[Bioperl-l] Re: Workbench3 to have das functionality?

David Block dblock@gene.pbi.nrc.ca
Tue, 13 Feb 2001 14:43:08 -0600 (CST)

Great, Lincoln!  I'm looking forward to it - I just downloaded das and
had a look at Geodesic, which is obviously in a state of development right
now - Go Robin!

The parts of your code that I want are the connecting bits and some of the
parsing bits- and then we draw GFF format pictures very easily.  My
concern is going to be in lining the sequences up.  I need to study das
and xml a bit more before I'm confident we can do this.

Meanwhile, I'm going to try to adapt your perl server to bioperl objects -
unless that's been done as well in ensembl or something?


On Tue, 13 Feb 2001, Lincoln Stein wrote:

> Good news about the Workbench!
> As it happens, yesterday I wrote a perl-based das client library for
> testing purposes.  It connects to multiple servers and draws pretty
> pictures.  I still have to write the CGI/mod_perl wrapper for it to
> make it easy to use on the web, but I'll go ahead and add it to the
> DAS CVS repository this week so that people can play with it.
> Lincoln
> David Block writes:
>  > Hello all - I am cross-posting so as not to miss anyone.  We at the PBI
>  > are slowly releasing Workbench2 (if you email me now, I can send it to
>  > you - it should work).  WB3 is starting off with a wish list, and one of
>  > the major items on my wish list is das.  Workbench should be a das client,
>  > and should include an optional das server, I think.
>  > 
>  > I know that most of das client code is in java - has anyone else done it
>  > with perl?  I expect our das client to be released open source in the same
>  > way that SeqCanvas (part of bioperl-gui) is open source.  I know that
>  > there is a das server implementation in perl, and I'd like to rework that
>  > for MySQL and our database/bioperl objects.
>  > 
>  > Anyone with any pointers, advice, or feedback, please let me know.  I'll
>  > start a new topic on our wiki (link below) as well.
>  > 
>  > Thanks!
>  > 

David Block
Plant Biotechnology Institute
National Research Council of Canada
Saskatoon, Saskatchewan