iOS apps for Science

I was going to list interesting iPhone/iPad apps months ago, but there is already an excellent list available here and I see no point in reinventing the wheel.

If you fancy hunting through the App Store, which isn't that great a search you'll generally find science apps under Books, Education, Reference or Utilities.

Now I have slightly more free time I might have a dabble with the iOS SDK.

Blog spring clean

Admittedly this is late for a spring clean, but Blogger has introduced a host of updates since I last looked. One being this nifty new template.

Also, something I've wanted to try out is a decent syntax highlighter and this one looks good. See http://alexgorbatchev.com/SyntaxHighlighter/. The instructions I followed for Blogger can be found here.

So now I can easily publish code like this:

<html>
  <head>
    <title>Tutorial: HelloWorld</title>
  </head>
  <body>
    <h1>HelloWorld Tutorial</h1>
  </body>
</html>

(You have escape angular brackets)

print "Hello, World!"

// Outputs "Hello, world!" and then exits
public class HelloWorld {
   public static void main(String[] args) {
       System.out.println("Hello world!");
   }
}

Don't use the Blogger WYSIWYG editor for this, switch to HTML else it will get very confused. I have used the pre method over script. I imagine if you switch templates this may break, but a quick copy and paste should bring the functionality back.

Fingers crossed it comes out ok through RSS readers as well!

New content... part II

I've finally submitted my PhD thesis! Therefore, I now have spare time, it might take a while to get used to. I've neglected this blog because of writing up but will start to post new content soon.

Eclipse Galileo

Eclipse continues it's annual eclipse release, this year with Galileo. Available to download from here.

33 projects have released new updates, so something for everyone. Of particular note for Mac users, is the option for Cocoa, the successor to the Carbon API. (Pick when you download).

I've tried a handful of plugins and they all seem to work fine:

• Subclipse
• CDT (new release)
• PyDev
• Aptana Studio

You can find numerous reviews on the eclipse website.

Eclipse with Django

Django is popular web framework written in Python. For Python users it is an obvious choice to deploy web applications. Once again I return to my favourite IDE to develop with Django - Eclipse.

Two plugins are needed to bring Django support to Eclipse. The second handles the Django template language. Grab the plugins:

1. PyDev (Python)
2. Aptana Studio (Python + Django)

Both plugins are from Aptana, PyDev is a plugin to their IDE. Thankfully, both work through Eclipse as well.

Eclipse with C++/OEChem

The final post in this series, allowing you to develop your OpenEye applications using Eclipse.

First off you will need to ensure the CDT plugin is installed, or download Eclipse for C++ developers.

Now we are set to go. Create a new C++ Project (Executable > Hello World). Edit/Add C++ files to the source folder. Next we need to inform the project about OpenEye.

• Open your project properties (Project > Properties).
• Pick C/C++ Build > Settings
• Edit [ All Configurations ] (by default Debug and Release)
• Set include paths (-I) under GCC C++ Compiler > Directories > Include paths
• Add $OE_DIR/toolkits/include
• Set library paths (-L) under GCC C++ Linker > Libraries > Library search path
• Add $OE_DIR/toolkits/lib
• Set specific libraries (-l) under GCC C++ Linker > Libraries > Libraries
• Add oeplatform, oesystem, oechem, m, z, pthread
• You can set further Makefile details from this panel (optimisation etc)

If you have multiple versions of the toolkit you can create a configuration for each one.

Between C++/Java/Python you should be able to code away happily within Eclipse.

Eclipse with Java/OEChem

Following up from a previous post, here I present the settings required to get Eclipse running with the OEChem Java wrapper.

Make sure you have Eclipse and and working OpenEye installation setup and running first.

1. Create a regular Java Project
2. Configure your build path to add:
3. a) Under sources add a linked source $OE_DIR/java/libs
4. b) Under libraries add external jars, $OE_DIR/java/*.jar (add them all)
5. Run your OEChem program, if you get license errors edit the run configuration; under environment add OE_LICENSE, with $OE_DIR/etc/oe_license.txt; OE_HOME with $OE_DIR and OEJAVA with $OE_DIR/java

Obviously substitute $OE_DIR with your actual absolute file path.

Now Eclipse's CDT can be used to use the C++ toolkit direct, so I'll post that - once I've started to use it!