Showing posts from 2009

CurvyCorners - Beautiful rounded corners for your HTML boxes

CurvyCorners is a javascript library that enables you to get boxes with beautiful rounded corners (very popular a few years ago). What I like about this library is that it is only used if the native CSS of the browser doesn't support it (i.e. only used for internet explorer). Also, if there is a declaration of your intention in the CSS source file (e.g. "-webkit-border-radius:10px;") then you just need to include the curvycorners script and it will sort everything else out for you. Nice.

Simon Hoggart's political review 2009

Simon Hoggart's political review 2009 | Politics | "Peter Mandelson on Boris Johnson 'We have a lot in common. We both spent a long time in Brussels. We both had very public resignations. And we both have an overwhelming ambition to do everything we can to undermine David Cameron.' Boris, at the same event, proved him right by singling out trimming wisteria as an example of expenses abuse. David Cameron was the only MP to claim for trimming wisteria. In a conference speech Boris made an open attack on Cameron's policy for the banks, but got the biggest cheer for promising to restore the river Thames to the London tube map."

Check out the full article.

Video of deepest undersea volcano eruption ever recorded

BBC News - Video of deepest undersea volcano eruption ever recorded: "Extraordinary video has been obtained by scientists of the deepest undersea eruption ever recorded."

Where Does My Money Go?

This is a nice interactive display of what the government spends the taxes on.

Natural Parenting

"On one hand, every single one of my ancestors going back billions of years has managed to figured it out.  On the other hand, that's the mother of all sampling biases."

Child abduction hoax with hair cutting

Since having children I have heard a number of stories about young girls being abducted and found with their hair cut off and in boys clothes. These stories didn't ring true but it concerned me anyhow.

Anyway, I finally looked them up on the web and they are clearly hoaxes:

I wish people would check up on these things before spreading fear in a "Daily Mail" like fashion.

BBC Comedy Blog: Robin Cooper Week

Rather humourous set of real phone calls between a comedian and a junk mailer.

What sort of place do I work at?

Last week, I came across the following notice in the male changing rooms at work:

It seems to be a mighty bizarre thing to do and makes me wonder what sort of person would poo all over the place like that. I can't say that I have noticed any of the stuff lying around but it makes me feel slightly queasy just thinking about the number of times that I have used those showers. And how do they know it is human faeces?

This is not the first "poo" related incident either. Last year all the towels on the towel rack outside the changing rooms (including one of mine) had to be destroyed because someone had wiped poo on a few of them. Previous to the great towel burning there was an infamous incident where someone had pooed in a cleaner's mug. At least one person seems to be on a serious bowel-related rampage. I would of thought that because the demographic of the workforce are mainly highly educated people that this sort of thing wouldn't happen but hey there can always be a rotten apple. I will be mighty peeved if they close the changing rooms though as I deperately require a shower after my daily commute.

The site management seemed to be on a mission last week as this notice appeared outside the girls' toilets near my office:

Makes me wonder what on earth the vandalism was and whether I should risk taking a peek.

The following notice appeared in the men's toilet near my office ages ago, after a few weeks where the toilets kept getting blocked:

I think the bit at the bottom that is unclear says "What about the poo?"

Very funny but I think good old site management hadn't cleared the blockage correctly the first time and thats why it kept getting blocked.

Splitting Time from Space—New Quantum Theory Topples Einstein's Spacetime

Splitting Time from Space—New Quantum Theory Topples Einstein's Spacetime: Scientific American: "Was Newton right and Einstein wrong? It seems that unzipping the fabric of spacetime and harking back to 19th-century notions of time could lead to a theory of quantum gravity."

Glad that people are continuing to come up with ideas for quantum gravity that avoid the over-parameterisation of string theory. I still like the sound of "Loop quantum gravity", I wonder how that is getting on.

Plotting a correlation matrix with ggplot2

This is a decent description on a decent way to display the results of multpile correlations in R using ggplot2.

Nationwide statement to QIF Format

Nationwide recently closed down the ability to get OFX statement files. These files were used to get transaction information into Microsoft Money and many other bits of accounting software. You can read more about it at the website.

I needed to find a way round this so that I could continue using Gnucash without resorting to typing everything in. Looking around I notices that the QIF format was pretty simple and so I have written two scripts:

  1. A Nationwide credit card statement to QIF converter

  2. A Nationwide flexaccount statement to QIF converter

They are tested to work on both OS X and Linux and have zero requirements.

Lets hope that Nationwide sort themselves out and produce a better way to do this.


