Monthly Archives: April 2007

Farewell OLPC

I had very high hopes for the “One Laptop Per Child” initiative.

The OLPC project was a genuine attempt to provide a cheap ($100) laptop for educating children in developing countries. Ruggedised, running Linux, well designed, it’s had many people wanting one for themselves, even if this meant paying a charitable premium back to the OLPC project.

However I’m deeply worried that the project is losing its focus. Firstly they refused to implement a premium option for private consumers, even though this could have swelled their charitable coffers.

Last week the news came that the $100 laptop would be a $175 laptop. The specifications had been ‘beefed up’.

Adding three quarters again to the price of the product seems to be crazy. But what is worst of all are the reasons why this has occurred. Apparently Microsoft want in on the OLPC good vibe, and provide a cut down version of Windows for it because – GOD FORBID – someone might actually start handing out Linux for free to children in developing nations.

Of course Linux runs on everything from toasters, to Linksys routers, PDA’s, phones and who knows what else. Windows on the other hand, doesn’t. So the OLPC specs appear to have been increased specifically to accommodate Microsoft, increasing the price of the unit, and allowing Bill Gates to make damn sure that no child is left behind from the great opportunity to be locked in to a DRM future.

My warm and fuzzies about this project just left the building. A real shame.

Papers 1.0

So finally this week there’s been a major software release that I’ve been eagerly anticipating.

Since moving to OS X as my primary computing platform I’ve noticed that I’ve bought a lot more software. I don’t mean in the hundreds of pounds category (because, quite frankly, that’s why the internet was invented), but in the £10 to £20 category.

The OS X community has quite a thriving scene that would once have been described as ‘shareware’. The term seems to have been dropped, but the principle is the same. Try for free, buy it when your trial expires.

As predominantly a Linux user for the last 12 years, this style of software sales has kind of passed me by, because everything I need on Linux is free.
I don’t know whether it’s because I can afford to buy software now without being concerned about it, or whether I’ve suddenly discovered the fact that there is magical trade off between ‘getting organised’ and realising that the open source solutions available really don’t fit my needs, but now I happily shell out for products that I think will benefit my GTD lifestyle (no still not yet implemented, wait ’till next week).

One of the things I have longed for is a decent reference management system. I had previously used KnowledgeTree for this purpose, and of course Endnote. KnowledgeTree had many excellent features, and it’s been 2 years since I used it, but there’s a reactionary little part of me that likes my stuff local. I’m not a great fan of running Apache on my laptop just to serve up an application, I’d rather just have a local application that works offline. Endnote is a package I’ve always regarded with utter contempt, so much so that when I wrote my PhD thesis I did all the referencing by hand.

So trying out Papers from mekentosj was a real revelation. At its heart Papers is a PDF bibliographic database. What makes it interesting to the life sciences community is the fact that you can tag the PDF’s up with appropriate metadata and the fact that it seamlessly integrates with Pubmed and Connotea.

That library of PDF’s sat on your hard disk can suddenly be organised in ways you previously only could have dreamed about. Sort by Author, Journal, Title – have smart folders of papers autocreated from custom keywords. Drag and drop papers into your library and pull bibliographic information directly from the internet using the DOI. What I especially liked was being able to feed back to a couple of well known OS X bioinformatics tool developers during the development of Papers. Feature requests and bug reports were gratefully received and the 1.0 release is infinitely more stable than the pre-release version, far more fully featured and better integrated to online resources. There’s already been occasions where I’ve been in meetings and had the PDF at my fingertips rather than having to rely on Spotlight to (maybe) find the PDF I’m interested in.

It doesn’t just work for papers – I’ve got PDF’s in there tagged with metadata that means something to *me*. When I imported my document libraries initially it took my Word documents in too. It now sports a Firefox plugin that allows you to summon its bibliographic services from the touch of a toolbar button.

It’s one of those pieces of software that conceptually is very simple, but after using it for a month you have no idea how you lived without it previously, nor – most importantly – why this hasn’t been implemented in this way before. I admit to have missed a trick here, because it was always in the back of my mind to develop something like this, but I don’t think I could ever have executed it with the panache this program offers.

OS X user? Over 100 PDF’s stuck in folders all over your drive? You do need this software, I cannot recommend it highly enough.

I’m not even going to explain how I got here

but this site just reminded me what the internet used to be like and it made me feel a bit warm and fuzzy inside, but also a little scared.

On linking topics, for some reason the blog has slipped down the Google rankings. Searching for “Dan Swan” I’m still on top but searching for “Daniel Swan” now brings up that sodding cross burning, racist namesake in the US who I will refrain from linking to, and spent many months trying to displace at the top of Google. But also now my *real* namesake (the other Dr Daniel C Swan) who is an Associate Professor and Director of the Chucalissa Museum has managed to get above me.

