movie, he does an *excellent* job playing Stephen Hawking in the early days of his diagnosis. The movie’s writer, Peter Moffat, also wrote the fairly-entertaining Einstein and Eddington, but the writing is sharper and more interesting in this older one. Well worth checking out for fans of biographies, science stories, or Benedict Cumberbatch.

An astrophysicist, Sarah H, offered her thoughts:

I came at this movie from two perspectives: First, as a fan of Benedict Cumberbatch, and second, as an astrophysicist and high school teacher. I thought the film had a good combination of “hard science”, but wrapped up in understandable terminology and a sweet human story. Benedict’s physical work as Hawking is

I can’t vouch for this, not having seen it before, but most reviews praise Benedict Cumberbatch’s efforts - it might be worth checking out.

Other articles on Code for life:

What do scientists look like?, redux

The littlest chameleon?

Epigenetics overview (video)

Do TED lectures need better vetting?

“We’re so used to getting a prescription that’s it’s surprising when we don’t”

Are bioinformaticians gods?

Finding a long-lost treasured item Grant Jacobs Apr 20

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Media loves those romantic, emotionally appealing, stories of someone rediscovering their favourite lost toy or book from their youth. What if that favourite thing was the computer source code of a project you put your all into?

This story could win a geek’s heart. Jordan Mechner, writer of the early graphical computer game* Prince of Persia, gets sent a box by his Dad. In the box is a 5¼” floppy disk containing the original source code, something though he’d lost. A trans-continential flight over a weekend, others’ work on hardware setup to read the disk, ensue – it’s a saga.

It’s all on his blog – read it, he writes well, recounting the arrival of the box and a post-event exploration of ’why?’ ArsTechnica also has coverage.

Aside from the story itself, some of the technology appeals to me. Read the rest of this entry »

Campbell Live on influenza vaccines Grant Jacobs Apr 19


Last night local current affairs program Campbell Live ran a story comparing two staff members and their decision to vaccinate or not, ’of course’ choosing one ‘for’ and one ‘against’ for balance.

You can view the footage* and read the comments they quoted and subsequent comments on-line. (To get back to the quoted comments from the video footage, you’ll need to keep pressing ‘View previous comments’ until you’ve got them all displayed – there’s a few hundred of them now!)

Overall the story seems well done. We’ve discussed communication of vaccine issues before here – what do think of Doctor Cameron‘s efforts?

Here’s what Aspiring Health, from twitter, thinks: ’Seriously Dr Cameron on @CampbellLiveNZ is the jolliest GP ever!’ He certainly presents with gusto and exudes bonhomie. Personally, I think he did an excellent job.

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What kind of scientist are you? Grant Jacobs Apr 15


In his novel COSM Gregory Benford describes* four types of scientists -

  1. I want to know – ’Prying into Mother Nature’s secrets.’
  2. Theory predicts – Exploring what theory says ought to happen.
  3. This is what I do – ’Habit often rather mindless. More deeply, it means This is who I am.’
  4. A sweet experiment – Doing a well designed/executed experiment itself.**

What kind of scientist are you?

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Epigenetics overview (video) Grant Jacobs Apr 11

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Below Jessica Tyler, from the University of Texas MD Anderson Cancer Center, introduces epigenetics, a topic I’ve touched on a few times and would like to elaborate further on. Her introduction is fairly gentle; hopefully some of the essence of the thing will come across to non-specialists!

You may need to wait until the video is buffered before it starts displaying. Feel free to ask questions in the comments below.

(Excuse the back-to-back videos and no articles – I’m very busy until at least Friday!)

Other articles on Code for life:

Epigenetics, growing old and identical twins becoming unique

Doggie ERVs

Transcribing a gene, free poster

Autism — looking for parent-of-origin effects

Coiling bacterial DNA

Epigenetics and 3-D gene structure

George Church on genomics and personalised medicine Grant Jacobs Apr 06

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Weekend video – for general readers.

This TEDxCambridge lecture by Professor George Church* offers an informal look at progress in genomics and personalised medicine. While very informal compared to some TED lectures, but it does give glimpses of where genomics and personalised medicine might be headed in a series of quick snapshots.**

In the middle of his talk you’ll hear about some kids sequencing genes for their own interest or school projects. For some like me who has been doing computational biology from before the genome projects*** it’s a measure of how far things have come.

There are some examples of new possible treatments being explored.

YouTube Preview Image

His talk assumes a bit of background in places – he’s giving a high-flying overview. Feel free to ask anything in comments below.

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And the top journals are… Grant Jacobs Apr 05


According to Google Metrics, top 20 of the top 100 journals are (if you find the writing a bit small, I’ve put the top 25 further down in the article):


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Forward to wikipedia – topic pages in computational biology Grant Jacobs Apr 04

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The PLoS (Public Library of Science) journal Computational Biology has offered it’s first Topic Page, Circular permutations in proteins,* along with a short editorial introducing the Topic Page concept.

Basically, authors write a wikipedia-style review of a topic that is reviewed and accepted by the journal, then forwarded to wikipedia to become a ‘living’ version of the Topic Page. Initial versions are developed on the PLoS Computational Biology Topic Page wiki site.**

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A bioinformatics periodic table Grant Jacobs Apr 03


A spin-off of the Eagle Genomics conference in Cambridge, UK, has been The Elements of Bioinformatics, a table of different tools in bioinformatics. (Update: an interactive web-based version of the periodic table is now available.)

You can offer thoughts on their blog (linked above), twitter (use the #egelements hashtag) or, of course, below.

bioinfo periodic table

Go explore it – you might find a few new tools to investigate.

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