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Dr Pan Pantziarka

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Dr Pan Pantziarka is a computer scientist, mathematical modeller and author, currently working with a diverse group of academics, oncologists and patient advocates in drug repurposing for oncology (publications in the works). He has previously published on Li Fraumeni Syndrome and is founder of the UK's only charity devoted to this rare genetic cancer pre-disposition condition – www.tp53.co.uk. He also blogs at www.anticancer.org.uk.
An obese belly, dangling freely. Pic: Tony Alter

Lies, damn pies and obesity statistics: We're NOT a nation of fatties

The messaging cannot be any clearer. We, like much of the developed world, are in the midst of an obesity crisis caused in large part by eating too much. Our super-size culture of fast food, sugary drinks and junk diets is turning us into a nation of over-sized and unhealthy slobs with expanding waist lines and it’s getting …
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Cutting cancer rates: Data, models and a happy ending?

In theory, the definitive treatment for early stage cancer patients should be surgical resection. Just get in there and cut the tumour out. If the lump is small and well-constrained, then surgical removal is all that should be needed. Unfortunately, this isn’t usually what happens. Even when the tumour is nice and small and …

Organic food: Pricey, not particularly healthy, won't save you from cancer

One of the primary drivers of the growth in organic food sales over the last couple of decades is the perception that organic food is healthier than conventionally farmed food. It stands to reason, doesn’t it? After all conventional crops depend on chemicals and organic food doesn't. And we all know that chemicals, in this case …
PHP

NetBeans extension makes simple work of PHP

Arriving with the NetBeans 6.1 release last week was the NetBeans IDE Early Access for PHP. This provides a complete PHP integrated development environment hosted in NetBeans, re-using the infrastructure NetBeans has already employed for Java and Ruby. Having walked through the main NetBeans IDE, I thought it worth looking …
Sun

NetBeans 6.1 packs welcome additions

Hot on the heels of a successful 6.0 release, which we covered here and here, Sun Microsystems has delivered NetBeans 6.1, just in time for the company's annual JavaOne and CommunityOne events in San Francisco, California. As you'd expect from an incremental release, the aim is to introduce enhancements and bug fixes rather than …
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Pump some IronPython with Studio IDE

When I looked at IronPython in part one, I focussed on how it marries the Python language and libraries with Microsoft's .NET framework. The sample code that was developed used the Python console (ipy) and a text editor - in other words with simple text-based tools for writing short scripts. But for bigger projects, or when …
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Quick scripting for .NET with IronPython

While Ruby and Groovy seem to get all of the attention, there's one scripting language that has been around for a lot longer and that has quietly been picking up in popularity over the long run. That language is Python, and, according to the TIOBE Programming Community Index Python was the language of the year for 2007. While …
Ruby on Rails teaser

Ruby runs on Rails with NetBeans

Having limped along in the wake of Eclipse, Sun Microsystems' NetBeans is getting its second wind. One thing that's helping is a fresh focus on scripting, particularly around Ruby on Rails. In this piece, I shall show how well Ruby on Rails has been integrated into NetBeans using the creation of a very simple application as an …
Ruby on Rails teaser

Polished NetBeans means Ruby

Let's be honest, the rise of the Eclipse development platform is the best thing to ever happen to Sun Microsystems' NetBeans integrated development environment (IDE). Eclipse rolled out a solid platform, with good performance, high levels of extensibility and a rapidly expanding ecosystem of commercial and open source plug ins. …
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Light reading for XML with Groovy

Groovy, unlike Java, provides a relatively streamlined way to read and write XML documents. In the first part of my two-piece tutorial, I looked at how you can use Groovy's flexible strings, closures and iterators to quickly create XML fragments and files. The emphasis was on making the most of Groovy as a scripting language …

Groovy: XML without the bloat

You may find this hard to believe, but there was a time before XML hell, when the idea was that XML was going to solve just about every tricky problem in software development. From swapping data between applications or platforms, to storing complex data structures in a portable format - XML was the answer. Growing up around the …
MySQL