Damn their eyes..

Finally a decent OS X calculator!

One of my major gripes with OS X is the lack of a decent built in scientific calculator. Yes there is one there, hidden (like in Windows) behind the standard interface, but they all lack a decent featureset.

It’s not like I don’t have a scientific calculator on every single desk I sit at, at home and in work, but there’s nothing like having one onscreen sometime.

I have just come across the Magic Number Machine, a really, really nice scientific calculator for OS X. Full history, more constants than you can shake a stick at, and easy to use.

Nice app!

Making progress in Rosetta@home

One of the things I’ve always loved to do with spare CPU cycles is contribute to distributed computing projects. I used to live quite high up in the SETI@home rankings, until I belatedly realised that whilst fun, there was very little scientific merit to hunting for aliens and decided to focus closer to home.

For I while I ran Folding@Home and whilst I’m sure things are better now, when I participated in it the project seemed to be run rather haphazardly, and I grew rather disillusioned with the projects progress.

More recently Simon and I (well mostly Simon actually) have been running Rosetta@Home in work. It’s superficially similar to Folding@Home, but focuses (as far as I am concerned) on more fundamental science.

Over the weekend we made possibly our second to last move in the Rosetta@Home stakes. Our team moved from 8th to 7th in the UK rankings for the project, with the chance to move into 6th place in about 4 months time.

We are the “Newcastle University Bioinformatics Support Unit” team on this page:

Top 100 ranking for UK teams

We should break into the top 300 worldwide teams soon too!

Please feel free to join us in our quest :)

Trolling bioinformaticians?

Spotted over the weekend in #bioinformatics on

01:07 [fabian2] hello
01:08 [orbitz] hi
01:09 [fabian2] what’s new
01:09 [fabian2] are you done fucking up all human agriculture yet ?
01:09 [fabian2] you wanna start making custom humans ?
01:09 [fabian2] mother fuckers
01:10 [fabian2] you’re the fuckers who truly belong in guantanamo
01:10 [orbitz] what?

nice to know bioinformaticians too can still get some of that sweet, ignorant trolling.

Nominative determinsim in genetics

So all over the news yesterday was the reports of a gene that controlled BMI. I had to look at this in a little more detail today, as I used to work in the obesity field, and wanted to know if any old colleagues were implicated in this.

The paper was published in science and certainly a couple of the authors (Graham Hitman and Mark McCarthy) are people I interacted with regularly when working at the Bart’s Genome Centre (QMW). When people push out Science papers you do really question your motivations for moving outside their sphere of influence just to get a new job.. oh well.

What caught my ear yesterday was the fact that not much is known about the gene involved (FTO) – certainly not why it should have any role in obesity. A little reading turns up the fact that it’s the gene that was derived from location of the ‘fused toes’ mouse mutant.

However the paper that reports the cloning of this gene has the most wonderful title:

“Cloning of Fatso (Fto), a novel gene deleted by the Fused toes (Ft) mouse mutation.”

So a gene that causes obesity in humans as identified in 2007, that was cloned in mice (which show developmental abnormalities but no weight ones) from a region causing “fused toes” was named Fatso back in 1999.

Isn’t that just perfect?

Bank charges part 2

OK so the interest calculation in my last post is off – that was the 8% statutory interest if I won in the courts. It seems that interest costs are about 10% of the claim, so my final claim went off today for £1666 to NatWest – recorded delivery.

They now have 14 days before I follow up my polite request for a settlement with a statement that I’m prepared to take legal action.

I was chatting online to someone who has been through this process recently and recouped £1900. I love the idea of thousands of consumers beating a path to threatened litigation with their banks and reclaiming all this money! Makes me all warm and fuzzy inside.

Getting back the bank charges

Because I’ve not always been as financially prudent as my peers, the last few years of my life have been replete with bank penalty charges for unauthorised overdraft fees and associated costs.

Seeing masses of consumers swinging into action over this (at and the Consumer Action Group in particular) I took the step of kicking off the process with my bank (NatWest) 2 weeks ago.

A couple of days ago a thick pack of statements arrived – the last 6 years of my financial life in paper form, leaving me to pore over them and decide when I have been unlawfully charged for services.
After careful consideration this afternoon the bank charges total £1500.

That’s £1500 of my money the bank has taken from me. £1500 that would have been very welcome as I tried to get myself out of debt in the first place. I had a feeling it would be around that sum, but seeing months when I was really struggling in the past have bank charges in excess of £110 levied against them was quite upsetting.

Onto stage 2 now.. calculate the statutory interest on these charges, and add them to the bill and then write to NatWest demanding prompt repayment.

I look forward to this windfall in a couple of months time, to bolster my ISA for the year (held elsewhere ;)) knowing that this money is rightfully mine.

Edit: The interest alone comes to a cool £400.