Torrential Web Dev

My 'day job' has nothing to do with PHP. It has nothing to do with any form of programming. I graduated in 2006 with a degree in Biochemistry and went on to do a MSc and now PhD in cardiovascular biology. The closest most of my colleagues come to programming is a formula in an Excel spreadsheet.

It was actually Excel which prompted this post. Yesterday I was analysing some data and bemoaning the poor search functionality that Excel makes available. I had already expanded the small set of experimental data I had with some values pulled from a web service using a quickly hacked together PHP script and it got me to wondering how much better things could be if I just stuck with PHP.

Where's the science?

This train of thought led on to whether PHP has been used all that often for scientific projects. There is an accelerating trend in Biology to make data and tools available via web interfaces. In my opinion this is an environment where PHP excels and yet all the literature I've seen discussing the development of these services uses Perl or occasionally Java.

Searching a little harder for PHP projects yields an equally depressing outlook. In PEAR Jesus Castagnetto released the Science_Chemistry and Math_Stats packages back in 2003. For my purposes though the Chemistry package is a little too 'chemical' and the stats package is a little too basic. In sourceforge there is a package named BioPHP which looks promising but again there has been no activity since 2003. A lot has happened since then.

Biology is increasingly data generative. There is going to be a steadily increasing need for tools to analyse all this data. These are likely to be centralised and made available via web interfaces.

Anyone out there?

I suspect I'm going to be increasingly creating automated solutions to remove some of the repetition involved in processing the, relatively, small amounts of data that I generate. A PHP toolkit able to leverage the latest online databases and perform 'advanced' statistics would be immensely valuable.

So my question is this. Is anyone out there using PHP in a scientific environment? Are there resources available which I've missed?

The web service for fetching contacts from MSN messenger / Windows Live Messenger has been hit by a series of problems over the past few days. First I hit the bandwidth limit for the account used to host the service. Next, the server used was hit by a DDoS attack. Finally after all that was sorted out the bandwidth limit again caused problems.

Hopefully everything should now be back to normal and the service will be stable.

As always, if you do have any problems, my contact details are available under the 'About' tab at the top of the page.

I have a love hate relationship with geo-targeting. The web wasn't designed with making it easy to get the geographical location of connected computers in mind. A users geographical location is interesting and potentially valuable though and so methods have been developed to make it (almost) possible.

These methods typically involve something akin to a brute force attack. Figure out where enough IP addresses have been assigned and you can get a good idea of where a user is from their IP address. Other methods involve identifying the computers through which they are communicating with you and assuming the user is in the surrounding geographical area. Neither method is perfect but in the majority of cases you can know which country a user is in with reasonable accuracy.

What I hate about geo-targeting is how some sites think they can locate you more accurately than the country you are in. Maxmind, which is probably the commercial leader, thinks it can guess your location to your nearest city with an accuracy of 81% in the US. Outside of the US I suspect this drops considerably. I'm seeing fewer sites than I once did trying to tell me where I'm connecting to the internet from (and getting it wrong) so I'll skip forward to what I love about geo-targeting.

Continue reading "Geotargeting in forms"

Over a full month after the fact I present my summary of the BarcampScotland2008 event.

The event was split over two days. It kicked off on the Friday evening (1st Feb) in the main room of Alison House at the School of Architecture. It was just the one room with a decent communal feeling. I think most people were holding back with their presentations for the following day. Despite this two presentations did take place. James Littlejohn made the first presentation after the welcome session and talked about data portability.



It was a good summary of the current situation. I also happen to agree with most of his positions. He has taken the decision of making his homepage the hub of his social network. Although I think he has perhaps taken things a little too far my main criticism is the implementation. Looking at the site it took me about 20 seconds to figure out that aboyne is where he is based and not his surname. I couldn't find his surname anywhere on his homepage. After navigating around for a while I found it in the byline for his blog. It wasn't an easy process. I highly doubt that data was machine readable despite the importance he attached to this during his talk.

Ewan Spence was next up with an improvised talk he largely made up on the spot. This rapidly migrated to a conversation with some interesting points raised.

Following on from this Dave McClure set a small competition going. A excessive number of random words were gathered from the audience which then broke up into 5 groups to brainstorm company ideas around any pair of words. Somehow the team I was in won with sexydyslexia.com, a couple that takes standard prose and converts it into netspeak and vice-versa. I notice that the domain name is still available so although rated as the best apparently no one in the audience wanted to run with it.

All the details on the second day after the jump . . .

Continue reading "BarCampScotland2008 Roundup"