  • Download the full statement in csv format from Nationwide

  • Download the relevant script into the same directory

  • Make the script executable: chmod +x

  • Create the QIF file: ./ NWCreditOct2009.csv > NWCreditOct2009.qif

  • Use the QIF file in your accounting application

Further Notes

Both simple scripts are variations of each other to adjust for the different columns and are written in awk. I have never done anything in awk before so it is likely that it is not the most efficient, but it works and I did enjoy learnig the basics.


I just noticed that someone has produced a Nationwide to OFX converter which would also produce files that can be used in Gnucash etc.

Trying to organise my library of PDF papers

I have recently been trying to find a better way to organise the library of papers I have got in the form of PDFs. I have tried two recently: Mendeley research networks and papers.


Papers is a superslick OS X application that I have trialled a couple of times. A few of my colleagues use it and it really is well designed and easy to use. What is especially powerful is that you can search for papers, download the pdf and have it put in your library all within the application. Another useful feature is that you can drag and drop pdfs into it and it will go out and get all the correct annotation information for you. It currently costs €29 or $42.

Mendeley research networks

Mendeley is an application that I came across a couple of days ago and overall I am really impressed. The company describes itself as "Like iTunes for research papers." and it has got quite a bit of positive press lately.

Mendeley consists of a desktop application and a social web application. The desktop application is cross-platform and allows you to import pdfs, organise your papers into libraries etc. and annotate your pdfs. As with papers it can rename your pdfs based on the annotation information. The real magic though is in the web part of the product. You can sync your libraries (annotations and pdfs) to the web allowing for easy cross-device shared libraries but more importantly it allows you to set up libraries as shared with different users. It also will allow you to see researchers with similar interests and give you statistics about your library and even about papers that you have authored.

In addition there is also a web sciptlet which they call a web importer that allows you to import paper annotations directly from pubmed, web of knowledge etc.. Unfortunately this doesn't import the pdfs too, that has to be downloaded separately. Also there are plugins for word and openoffice so that you can cite and provide reference lists in your papers. Finally, for the latex fan boys it outputs to bibtex.

Rough comparison of Mendeley with papers


  • Free

  • Inbuilt annotation and notes of pdfs

  • Can store your library and even the pdfs on the web

  • Easy to sync libraries between computers

  • Can share libraries between people

  • Cross platform i.e. windows, mac and Linux

  • Easier to use your citations in word and openoffice


  • Can't download the pdf within the application (can download the pdf independently and then import it, on which it will automatically get the metadata)

  • Not as slick as a native OS X app

Molecular Systems Biology - Dissection of a complex transcriptional response using genome-wide transcriptional modelling

A paper has finally been published based on some of the work I did during my PhD. Really thrilled about it and in a top journal too. Thanks go to Martino for a lot of hard work.


Modern genomics technologies generate huge data sets creating a demand for systems level, experimentally verified, analysis techniques. We examined the transcriptional response to DNA damage in a human T cell line (MOLT4) using microarrays. By measuring both mRNA accumulation and degradation over a short time course, we were able to construct a mechanistic model of the transcriptional response. The model predicted three dominant transcriptional activity profiles—an early response controlled by NFkappaB and c-Jun, a delayed response controlled by p53, and a late response related to cell cycle re-entry. The method also identified, with defined confidence limits, the transcriptional targets associated with each activity. Experimental inhibition of NFkappaB, c-Jun and p53 confirmed that target predictions were accurate. Model predictions directly explained 70% of the 200 most significantly upregulated genes in the DNA-damage response. Genome-wide transcriptional modelling (GWTM) requires no prior knowledge of either transcription factors or their targets. GWTM is an economical and effective method for identifying the main transcriptional activators in a complex response and confidently predicting their targets.

Correctly map iPhoto ‘09 Faces to contacts on Facebook

This has been doing my head in!

Correctly map iPhoto ‘09 Faces to contacts on Facebook - Derek Punsalan – 5THIRTYONE: "Correctly mapping iPhoto Faces with Facebook contacts

Apple does not make the most important detail for integration between iPhoto and Facebook easy to find. In order for Faces tagged in iPhoto to correctly link to their corresponding profile(s) on Facebook, the email address for the contact in iPhoto must match the address on file in Facebook.

If the email addresses do not match, contact tags in Facebook will not link to a profile page or notify a contact new photos have been uploaded."

FastPorts - Mac OS X user-friendly ports repository

FastPorts is a precomplied set of unix applications that are compiled from the MacPorts project. Could be pretty useful as I use MacPorts at the moment to get all the necessary unix tools but get frustrated at how long it sometimes takes to compile them.

The no-framework PHP MVC framework

This is just an interesting article I want to keep around.

