[BioSQL-l] Web front-ends to BioSQL

[mark.schreiber at novartis.com]

Hi -

I have partly auto and partly manually generated an EJB 3 binding to 
BioSQL that can be used with JPA. Notably this uses the new EJB model not 
the nasty old one so it is very easy to use. As all EJB's are now plain 
old java beans it is also very easy to use these objects in web services 
and JSP pages (maybe PHP too??).

Also, because the EJB's and JPA is now more flexible you don't need a full 
java app container (JBOSS, Glassfish) but can instead use them in 
standalone programs although with a container you do get other benefits of 
transaction control/ security/ load balance etc for free.  Also if you do 
use a web interface the web front end will probably be in Tomcat and you 
can use this as a light container for talking to the biosql entity beans. 
If you think there will be more than a few users I would probably advocate 
using Glassfish or similar app server because there are many advantages 
that out weigh the relatively small overhead.

The EJB binding is not part of BioJava but is a candiate for inclusion in 
BioJava3.  I can provide you with code if you are interested. I would also 
be keen to see this get some use.

Best regards,

- Mark

biosql-l-bounces at lists.open-bio.org wrote on 01/30/2009 02:45:05 AM:

> 
> On Jan 29, 2009, at 11:44 AM, James Procter wrote:
> 
> >
> > Chris Fields wrote:
> >> Gbrowse, maybe?  There is a BioSQL plugin for it 
> >> (Bio::DB::Das::BioSQL):
> >>
> >> http://gmod.org/wiki/GBrowse#About_Databases
> > I'm also in the market for a quick and easy front end - from what I've
> > heard from a colleague, GBrowse can be tricky to install. Also - for 
> > my
> > application we'd like to easily gather sets of proteins and then 
> > explore
> > their annotation. This is a little out of the scope of GBrowse.
> 
> I don't find Gbrowse itself tricky as much as getting BioPerl 
> installed.  One can use Gbrowse for what you want but there are 
> probably better resources (Ensembl, maybe).
> 
> chris
> 
> > I think there might be a niche needing filling here - would anyone be
> > interested in pooling code/resources ?
> >
> > Jim.
> >
> > -- 
> > -------------------------------------------------------------------
> > J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
> > Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> > The University of Dundee is a Scottish Registered Charity, No. 
> > SC015096.
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> 
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