[BioSQL-l] Web front-ends to BioSQL

[Mark Schreiber]

Interestingly a few years back Richard Holland and I tried to publish a web
front to BioSQL that used Java, Struts and some bits of BioJava. It got shot
down by the reviewers on the basis that there was already too many of these
kinds of things like GMOD etc. Unfortunately no-one agreed with the idea
that a front end to BioSQL was the unique part.
Not that one or two opinionated reviewers (possibly reading this list)
should be enough to put you off. I think they missed the point.

- Mark

On Wed, Feb 4, 2009 at 7:01 PM, michael watson (IAH-C) <
michael.watson at bbsrc.ac.uk> wrote:

> Hi
>
> I think the conversation is splitting in two, which is great!
>
> First of all, I can see a need for an API, and web-services are a very
> interesting way forward, especially as they can be used in many
> different systems.  I'd certainly like to see something develop along
> those lines.
>
> However, I would like to continue the front-end conversation.  A
> web-services API isn't a front-end, it's a means to a front-end, and I
> disagree that there is not enough commonality to develop a web-based
> front-end.  There are a huge number of groups who want to manage a
> sequence collection, they want to be able to search that sequence
> collection, list and browse it, export them as EMBL/GenBank, import from
> EMBL/GenBank.  Now, if someone was to write import.php, export.php,
> search.php and browse.php - well, on top of a BioSQL database, I think
> that would be an incredibly powerful app.
>
> Mick
>
> -----Original Message-----
> From: biosql-l-bounces at lists.open-bio.org
> [mailto:biosql-l-bounces at lists.open-bio.org] On Behalf Of Mark Schreiber
> Sent: 31 January 2009 11:04
> To: Chris Fields
> Cc: biosql-l at lists.open-bio.org
> Subject: Re: [BioSQL-l] Web front-ends to BioSQL
>
> Hi -
>
> My feeling is that the diversity of languages and frameworks within
> languages would mean that a generic web front end to BioSQL will and
> should never materialize. What would be a lot more sensible is a
> generic API in the form of a webservice or collection of webservices
> that could be used by (theoretically) any web frame work to generate a
> website.
>
> User preferences and requirements will be far too diverse for a
> generic web front end.
>
> - Mark
>
> On 1/31/09, Chris Fields <cjfields at illinois.edu> wrote:
> > Another article (as pointed out by Heikki on bioperl-l):
> >
> >
> http://www.heise-online.co.uk/open/Healthcheck-Perl-The-Perl-Future--/fe
> atures/112388/0
> >
> > The last section is all on MVC-oriented frameworks.
> >
> > chris
> >
> > On Jan 30, 2009, at 1:57 PM, Gudmundur A. Thorisson wrote:
> >
> >> We use Catalyst MVC framework for our project
> (http://www.hgvbaseg2p.org
> >> ). Very good stuff, we combine it with the DBIx::Class ORM and
> >> Template Toolkit as the templating engine. Totally recommended.
> >>
> >>
> >>                Mummi
> >>
> >> On 30 Jan 2009, at 19:45, Chris Fields wrote:
> >>>>
> >>>
> >>> Perl web application framework: Catalyst and Jifty (have not tried
> >>> them myself).  RoR gets a lot of press, but I understand the RoR
> >>> devs tend not to listen to the core ruby devs and (as a
> >>> consequence) had recently run into issues with the 1.8.7 ruby
> >>> release, detailed by the always-entertaining chromatic here:
> >>>
> >>> http://use.perl.org/~chromatic/journal/37125
> >>>
> >>> chris
> >>>
> >>>> 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
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> >>
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