DNA sequencing - Ars Technica

Ars Technica have started an interesting series on DNA sequencing. I will update this post as the new articles are published

Google Picasa 3.5 Review | Photography | Macworld

This is a Google Picasa 3.5 review. Toying with the idea of switching from iphoto once my current version gets a bit dated. I really do dislike the way that iphoto organises your photos, but apart from that I like it.

xkcd - Movie Narrative Charts

Oxfam's second-hand online shop

Who would have guessed that Oxfam has a second hand online shop. What's even better is that the delivery is free. Gotta be some bargins in there somewhere.

Universal Scrobbler

Universal Scrobbler is an app that allows you to update with tracks you have heard, but not on iTunes. Most importantly this allows you to select tracks played by BBC radio in the last 9 hours.

Grooveshark -- Listen to Free Music

Grooveshark -- Listen to Free Music

Tiny song -- Type in a song and make a free music link to share music with friends

Use X vis SSH with a su'ed user

xauth list
Copy relevant line (one with the same display number)
sudo su rbaird
xauth add relevantLine

GnuCash OSX

Finally, Gnucash (the personal accounting software that I use) has gone OS X native. Well apparently you have been able to do it for a while but it was super messy. That has really made my day - sad aren't I. I got into Gnucash when Ubuntu was my main desktop at work and have been stuck with the X11 version until now. You can download it from here and there are further deatils on the wiki page.


shootShifter 1.1.1 ... redate and rename folders of images on a Mac.

PicFog - real-time image search

This is a real time stream of images that have been posted by twitpic. Strangely fascinating.

HOWTO: Move your iTunes music while preserving library data (when you don’t let iTunes manage your music library)

This gives a good method to transfer your music to a new location and still keep it in the iTunes library. I probably will use it shortly, but why isn't this easier?

How the ipod touch can find your location

The ipod touch does an amazingly good job at finding your current location with no gps and no mobile phone masks. At home we are located to my street! These, two articles explain it ... remarkable.

Basically there is a database of WIFI access points and there locations that have been gathered by Skyhook. Basically it sounds like they periodically drive around gathering data ... mad. There are coverage maps and you can also submit the location of your own router.


Checkatrade is a really useful site to find tradesmen, with lots of reviews. Just found a decent gas fitter through them.

Bike blog: It's never too early to get in the saddle

Bike blog: It's never too early to get in the saddle | James Sturcke

Has an alternative to the wooden learner bikes

6 extraordinarily stubborn 'nail houses'

6 extraordinarily stubborn 'nail houses'

mairix - email index and search tool

mairix - email index and search tool

Could this be the way forward for searching all mail folders @ once? or is that google?

Or maybe this.

Cannabis may help the war on cancer

Some work of a friend of mine (Dr Liu) hit metro's front page a while back!

Genetic test in three years to detect prostate cancer | Science | The Guardian

This is a newspaper article on some work that some colleagues of mine have done.

Football dataset

Here are some links that might help get a good premiership football result dataset:
The Rec.Sport.Soccer Statistics Foundation.

Free Online Backup, File and Folder Sync, Share & Storage for Windows, Mac, and Linux -

This looks like an interesting alternative to dropbox.

Free Online Backup, File and Folder Sync, Share & Storage for Windows, Mac, and Linux -
"SpiderOak provides an easy, secure and consolidated free online backup, sync, sharing, access & storage solution for Windows, Mac OS X, and Linux (Ubuntu, Debian & Fedora)

* Access all your data in one de-duplicated location
* Configurable multi-platform synchronization
* Preserve all historical versions & deleted files
* Share folders instantly in web ShareRooms w / RSS
* Retrieve files from any internet-connected device
* Comprehensive 'zero-knowledge' data encryption
* 2 GBs Free / $10 per 100 GBs / Unlimited devices"

95 Old School Games You Can Play Online

Do you like the web?

Do you like old school games?

Well now you can combine them and play old school games online.

Special mentions to "spy hunter", "bubble bobble", "millipede", "gauntlet", "qbert" and "dragon's liar".

Undo Closed Window Coming in Firefox 3.5

I never knew that Ctrl+Shift+t opened the last tab you closed in firefox. So I've learnt something useful for the day. Whoop!

More praise for Dan!

Cancer treatments get personal - 15 April 2009 - New Scientist: "The rapid pace of change has left many feeling ill-equipped to deal with the vast quantity of data they are now faced with. 'I only survive in this area because I have a right-hand man who has a PhD in maths,' says Cooper."

That would be me then!

Segway Puma

Is this the fuuuuuuutttttttuuuuurrrrrrrrr

Apparently it can go up to 35mph.

