Blue Collar Bioinformatics

BioSQL on Google App Engine

with 4 comments

The BioSQL project provides a well thought out relational database schema for storing biological sequences and annotations. For those developers who are responsible for setting up local stores of biological data, BioSQL provides a huge advantage via reusability. Some of the best features of BioSQL from my experience are:

  • Available interfaces for several languages (via Biopython, BioPerl, BioJava and BioRuby).
  • Flexible storage of data via a key/value pair model. This models information in an extensible manner, and helps with understanding distributed key/value stores like SimpleDB and CouchDB.
  • Overall data model based on GenBank flat files. This makes teaching the model to biology oriented users much easier; you can pull up a text file from NCBI with a sequence and directly show how items map to the database.

Given the usefulness of BioSQL for local relational data storage, I would like to see it move into the rapidly expanding cloud development community. Tying BioSQL data storage in with Web frameworks will help researchers make their data publicly available earlier and in standard formats. As a nice recent example, George has a series of posts on using BioSQL with Ruby on Rails. There have also been several discussions of the BioSQL mailing list around standard web tools and APIs to sit on top of the database; see this thread for a recent example.

Towards these goals, I have been working on a BioSQL backed interface for Google App Engine. Google App Engine is a Python based framework to quickly develop and deploy web applications. For data storage, Google’s Datastore provides an object interface to a distributed scalable storage backend. Practically, App Engine has free hosting quotas which can scale to larger instances as demand for the data in the application increases; this will appeal to cost-conscious researchers by avoiding an initial barrier to making their data available.

My work on this was accelerated by the Open Bioinformatics Foundation’s move to apply for participation in Google’s Summer of Code. OpenBio is a great community that helps organize projects like BioPerl, Biopython, BioJava and BioRuby. After writing up a project idea for BioSQL on Google App Engine in our application, I was inspired to finish a demonstration of the idea.

I am happy to announce a simple demonstration server running a BioSQL based backend: BioSQL Web. The source code is available from my git repository. Currently the server allows uploads of GenBank formatted files and provides a simple view of the records, annotations and sequences. The data is stored in the Google Datastore with an object interface that mimics the BioSQL relational model.

Future posts will provide more details on the internals of the server end and client interface as they develop. As always, feedback, thoughts and code contributions are very welcome.

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Written by Brad Chapman

March 15, 2009 at 8:45 am

4 Responses

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  1. great post – and a nice demo! Finger’s crossed someone takes up the Google Code challenge…

    Jim Procter

    March 16, 2009 at 11:21 am

    • Thanks for the kind words Jim. Unfortunately, it looks as if the Google Code project won’t be on this year but we’ll keep chugging away with it regardless. I’m happy to have it out there so others can play with it.

      Brad Chapman

      March 22, 2009 at 6:54 pm

  2. Whoah – a bit late in commenting on this but it looks good. Having worked in a few labs – I see a strong need for an easy to deploy + maintain website (web-framework based) for managing genetic data (and maybe phenotypic, etc.). I have worked with Chado, which was quite challenging. BioSQL appears to be a lot simpler – do you know of any projects out there being developed that would allow users to easily deploy a site, and import/export/manage and maybe view/visualize their data?

    Daniel Cook

    August 29, 2013 at 12:44 pm


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