Get into data with Groovy

In the first part of this two-part series we looked at how Groovy provides a simple and intuitive approach to accessing MySQL. Compared to Java, Groovy is less verbose and more focused on what the developer wants to do with the database. Additionally, things like opening and closing database connections, writing boilerplate …
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Learning Ruby

To some, Ruby is going to take over the world. With prominent Java developers and propagandists jumping ship, there has seemed to be no stopping its momentum, particularly in web development. Part of the reason for the popularity with hackers (in the programming sense of the word), is that it's easy for a programmer in an …
MySQL

Groovy way to MySQL

A very traditional niche of scripting languages, (such as Perl, Python or Ruby), has been in the ad hoc manipulation of databases – from grabbing data, transforming it, performing bulk updates, right on through to full-on data migration projects that move data from one platform or RDBMS to another. Scripting languages are …
Google

Getting Google’s Web Toolkit going

Developers looking to build Ajax-style rich internet applications (RIA) are pretty much spoilt for choice at the moment. There are dozens of RIA tools and frameworks littering the development landscape, from those providing minimal sets of JavaScript libraries to heavyweight contenders such as Adobe’s Flex, Microsoft’s …
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Continuous Integration: Improving Software Quality and Reducing Risk

Like unit testing and automated builds, continuous integration is one of those development best practices that everyone can agree on, from the most extreme programmers to the most dogmatic of RUPistas. System integration – the moment when all of the different components of an application come together to produce a harmonious and …
beautiful code

Shall I compare thee (code) to a summer's day?

Beautiful code? Well, we've all seen plenty of ugly code in our time. If we're being honest, we'd probably even admit to have written some dog-ugly code at one time or other (no doubt with every intention to refactor it later so that it's a bit less brutally repulsive). But code that's beautiful? What does that even mean? Code …
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Introducing Microsoft LINQ

Microsoft's Language Integrated Query (also known as LINQ), is one of the key features on the .NET horizon. Already out as a beta, it's slated for release as part of Visual Studio 2008 (which goes under the code name of Orcas, which conjures images of packs of killer whales rather than shrink-wrapped development software). …
Smart and gets things done

'Smart and gets things done'

Smart and gets things done is a pretty apt description of the kind of people we want to recruit into our development teams. Unfortunately, this is no easy matter. And, given the consequences of a wrong choice for either party, it can often be a pretty hit and miss affair. Joel Spolsky, of VBA and Joel On Software fame, has put …
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Programming Flex 2

The move towards rich internet applications (RIA) seems to be unstoppable. Aiming to offer browser-based applications with the speed, flexibility and functionality of traditional desktop applications, companies like Google and others continue to raise the bar as to what you can do in a browser. One of the key technologies in …
JBoss Seam

Ironing down the JBoss Seam

We might as well get this over and done at the outset. Yes, JBoss Seam is another Java framework. I know, you thought there couldn't possibly be any room for another one, but you're wrong. What's more, it's another Java EE framework, built to make life for the enterprise developer more productive, more efficient, more …
Linux Programmers Toolbox

The Linux programmer's toolbox

Linux, like the other *nix platforms, has a reputation of being a good environment for developers. In fact, Linux and hacking – in the original sense of the word – seem to go hand in hand, so much so that some commentators still find it hard to conceive of it as anything but a server and/or development platform. Whether the …
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Compelling Linux server slithers into the open

The Linksys NSLU2 is a cheap and compact Network Attached Storage (NAS) device with an Ethernet connection and two USB ports for connecting hard drives and/or USB flash disks to a LAN. It sports a simple web-based interface that is used to configure the device, format any attached disks, set up disk shares and so on. It's a …
Java

