I created a project website for my newly released Android app cmBot at SourceForge.
It will be filled with more content in the next weeks.

This is the address: http://code.google.com/p/cmbot/

Last summer I bought my first smartphone. It runs Google’s Linux-based operating system Android. When a professor told me that mobile computing didn’t have anything to do with bioinformatics, I asked myself “… or does it?”. Since then I wanted to apply mobile computing to topics from computational molecular biology. Today I introduce my first shot at doing so.

I proudly announce the release of a PDB app for Android smartphones!
It is called cmBot (computational molecular biology roBot) and is freely available for download here.

The app consumes the PDB API. This means it looks up PDB ID’s and then parses the XML file the database returns in response. Finally, cmBot displays a nice overview of the file’s major facts - including a graphic visualization of the protein.

Who needs the app?

Not only computational molecular biologists or bioinformaticians like me use the Protein Data Bank PDB. But also biologists, chemists, pharmacists, and all those who are somewhere in between. If you are interested in a particular protein and your PC or laptop is not available, you may want to look up the basic information on your mobile phone. cmBot makes this possible in no time at all!

How to use the app?

When you start the app, your phone displays a search field with the default text “Enter PDB ID…”.
It’s not that difficult, you see…

After entering the PDB identifier of your protein, which may be something like 2KTG for example, you submit it. Now the app connects to the PDB and retrieves the corresponding data, if the identifier exists.
The app then prompts a structure image and a data sheet containing the following textual information:

• Structure ID
• Title
• PubMed ID
• Keywords
• Number of entities
• Number of residues
• Number of atoms
• Published on
• Released on
• Authors
• Status

“Structure ID” and “PubMed ID” are displayed as links so the corresponding PDB and PubMed sites are just one click away.

How to get cmBot?

cmBot is not (yet) available from the Android app store, but you can install it following the instructions given below. There’s only one prerequisite: You need a smartphone running Android 2.2 or higher.

1. Download the archive from http://bioinformatik.o-dyn.de/cmbot/cmBot.apk to the SD card of your smartphone.
2. Install it using one of the popular app installer apps (e.g. Easy Installer).

What does it look like?

What’s in the future?

This is just the first release of my app. I am going to improve it in the coming weeks and months. I’m planning on integrating more functionality, including better integration with other databases, and a molecule viewer (actually I’ve already written a bunch of code for this).
And finally there will be a website dedicated to this project exclusively.

Your feedback is greatly appreciated, so I can improve my app’s usability, too.