[BioSQL-l] Web front-ends to BioSQL

[Hilmar Lapp]

Having such a webapp would be pretty cool, and I agree with the  
argument below that there are numerous small groups or individuals  
with this need. (we have some ourselves here ...)

One word of caution as to where to look for lessons I think is the  
infamous GMOD gene page and standard web front-end, which has been  
labored on in various incarnations for more than half a decade,  
without producing a compelling and broadly adopted result. People's  
needs and technology obsessions vary from place to place.

One possibly hugely complicating factor for the GMOD web front-end was  
that the target audience were model organism websites, which  
themselves have a large and diverse stakeholder community, so  
flexibility and configurability became overriding requirements  
resulting in bloat of code stacks and features.

My personal take is that for this to be broadly useful, the primary  
target audience should probably be programmers, or programming-savvy  
scientists, who can extend and customize a core application at will.  
In other words, much in line with the philosophy behind the Bio*  
libraries.

Other than that, keep it simple so I don't have to learn yet another  
(namely your templating or clever XML configuration scheme) language  
to extend it. I sat next to Mark when he generated a bare-bones BioSQL- 
binding in EJB literally in minutes, which I thought was cool. People  
rave about Ruby and RoR too as for ease of getting started. By far the  
most people out there will be familiar with Perl, but I'm not sure  
what the web application framework would be there that would put me at  
ease. In the end what may count more than anything else is critical  
mass even if it's not everyone's darling language.

My $0.02, and I'd be keen so see what comes out of this. If there's  
something I can do to tip the balance towards something tangible  
happening, let me know.

	-hilmar

On Jan 30, 2009, at 6:03 AM, michael watson (IAH-C) wrote:

> Dear All
>
> Thank you for the responses.  I think it is clear there is a need -  
> all
> over the World there are groups of various sizes who try to collate  
> and
> curate sequences for their organism of choice, from fish virus  
> databases
> with 200 records, to flu databases with many thousands.  I'm in  
> contact
> with a tiny percentage of these groups, and there is a clear need for:
>
> - common DB schema (tick, we can use BioSQL)
> - Web app for:
> 	- submitting new sequences
> 	- curating and editing sequences
> 	- comparing sequences - align, draw trees etc
> 	- showing sequences on maps (i.e. location of sample)
> 	- submitting sequences to GenBank
> 	- retrieving sequences from GenBank
>
> With all of the Bio* projects, this shouldn't be too hard to do, but  
> as
> ever it needs bodies to do it... I took a quick look at Galaxy but  
> that
> isn't really what was needed.
>
> Thanks again
>
> Mick
>
> -----Original Message-----
> From: biosql-l-bounces at lists.open-bio.org
> [mailto:biosql-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: 29 January 2009 18:45
> To: James Procter
> Cc: biosql-l at lists.open-bio.org
> Subject: Re: [BioSQL-l] Web front-ends to BioSQL
>
>
> 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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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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