Is PHP good enough for science?
Tuesday, July 15th, 2008My ‘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?