Tryangled Solutions web designing tips tricks

Think back to the library card catalogue analogy.  In the old card files, and even in today’s computer terminal library catalogues, you find information by searching on either the author, the title, or the subject.  You usually choose the subject option when you want to cover a broad range of information.

Example:  You’d like to create your own home page on the Web, but you don’t know how to write HTML, you’ve never created a graphic file, and you’re not sure how you’d post a page on the Web even if you knew how to write one.   In short, you need a lot of information on a rather broad topic–Web publishing.

Your best bet is not a search engine, but a Web directory like the Open Directory Project,  Google Directory or  Yahoo.  A directory is a subject-tree style catalogue that organizes the Web into major topics, including Arts, Business and Economy, Computers and Internet, Education, Entertainment, Government, Health, News, Recreation, Reference, Regional, Science, Social Science, Society and Culture.  Under each of these topics is a list of subtopics, and under each of those is another list, and another, and so on, moving from the more general to the more specific.

Example: To find out about Web page publishing from Yahoo, select the Computers and Internet Topic, under which you find a subtopic on the Wide World Web. Click on that and you find another list of subtopics, several of which are pertinent to your search: Web Page Authoring, CGI Scripting, Java, HTML, Page Design, Tutorials.  Selecting any of these subtopics eventually takes you to Web pages that have been posted precisely for the purpose of giving you the information you need.

If you are clear about the topic of your query, start with a Web directory rather than a search engine.  Directories probably won’t give you anywhere near as many references as a search engine will, but they are more likely to be on topic.

Web directories usually come equipped with their own keyword search engines that allow you to search through their indices for the information you need.

Important note:  Search engines and  Web directories are being integrated in interesting ways.    For example, if you use the Google search engine and one of the results happens to be found in the Google’s Directory (which is based on the dmoz directory), Google will offer you a link to that section of the directory. Meanwhile, if you conduct your search in the Google directory, Google will order the results according to PageRank, which is   Google’s all-important measure of  “link popularity.”

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?