Making Java Groovy

It is increasingly important to differentiate between Java the programming language and Java the platform. While there have long been other languages that have targeted the platform, the best known being Jython – a version of the Python language that compiled down to Java byte code to be executed by the Java Virtual Machine ( …
Programming in Haskell

Programming in Haskell

While it may appear that object oriented programming has achieved dominance in terms of programming language paradigms, there still exist outposts that refuse to submit to the benefits of polymorphism, encapsulation, and object inheritance. It's not just that there is a hard-core group sticking to procedural coding in C and …
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Process improvement essentials

Process improvement, in the guise of the ‘big three’ frameworks of ISO 9001, CMMI and Six Sigma on the face of it would seem to have much in common and all aim to produce the same end result – improved quality through established and proven processes. With compliance to one or other of these frameworks increasingly being sought …
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Use case driven object modelling with UML: Theory and practice

While the methodology wars continue to flourish, and advocates of this process versus that process slug it out to show that they alone are following the one true path, there is one technique that all seem to agree on: the use case. While extreme programmers prefer the term user story, (and still others talk about storyboards), …
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VSTO For Mere Mortals

In addition to the legions of professional Visual Basic programmers, there are still more developers who use VBA and Microsoft Office for automation, customisation or the development of tailored office applications. Many of these are super-users rather full-time developers, but they have depended on VBA to extend and expand what …
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The Ruby Way

It is, perhaps, inevitable that the first code you write in a new programming looks suspiciously like code from the language you already know. I can remember my own first Java applications looking suspiciously procedural and C-like. In making those first moves into object orientation, it takes a while before it all makes sense. …
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The Java Phrasebook

Elliote Rusty Harold, acclaimed Java and XML author, recently described Java as the lingua franca of the programming world. According to Harold he can write basic Java and have it understood by non-Java programmers more often than not. It’s the language of choice for computer science education and is so ubiquitous in …
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Acquiring Code Craft

Books on programming language x, technology y, and methodology z are 10 a penny. Bookshop shelves groan under the weight of books promising to teach programming x, y or z in 21 days, 7 days, 24 hours, 10 minutes, 30 seconds... Developers are not exempt from the lure of instant wisdom and there are plenty of publishers and …
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Linux Live CDs

I can still remember the wow factor when first seeing a copy of Knoppix booting up on a Windows machine. It was many moons again and the idea of a bootable Linux CD seemed strangely miraculous. Assuming you had a BIOS that could boot from a CD, (pretty much a standard now but not so common a few years ago), Knoppix would …
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Mastering Regular Expressions

Like SQL and XML, regular expressions are an essential tool in every developers’ toolbox. Processing text, which is pretty much what most programs do when you think about it, is so central a concern that even without regular expressions most developers quickly build up a library of functions and idioms for text matching, …
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Escape from Access DB

Do you like Microsoft Access? Well, thanks to an intuitive and powerful user interface and being bundled as part of Office, it has established a niche for itself in many organisations, sometimes unofficially. The combination of recordable macros, wizard-generated reports, query-by-example and, crucially, the provision of …
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Agile Software Development

Alistair Cockburn is one of the most prominent and influential of the Agile development gurus. As well as being one of the original authors of the Agile Manifesto, he is also the developer of the Crystal family of agile methodologies and a pivotal figure in the evolution of the Use Case. He is also an articulate and passionate …
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Beginning Hibernate

Although it sounds like something to do with electrical resistance in AC circuits, "impedance mismatch" describes the issues that arise when dealing with the different conceptual bases of object oriented development and relational databases. Developers model their domain with classes and objects, but when it comes to persisting …
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Ajax Hacks

Everybody loves Ajax. Javaists, Rubyists, Pythonistas; even Microsofties get to play with Ajax in the form of Atlas. Book publishers love Ajax too, judging by the stack of new titles coming hot off the presses. O'Reilly has added to the pile with a new title in their long-running "Hacks" series. The aim of the series is to …
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Java databasing with Derby

It sometimes feels as if open source databases are a dime a dozen. There are the big names like MySQL, PostgreSQL, and Ingres. There are plenty of other lesser known but no less powerful open source databases: Firebird, SQLite, HSQLDB, Apache Derby, IBM Cloudscape, and Java DB. Actually, I cheated there at the end, those last …
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Off the Rails?

