Gene Set Builder

There's an interesting application note by Yusuf et al. from the Wasserman lab at Vancouver's Centre for Molecular Medicine and Therapeutics this week, in BMC Bioinformatics. Gene Set Builder - what, no acronym? - does exactly what is says on the tin. It's an online database which allows you to create, store and manipulate sets of genes.

It's a fairly basic idea. The rationale behind GSB is that:

while tremendous effort has been invested in developing tools that can analyze a set of genes, minimal effort has been invested in developing tools that can help researchers compile, store, and annotate gene sets in the first place.

For something like this to actually be useful the benefits of using it have to outweigh the hassle of involving yet another system and its associated peculiarities in your scripts and analyses. Luckily that seems to be the case here - it's a simple system that's straightforward to access via the web, it exports different kinds of data quite happily and it comes with tutorials and a Perl API.

The benefits of keeping gene sets on GSB rather than in, say, a text file on your hard drive are to do with GSB's built-in functionality. The GSB backend integrates with Ensembl and the Wasserman's lab own GeneLynx database to allow users to

search and import genes in batches; synchronize missing and outdated gene annotations with currently available information; compile and export gene sets as FASTA sequences, cDNA transcripts, tables, or as lists of identifiers; share data with other users; and create sets of homologs to facilitate comparative studies across species.

Nothing ground breaking - but then that's not the point. It works, and it's easy to use. It reminded me a bit of ORegAnno, in that it's a simple concept well executed. The only problem I'd have with it is... is it going to disappear six months after I put my data on it? Are the authors going to update it when Ensembl changes its API or database schema and the backend code breaks?