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C is the canonical procedural programming language and the greatest pitfall for a programmer looking to show off his database-fu is that he fails to realize that SQL is not procedural (nor is it functional or object-oriented, for that matter). Rather than thinking in terms of data and operations on data one must think of sets of data and relationships among those sets. This usually crops up with the improper use of a subquery:
SELECT a.id,
(SELECT MAX(created)
FROM posts
WHERE author_id = a.id)
AS latest_post
FROM authors a

Since this subquery is correlated, i.e., references a table in the outer query, one should convert the subquery to a join.
SELECT a.id, MAX(p.created) AS latest_post
FROM authors a
INNER JOIN posts p
ON (a.id = p.author_id)
GROUP BY a.id

Although the names are much alike, JavaScript is primarily a scripting language for use within HTML pages, while Java is a real programming language that does quite different things from JavaScript. In addition Java is much harder to learn. It was developed by Sun for use in pretty much anything that needs some computing power.

JavaScript was developed by Brendan Eich, then working at Netscape, as a client side scripting language (even though there’s no fundamental reason why it can’t be used in a server side environment).

Originally the language was called Live Script, but when it was about to be released Java had become immensely popular (and slightly hypey). At the last possible moment Netscape changed the name of its scripting language to “JavaScript”. This was done purely for marketing reasons. Worse, Eich was ordered to “make it look like Java”. This has given rise to the idea that JavaScript is a “dumbed-down” version of Java. Unfortunately there’s not the slightest shred of truth in this story.

Java and JavaScript both descend from C and C++, but the languages (or rather, their ancestors) have gone in quite different directions. You can see them as distantly related cousins. Both are object oriented (though this is less important in JavaScript than in many other languages) and they share some syntax, but the differences are more important than the similarities.

If you are a C++ or Java programmer you will be surprised by some of JavaScript’s features. Since I don’t have any previous programming experience, the differences are not described on this site. The best you can do is buy David Flanagan, “JavaScript, the Definitive Guide”, 5th edition, O’Reilly, 2006. In this book the differences between C++/Java and JavaScript are clearly explained. I co–edited a few chapters of this book.

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?

Compositional programming style
In the object oriented programming style, it’s preferable to split functionality out to multiple objects, that can work together to solve a single task. Taken to the extreme, this results in more, but smaller, classes and generally relies less on inheritance and more on composition. In lack of better words, I’ll call this compositional programming style. It’s a style which is usually more prevalent with experienced programmers.

For someone coming from an imperative style of programming, this style can appear abstract and confusing, but the benefits are in the flexibility of the code. If different objects are related through composition, parts can be replaced, without changing the code. This makes it easier to reuse components, and to hook into the code, by providing a wrapper here or there. This is especially useful during testing, since it becomes easier to mock out external dependencies (Such as a database or an smtp server).

There is, however, a dark side to composition — dependencies.

So what is a dependency?
For the sake of this post, I’ll use a rather naïve example. Assume, that we were building an addressbook application. This would feature an entity of type Person. In our code, we might have a class …

When it comes to web programming languages, PHP probably holds the record for copping criticism from the community at large. Comparisons with alternatives such as Ruby on Rails and Python/Django are common; defenders of PHP are quick to criticise the comparison of a language and a framework. But at the end of the day, developers work with Ruby on Rails, and with Python/Django, and with PHP. Just PHP. For most of the PHP applications out there, the language is just perfect, because PHP, to an extent, is the framework.

PHP is designed for the web. You could plug vanilla Ruby or Python into a web server and get up and running pretty quickly. But, at least at a basic level, you’d want a framework to deal with common issues of web development. In PHP, you just get started. PHP and Apache work out request data, output handling and more, right out of the box. (PHP also masters deployment.) David Heinemeier Hanson, the creator of the Ruby on Rails framework, calls this the immediacy of PHP.

Now, consider the “average” PHP frameworks. They help you handle request data, manage your output, control app flow - essentially, extending …

PHP Programming has become one of the trends today. To learn more about it, you can first start through the internet. Although you may also try books however internet provides more comprehensive information. Think what topics about PHP are you most interested about. You can visit and join forums discussing PHP programming. You can even ask questions in the forums. Friends who are into the field of programming might help.

If you want to know more about PHP Programming, it should not be limited to that there are also other areas that you need to learn about like JavaScript, HTML and CSS. It is helpful to always have knowledge on the latest trends and innovations regarding PHP Programming.