Billed as a possible Java-killer, the huge amount of interest in the Ruby programming language is in no small part due to the popularity of the Ruby On Rails framework. An application framework that implements the Model View Controller architecture, Ruby On Rails enables the creation of data-driven web applications with minimal …
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Practices of an Agile Developer

If nothing else, the Agile development movement has hit on a good brand. Agile has so many positive connotations – fast, graceful, dynamic. Come on, who doesn’t want to be Agile? Besides, the alternatives don’t have a handy label to grab on to. Formal methodologies? The Unified Process? Arthritic programming… Nope, Agile wins …
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The No Fluff Just Stuff 2006 Anthology

The No Fluff Just Stuff (NFJS) symposia have achieved a reputation for providing the geekiest content to its developer audiences. Primarily focused on Java and open source technologies, the symposia major on delivering sessions devoted to leading edge technologies presented by the leading practitioners. Audiences are …
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Building websites with PHP-Nuke

Building a configurable, flexible and highly interactive community web site from scratch is no mean feat. Get the technical implementation right and you might have a vibrant and active community coalesce around your site. Get it wrong and you’re left with dead web real-estate that’s dressed right but is going nowhere. However, …
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Get yourself up to speed with UML 2.0

The Unified Modelling Language (UML) has firmly established itself as the lingua franca of the object oriented development world. It offers the right levels of abstraction, independence from programming language implementation to make it pretty much ubiquitous. Use cases and class diagrams have entered the vernacular, even …
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Java 6 Platform Revealed

It seems it was only yesterday that the Tiger was escaping into the wild, and here we are today with Mustang rearing up ahead, and the Dolphin already surfacing here and there. Javaists will recognise Tiger, Mustang and Dolphin as Java 5.0, 6.0 and 7.0 respectively, and everyone else can now stop scratching their heads and …
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Micro-ISV: From vision to reality

Every developer working for an employer dreams, at one time or another, about striking out alone. Whether it's a dream of starting up the next Microsoft, or simply the chance to create the perfect widget, it's a common enough fantasy for those working for someone else. And, like all such dreams, there are a few souls brave …
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Anti-Hacker’s Toolkit

Sometimes it just pays to think bad thoughts. And, sometimes, it might even be a good idea to act on those bad thoughts. No, that doesn't mean you go out and shoot your boss. It does mean thinking bad thoughts about security. It means thinking like a hacker (no, not that sort of hacker, the sort that attacks your software/server …
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Code Quality

With his first book, Code Reading, Diomidis Spinellis broke new ground. Here was a major book on the oft-neglected but important skill of reading source code. Given that software maintenance is a huge and ever-growing burden that all developers have to endure, it is surprising that the major emphasis in education and in the …
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Finding bugs with FindBugs

A good compiler does more than simply refuse to compile syntactically incorrect code. Most modern compilers can issue warnings about many different types of potential problem, from reporting on the use of deprecated libraries and packages, to sounding alarm bells about uninitialised variables, or ignoring return values from …
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The state of POJO play

Few could deny that one of the biggest drivers of change in the Java world recently has been the complexity of "enterprise Java". The complexities of EJB 2.x, with forests of XML configuration files, boiler plate script, the slow edit-compile-debug cycle forced by having to deploy to a server, the reliance on procedural code …
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A Java - .NET 'welding' course

Like it or not, (and there are plenty of zealots who don't), the Java and .NET worlds have to learn to live with one another nicely. In practice this means that applications have to be able to cross platform boundaries easily - no more hiding behind proprietary interfaces, no more trying to own the entire software stack, and no …