[BioSQL-l] Web front-ends to BioSQL

[michael watson (IAH-C)]

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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