A mobile interface to the Registry of Standard Biological Parts

Recently I developed a simple mobile interface to the Registry of Standard Biological Parts – the database that is currently the focal point for parts-based synthetic biology. I’ve called this mobile interface mPartsRegistry and I thought it would be worth outlining it’s features and sharing some notes about the project, in case someone else finds it useful.

mPartsRegistry is a simple interface to the Registry of Standard Biological Parts aimed at mobile smartphone browsers. It’s powered by the Parts Registry API, which provides a simple RESTful interface to key metadata about parts in the database. It features:

  • A simple interface tailored for mobile WebKit browsers (Android browser, mobile Safari, probably others). Web-based, zero-installation required.
  • Basic search of the Registry by part name.
  • “Favorite parts” to locally bookmark parts on your device.
  • Provides basic metadata associated with parts, including size, description, authors, DNA sequence, categories and availability.
  • Freely available and recyclable source code, released under the MIT License (fork it on GitHub).

The idea for a mobile interface to the Registry came out of a moment in the wet lab, where I was supervising the Monash iGEM team, and someone asked “How many basepairs is that part again ?”. I’ve found most ideas for smartphone apps in the lab a little contrived; nothing more than an excuse to jump on the Android or iOS app bandwagon, with limited practical utility. This was a situation where I could genuinely see a use for a simple mobile interface to look up some reference information, so I thought I’d create it.

The goal is not to completely replicate the functionality of the Registry (at this stage the API would not allow that anyhow), but to provide simple mobile-friendly interface to quickly look up important data about a Biobrick(tm) parts in a laboratory setting, where accessing a desktop computer is often less convenient. In this context, you generally know the part name (eg B0034) that is written on a tube, but would like to quickly lookup some details.

The project consists of two main parts: the web frontend, build using jQTouch and Django templates hosted on Google App Engine, and the parser backend (partsregistry.py) that deals with directly querying the Registry API.

The application uses BeautifulSoup on the server side to parse the XML served by the Registry’s API. This parser may be useful as a generic Python interface to the Registry API for other projects, although it is not yet feature complete. Why parse the XML on the server rather than the client ? The Registry API does not offer JSONP callbacks, making direct client-to-API queries by a web app served from another domain tricky (Same Origin Policy, yadda yadda). While this probably could have been done in straight clientside Javascript if I’d used some type of cross-domain AJAX hack, parsing on the server side also opens the possibility in the future to ‘value-add’ to the data in some way, potentially incorporating extra data not served directly by the Registry API, before it’s sent to the client.

Google App Engine works as a cheap hosting solution for a low traffic app like this, which is likely to stay within the free quotas. Also, GAE supports Python, and I like Python. jQTouch makes for a reasonable cross-platform mobile web interface, since it is optimized for WebKit-based browsers. While officially jQTouch supports iPhone/iPod Touch and doesn’t have official Android support, in my hands it works well enough on Android (and in fact displayed some minor bugs on Mobile Safari that were not evident on Android). Typically when using jQTouch you are expected to load multiple ‘pages’ all into several div-sections, lumped into a single HTML document. jQTouch then does the Javascript+CSS magic to render fast page switching, which actually working within a single HTML document. Since the main action of this app is to ‘search’, we don’t yet know what the results page will be, so this nice feature of jQTouch is barely used.

Searching for the same part all the time can get annoying, so mPartsRegistry provides a simple ‘bookmarking’ feature where a list of favorite parts can be managed and stored on the device. This is implemented via HTML5 localStorage – if there was demand then this could easily be turned into server side storage, but I doubt it’s necessary. In the future, it might make sense to pre-cache the metadata for any of these “favorite parts” so that the fast page switching features in jQTouch can be used to full advantage.

Currently, the interface does not show information about sequence features, subparts and twins, however I plan to implement these at some point. The Registry API currently does not provide information about samples, literature references or lab groups, but once these are enabled I plan to support this metadata within mPartsRegistry too.

Okay, that’s all kids .. and remember .. take off your gloves before using your smartphone in the lab !

Occyd : tagging for locations

Occyd Map View (search results)

Those who have been watching may have noticed I quietly started developing an Android application in the last month or so. It’s still super-buggy and far from feature complete, but I thought it was time to announce it here (“release early, release often”). It’s not ready for real users yet, but developers may like to take a little look.

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QR-code bookmarklets

A quick post to share some bookmarklets I made.

I’ve found QR-code “2D barcodes” really handy when playing with my Android phone.

qrcode

Sometimes, I have a web page open on my desktop PC, and I want to quickly load it in the Android Chrome browser to see what it looks like. Rather than re-typing it with my thumbs, the Barcode Scanner application allows me to scan a QR-code from the screen of my computer, and if the decoded text contains a URL, open it in the Android browser.

These two bookmarklets turn the URL of the current page that is open in your browser into a scannable QR-code:

Google Charts API based bookmarklet: Drag this link –>Current URL to QR-code to your bookmarks toolbar.

The code is:
javascript:location.href='http://chart.apis.google.com/chart?cht=qr&chs=350x350&chl='+escape(location.href);

Alternatively, I made a Kaywa QR-code generator version. Drag this link –>Current URL to QR-code to your bookmarks toolbar.

The code is:
javascript:location.href='http://qrcode.kaywa.com/img.php?s=8&d='+escape(location.href);

They both do the same thing, so you probably only want one. Only tested on Firefox.

(Update:  seemed WordPress ate the javascript in the bookmarklet links … should be okay now)

Delicious geohashes … mmmm … tagging *drool*

Since I got a new toy for Christmas, I’ve become interested in geolocation and the fun things you can do when you have an internet-connected GPS-enabled device in your pocket. I’m also a compulsive delicious tagger, so I quickly discovered the existing practice for geotagging delicious bookmarks.

Essentially, this seems to be: add the tag ‘geotagged‘, along with the tags ‘geo:lat=X.xxx‘ and ‘geo:lon=X.xxx‘, where the X.xxx‘s are the latitude and longtitude numbers that are likely to come straight out of your GPS, in decimal degrees (WGS84).

This is all very nice, but the problem with tags in this format is that there is no easy or efficient way to use them to retrieve all items tagged for a particular locality. Sure, if I’m standing right on top of the Eureka Tower at -37.821362,144.964213, I can search for tags geo:lat=-37.821362 and geo:lon=144.964213 to find all the geotagged links for that exact location, but what if I’m standing 50 metres across the street looking up at the tower and want to search for links near my current location ? Continue reading