How to ship big stuff around the UK | BitterWallet

How to ship big stuff around the UK | BitterWallet

Baby chicks do basic arithmetic

Smarter than the average chick

Sweet Home 3D

This looks like a useful open-source app to design rooms. I've got a bedroom + partition wall and kitchen in mind.

Persepolis on freeview

"Persepolis Premiere

Saturday 11 April
11:00pm - 12:50am
Channel 4

Animated feature based on Marjane Satrapi's graphic novel about her life in Iran, before and after the country's revolution in 1979, and Europe. After being sent to Vienna by her parents to study, she discovers politics, drugs and sex, but also a feeling of dislocation caused by the attitudes of those around her. She returns to her homeland to find that much has changed, but not for the better." Shares Your Email on the Internet, Protects It from Spambots

This looks like a good way to protect your email address in the big dark den of the world wide web.


"Sequential is an image viewer for Mac OS X. It was originally designed for opening a folder of images and displaying them in order. It works well for viewing comics and manga.

Sequential can display folders and archives (ZIP, RAR, CBZ and CBR) of images (including JPEG, PNG, and GIF) and PDF files. It is able to load images on the internet from a page or image URL.

Sequential has mature full screen support and can display images' Exif data."

BBC Two to show US TV's The Wire

Wow! I've been waiting for this to come onto freeview ever since Charlie Brooker started going on about it. Let's just hope that it's as good as everyone says.

===EDIT 29/03/09===
In actually fact it starts tomorrow (Monday 30th March) on BBC2. It's on everynight!

Danny Fingeroth's top 10 graphic novels

Danny Fingeroth's top 10 graphic novels | Books |


This looks like a useful program to easily convert files from the Toppy (PVR) to DVDs.

Personal Inflation Calculator

Personal Inflation Calculator

SSH Bouncing

This is an interesting article about how to get to a computer behind your NAT via SSH without using port forwarding.

Free Map Tools

Free Map Tools

Brilliant website that provides, as the name says, free map tools. I particularly like the "Free WiFi points map" and "Measure Distance".

GCC To Receive Automatic Parallelization Support

[Phoronix] GCC To Receive Automatic Parallelization Support

Wow something that might help normal programs use all the cores we've got these days.

Films on Freeview

An interesting site that allows you to rank the next week's films on freeview by IMDB score and filter on genre, date etc.. There are also plenty of different views of the data. Bon!

-- Edit -- A similar one

Incredible JavaScript Canvas 3D demos from Japan! Tech Blog: Incredible JavaScript Canvas 3D demos from Japan!

This is a blog post about some amazing demos of 3D web stuff using just canvas and javascript - no flash etc. here.

Here are the demos.

On a similar note, you can now play quake from within the browser. No installation of anything necessary, well apart from flash.

Web technologies seem to be coming in leaps and bounds.


tsocks - Transparent SOCKS Proxying Library

At work they have just installed a new web filtering system and it seems to be destroying half my life: ical/webdav doesn't work, Firefox maximises when it downloads a file, tasque (my task manager) does not download all my tasks from rememberthemilk.

One particular problem is that I can't reliably use R to download gene annotation data from ensembl using the biomaRt library. I thought I might try and use ssh with a SOCKS proxy to isolate the problem but couldn't work out how to make R uses the SOCKS proxy. tsocks is a wrapper program that intercepts any network requests from the child program and passes to the SOCKS proxy.

I'm having trouble getting it to work with R at the moment, but its a good idea anyhow.

Guardian Football Chalkboards

Chalkboards | Football |

The Guardian have just recently put up a football chalkboards flash webapp. You can pick any match and look at how any player or the whole team did certain things like shot, pass, tackle etc.. Its also quite nice how you can set the time in the match to look at. Very interesting and definitely worth a look.

Bring On The Trumpets

Matt Berry we love you

CryoPID - A Process Freezer for Linux

CryoPID - A Process Freezer for Linux

This looks like a nifty utility. Basically, it allows one to save the state of a process (program) to file and then resume it. So you can for example restart the computer without having to run the program again. I can see this being very useful for some of the analysis that I do that takes a long time.


This is a plugin for XBMC (the media centre application on my modded xbox) which should allow access to BBC iplayer. As the xbox is attached to the TV we can missed BBC stuff on the nice screen.

Looks easy enough to install, I will try and have a go this weekend.

MP3s = Communism


Software so A can smash the keyboard and get a response

Here is some software designed to entertain babies when they try to destroy your laptop/computer:

OS X: AlphaBaby
Windows: baby smash

How to Keep Fruits and Veggies Fresh

A useful table on what fruit and veg to store where.